51
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Zhu WS, Litterman AJ, Sekhon HS, Kageyama R, Arce MM, Taylor KE, Zhao W, Criswell LA, Zaitlen N, Erle DJ, Ansel KM. GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins. Genome Biol 2023; 24:281. [PMID: 38062486 PMCID: PMC10701951 DOI: 10.1186/s13059-023-03125-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags correspond with known RBP binding sites and are enriched for sites detected by RBP-specific crosslinking immunoprecipitation (CLIP) for abundant cytosolic RBPs. Comparison of human Jurkat T cells and mouse primary T cells uncovers shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a conserved mRNA-destabilizing cis-regulatory element. GCLiPP signal overlapping with immune-related SNPs uncovers stabilizing cis-regulatory regions in CD5, STAT6, and IKZF1.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam J Litterman
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Harshaan S Sekhon
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
| | - Robin Kageyama
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Kimberly E Taylor
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Wenxue Zhao
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
- School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
| | - Lindsey A Criswell
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Noah Zaitlen
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - David J Erle
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
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52
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Booth GT, Daza RM, Srivatsan SR, McFaline-Figueroa JL, Gladden RG, Mullen AC, Furlan SN, Shendure J, Trapnell C. High-capacity sample multiplexing for single cell chromatin accessibility profiling. BMC Genomics 2023; 24:737. [PMID: 38049719 PMCID: PMC10696879 DOI: 10.1186/s12864-023-09832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challenging and costly. Here we describe a novel approach, sciPlex-ATAC-seq, which uses unmodified DNA oligos as sample-specific nuclear labels, enabling the concurrent profiling of chromatin accessibility within single nuclei from virtually unlimited specimens or experimental conditions. We first demonstrate our method with a chemical epigenomics screen, in which we identify drug-altered distal regulatory sites predictive of compound- and dose-dependent effects on transcription. We then analyze cell type-specific chromatin changes in PBMCs from multiple donors responding to synthetic and allogeneic immune stimulation. We quantify stimulation-altered immune cell compositions and isolate the unique effects of allogeneic stimulation on chromatin accessibility specific to T-lymphocytes. Finally, we observe that impaired global chromatin decondensation often coincides with chemical inhibition of allogeneic T-cell activation.
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Affiliation(s)
- Gregory T Booth
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - José L McFaline-Figueroa
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA
| | - Rula Green Gladden
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew C Mullen
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Scott N Furlan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
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53
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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54
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Moyers BA, Partridge EC, Mackiewicz M, Betti MJ, Darji R, Meadows SK, Newberry KM, Brandsmeier LA, Wold BJ, Mendenhall EM, Myers RM. Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells. Genome Res 2023; 33:1879-1892. [PMID: 37852782 PMCID: PMC10760452 DOI: 10.1101/gr.278205.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins (DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in distal-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and show the usefulness of large genomic analyses for elucidation of individual TF functions.
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Affiliation(s)
- Belle A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Michael J Betti
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Roshan Darji
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | | | - Barbara J Wold
- Merkin Institute for Translational Research, California Institute of Technology, Pasadena, California 91125, USA
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
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55
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Park SG, Kim WJ, Moon JI, Kim KT, Ryoo HM. MESIA: multi-epigenome sample integration approach for precise peak calling. Sci Rep 2023; 13:20859. [PMID: 38012291 PMCID: PMC10681995 DOI: 10.1038/s41598-023-47948-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is the most widely used method for measuring chromatin accessibility. Researchers have included multi-sample replication in ATAC-seq experimental designs. In epigenomic analysis, researchers should measure subtle changes in the peak by considering the read depth of individual samples. It is important to determine whether the peaks of each replication have an integrative meaning for the region of interest observed during multi-sample integration. We developed multi-epigenome sample integration approach for precise peak calling (MESIA), which integrates replication with high representativeness and reproducibility in multi-sample replication and determines the optimal peak. After identifying the reproducibility between all replications, our method integrated multiple samples determined as representative replicates. MESIA detected 6.06 times more peaks, and the value of the peaks was 1.32 times higher than the previously used method. MESIA is a shell-script-based open-source code that provides researchers involved in the epigenome with comprehensive insights.
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Grants
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 Korean government (MSIT)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 Korean government (MSIT)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 Korean government (MSIT)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 Korean government (MSIT)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 Korean government (MSIT)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 National Research Foundation of Korea (NRF)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 National Research Foundation of Korea (NRF)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 National Research Foundation of Korea (NRF)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 National Research Foundation of Korea (NRF)
- RS-2023-00207971, 2020R1A4A1019423, 2022R1I1A1A01062894 and 2021R1C1C2095130 National Research Foundation of Korea (NRF)
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Affiliation(s)
- Seung Gwa Park
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry and Dental Multiomics Center, Dental Research Institute, Seoul National University, Seoul, South Korea
- Epigenetic Regulation of Aged Skeleto-Muscular System Laboratory, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Woo-Jin Kim
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry and Dental Multiomics Center, Dental Research Institute, Seoul National University, Seoul, South Korea
- Epigenetic Regulation of Aged Skeleto-Muscular System Laboratory, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Jae-I Moon
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry and Dental Multiomics Center, Dental Research Institute, Seoul National University, Seoul, South Korea
- Epigenetic Regulation of Aged Skeleto-Muscular System Laboratory, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Ki-Tae Kim
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry and Dental Multiomics Center, Dental Research Institute, Seoul National University, Seoul, South Korea.
- Epigenetic Regulation of Aged Skeleto-Muscular System Laboratory, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea.
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry and Dental Multiomics Center, Dental Research Institute, Seoul National University, Seoul, South Korea.
- Epigenetic Regulation of Aged Skeleto-Muscular System Laboratory, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, South Korea.
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56
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Chen Y, Paramo MI, Zhang Y, Yao L, Shah SR, Jin Y, Zhang J, Pan X, Yu H. Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants. Annu Rev Genet 2023; 57:201-222. [PMID: 37562413 DOI: 10.1146/annurev-genet-030723-120717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Despite accumulating evidence implicating noncoding variants in human diseases, unraveling their functionality remains a significant challenge. Systematic annotations of the regulatory landscape and the growth of sequence variant data sets have fueled the development of tools and methods to identify causal noncoding variants and evaluate their regulatory effects. Here, we review the latest advances in the field and discuss potential future research avenues to gain a more in-depth understanding of noncoding regulatory variants.
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Affiliation(s)
- You Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Mauricio I Paramo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Yingying Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Li Yao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Sagar R Shah
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Yiyang Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Junke Zhang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Xiuqi Pan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
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57
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Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, Georgakopoulos-Soares I, Ahituv N. MPRAbase: A Massively Parallel Reporter Assay Database. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567742. [PMID: 38045264 PMCID: PMC10690217 DOI: 10.1101/2023.11.19.567742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene regulatory activity. There are several different variations of MPRA technology and they are used for numerous applications, including regulatory element discovery, variant effect measurement, saturation mutagenesis, synthetic regulatory element generation or characterization of evolutionary gene regulatory differences. Despite their many designs and uses, there is no comprehensive database that incorporates the results of these experiments. To address this, we developed MPRAbase, a manually curated database that currently harbors 129 experiments, encompassing 17,718,677 elements tested across 35 cell types and 4 organisms. The MPRAbase web interface ( http://www.mprabase.com ) serves as a centralized user-friendly repository to download existing MPRA data for independent analysis and is designed with the ability to allow researchers to share their published data for rapid dissemination to the community.
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58
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Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Lieberman Aiden E, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM. An encyclopedia of enhancer-gene regulatory interactions in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.563812. [PMID: 38014075 PMCID: PMC10680627 DOI: 10.1101/2023.11.09.563812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease1-6. Here we create and evaluate a resource of >13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and largescale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 elementgene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancerpromoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.
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Affiliation(s)
- Andreas R. Gschwind
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - Kristy S. Mualim
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institute of Science, Stanford, CA, USA
| | - Alireza Karbalayghareh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maya U. Sheth
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kushal K. Dey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Evelyn Jagoda
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramil N. Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Wang Xi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anthony S. Tan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - Hank Jones
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - X. Rosa Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - David Yao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Present Address: Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Benjamin T. James
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Muhammad S. Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA
| | - Neva C. Durand
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Suhas S. P. Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Ragini Mahajan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Benjamin R. Doughty
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kalina Andreeva
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob C. Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Present Address: Artificial Intelligence Laboratory, Illumina, Inc., San Diego, CA, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Present Address: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Tri C. Nguyen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | | | - Hilary K. Finucane
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill E. Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Michael A. Beer
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - John A. Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Erez Lieberman Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Lars M. Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jesse M. Engreitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Sciences and Engineering Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
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Tu Z, Bi Y, Mao T, Wang H, Gao S, Wang Y. Discordance between chromatin accessibility and transcriptional activity during the human primed-to-naïve pluripotency transition process. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:35. [PMID: 37938437 PMCID: PMC10632355 DOI: 10.1186/s13619-023-00179-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Naïve pluripotent state can be obtained by several strategies from various types of cells, in which the cell fate roadmap as well as key biological events involved in the journey have been described in detail. Here, we carefully explored the chromatin accessibility dynamics during the primed-to-naïve transition by adopting a dual fluorescent reporter system and the assay for transposase-accessible chromatin (ATAC)-seq. Our results revealed critical chromatin remodeling events and highlight the discordance between chromatin accessibility and transcriptional activity. We further demonstrate that the differential epigenetic modifications and transcription factor (TF) activities may play a critical role in regulating gene expression, and account for the observed variations in gene expression despite similar chromatin landscapes.
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Affiliation(s)
- Zhifen Tu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yan Bi
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Tengyan Mao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Hong Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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Schleussner N, Cauchy P, Franke V, Giefing M, Fornes O, Vankadari N, Assi SA, Costanza M, Weniger MA, Akalin A, Anagnostopoulos I, Bukur T, Casarotto MG, Damm F, Daumke O, Edginton-White B, Gebhardt JCM, Grau M, Grunwald S, Hansmann ML, Hartmann S, Huber L, Kärgel E, Lusatis S, Noerenberg D, Obier N, Pannicke U, Fischer A, Reisser A, Rosenwald A, Schwarz K, Sundararaj S, Weilemann A, Winkler W, Xu W, Lenz G, Rajewsky K, Wasserman WW, Cockerill PN, Scheidereit C, Siebert R, Küppers R, Grosschedl R, Janz M, Bonifer C, Mathas S. Transcriptional reprogramming by mutated IRF4 in lymphoma. Nat Commun 2023; 14:6947. [PMID: 37935654 PMCID: PMC10630337 DOI: 10.1038/s41467-023-41954-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/20/2023] [Indexed: 11/09/2023] Open
Abstract
Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University Medical Center Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, 60-479, Poland
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Ioannis Anagnostopoulos
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Thomas Bukur
- TRON gGmbH - Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Marco G Casarotto
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Frederik Damm
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Michael Grau
- Department of Physics, University of Marburg, 35052, Marburg, Germany
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Stephan Grunwald
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Martin-Leo Hansmann
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
- Institute for Pharmacology and Toxicology, Goethe University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lionel Huber
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Eva Kärgel
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Simone Lusatis
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Daniel Noerenberg
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Reisser
- Department of Physics, Institute of Biophysics, Ulm University, Ulm, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg-Hessen, Ulm, Germany
| | - Srinivasan Sundararaj
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andre Weilemann
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Wiebke Winkler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Wendan Xu
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, 13125, Berlin, Germany
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claus Scheidereit
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Ralf Küppers
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany.
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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61
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Li S, Luo Y, Wei G, Zong W, Zeng W, Xiao D, Zhang H, Song Y, Hao Y, Sun K, Lei C, Guo X, Xu B, Li W, Wu Z, Liu Y, Xie X, Guo J. Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:239. [PMID: 37930441 DOI: 10.1007/s00122-023-04489-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE We developed an efficient promoter editing method to create different weak Ehd1 alleles in elite japonica rice variety ZJ8 with slightly delayed heading and improved yield for use in breeding. Heading date is an important agronomic trait of rice (Oryza sativa) that determines the planting areas and cultivation seasons of different varieties, thus affecting final yield. Early heading date 1 (Ehd1) is a major rice integrator gene in the regulatory network of heading date whose expression level is negatively correlated with heading date and grain yield. Some elite japonica varieties such as Zhongjia 8 (ZJ8) show very early heading with poor agronomic traits when planted in South China. This problem can be addressed by downregulating the expression of Ehd1. In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be created to expand the planting area of rice and improve grain yields.
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Affiliation(s)
- Shengting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanqiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
| | - Guangliang Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanyong Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dongdong Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Han Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingang Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kangli Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chen Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Bingqun Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weitao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zeqiang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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62
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Devens HR, Davidson PL, Byrne M, Wray GA. Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species. Mol Biol Evol 2023; 40:msad222. [PMID: 37823438 PMCID: PMC10638671 DOI: 10.1093/molbev/msad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/14/2023] [Accepted: 07/27/2023] [Indexed: 10/13/2023] Open
Abstract
Chromatin accessibility plays an important role in shaping gene expression, yet little is known about the genetic and molecular mechanisms that influence the evolution of chromatin configuration. Both local (cis) and distant (trans) genetic influences can in principle influence chromatin accessibility and are based on distinct molecular mechanisms. We, therefore, sought to characterize the role that each of these plays in altering chromatin accessibility in 2 closely related sea urchin species. Using hybrids of Heliocidaris erythrogramma and Heliocidaris tuberculata, and adapting a statistical framework previously developed for the analysis of cis and trans influences on the transcriptome, we examined how these mechanisms shape the regulatory landscape at 3 important developmental stages, and compared our results to similar analyses of the transcriptome. We found extensive cis- and trans-based influences on evolutionary changes in chromatin, with cis effects generally larger in effect. Evolutionary changes in accessibility and gene expression are correlated, especially when expression has a local genetic basis. Maternal influences appear to have more of an effect on chromatin accessibility than on gene expression, persisting well past the maternal-to-zygotic transition. Chromatin accessibility near gene regulatory network genes appears to be distinctly regulated, with trans factors appearing to play an outsized role in the configuration of chromatin near these genes. Together, our results represent the first attempt to quantify cis and trans influences on evolutionary divergence in chromatin configuration in an outbred natural study system and suggest that chromatin regulation is more genetically complex than was previously appreciated.
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Affiliation(s)
| | | | - Maria Byrne
- School of Medical Science, The University of Sydney, Sydney, New South Wales, Australia
- School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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63
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Rapakoulia T, Lopez Ruiz De Vargas S, Omgba PA, Laupert V, Ulitsky I, Vingron M. CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction. Bioinformatics 2023; 39:btad687. [PMID: 37982748 PMCID: PMC10666202 DOI: 10.1093/bioinformatics/btad687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023] Open
Abstract
MOTIVATION Identifying target promoters of active enhancers is a crucial step for realizing gene regulation and deciphering phenotypes and diseases. Up to now, several computational methods were developed to predict enhancer gene interactions, but they require either many epigenomic and transcriptomic experimental assays to generate cell-type (CT)-specific predictions or a single experiment applied to a large cohort of CTs to extract correlations between activities of regulatory elements. Thus, inferring CT-specific enhancer gene interactions in unstudied or poorly annotated CTs becomes a laborious and costly task. RESULTS Here, we aim to infer CT-specific enhancer target interactions, using minimal experimental input. We introduce Cell-specific ENhancer Target pREdiction (CENTRE), a machine learning framework that predicts enhancer target interactions in a CT-specific manner, using only gene expression and ChIP-seq data for three histone modifications for the CT of interest. CENTRE exploits the wealth of available datasets and extracts cell-type agnostic statistics to complement the CT-specific information. CENTRE is thoroughly tested across many datasets and CTs and achieves equivalent or superior performance than existing algorithms that require massive experimental data. AVAILABILITY AND IMPLEMENTATION CENTRE's open-source code is available at GitHub via https://github.com/slrvv/CENTRE.
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Affiliation(s)
| | | | | | - Verena Laupert
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Igor Ulitsky
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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64
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Burris TP, de Vera IMS, Cote I, Flaveny CA, Wanninayake US, Chatterjee A, Walker JK, Steinauer N, Zhang J, Coons LA, Korach KS, Cain DW, Hollenberg AN, Webb P, Forrest D, Jetten AM, Edwards DP, Grimm SL, Hartig S, Lange CA, Richer JK, Sartorius CA, Tetel M, Billon C, Elgendy B, Hegazy L, Griffett K, Peinetti N, Burnstein KL, Hughes TS, Sitaula S, Stayrook KR, Culver A, Murray MH, Finck BN, Cidlowski JA. International Union of Basic and Clinical Pharmacology CXIII: Nuclear Receptor Superfamily-Update 2023. Pharmacol Rev 2023; 75:1233-1318. [PMID: 37586884 PMCID: PMC10595025 DOI: 10.1124/pharmrev.121.000436] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
The NR superfamily comprises 48 transcription factors in humans that control a plethora of gene network programs involved in a wide range of physiologic processes. This review will summarize and discuss recent progress in NR biology and drug development derived from integrating various approaches, including biophysical techniques, structural studies, and translational investigation. We also highlight how defective NR signaling results in various diseases and disorders and how NRs can be targeted for therapeutic intervention via modulation via binding to synthetic lipophilic ligands. Furthermore, we also review recent studies that improved our understanding of NR structure and signaling. SIGNIFICANCE STATEMENT: Nuclear receptors (NRs) are ligand-regulated transcription factors that are critical regulators of myriad physiological processes. NRs serve as receptors for an array of drugs, and in this review, we provide an update on recent research into the roles of these drug targets.
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Affiliation(s)
- Thomas P Burris
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Ian Mitchelle S de Vera
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Isabelle Cote
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Colin A Flaveny
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Udayanga S Wanninayake
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Arindam Chatterjee
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - John K Walker
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Nickolas Steinauer
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Jinsong Zhang
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Laurel A Coons
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Kenneth S Korach
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Derek W Cain
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Anthony N Hollenberg
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Paul Webb
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Douglas Forrest
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Anton M Jetten
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Dean P Edwards
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Sandra L Grimm
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Sean Hartig
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Carol A Lange
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Jennifer K Richer
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Carol A Sartorius
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Marc Tetel
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Cyrielle Billon
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Bahaa Elgendy
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Lamees Hegazy
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Kristine Griffett
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Nahuel Peinetti
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Kerry L Burnstein
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Travis S Hughes
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Sadichha Sitaula
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Keitch R Stayrook
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Alexander Culver
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Meghan H Murray
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - Brian N Finck
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
| | - John A Cidlowski
- University of Florida Genetics Institute, Gainesville, Florida (T.P.B., I.C.); Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (I.M.S.d.V., U.S.W., A.C., J.K.W., N.S., J.Z.); Pfizer, San Diego, California (C.A.F.); Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina (L.A.C., K.S.K.); Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina (L.A.C.); Duke Human Vaccine Institute, Durham, North Carolina (D.W.C.); Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts (A.N.H.); The California Institute of Regenerative Medicine, South San Francisco, California (P.W.); Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (D.G.); National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina (A.M.J.); Department of Molecular and Cellular Pharmacology, Baylor College of Medicine, Houston, Texas (D.P.E., S.L.G., S.H.); Department of Medicine, Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota (C.A.L.); Department of Pathology, University of Colorado, Aurora, Colorado (J.K.R., C.A.S.); Neuroscience Program, Wellesley College, Wellesley, Massachusetts (M.T.); Center for Clinical Pharmacology, University of Health Sciences and Pharmacy, Saint Louis, Missouri (C.B., B.E., L.H.); Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, Alabama (K.G.); Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, Florida (N.P., K.L.B.); Department of Biomedical and Pharmaceutical Sciences, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana (T.S.H.); Asteroid Therapeutics, Inc. Indianapolis, Indiana (S.S., K.R.S., A.C.); Saint Louis University School of Medicine, St. Louis, Missouri (M.H.M.); Department of Medicine, Washington University School of Medicine, St. Louis, Missouri (B.N.F.); and Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina (J.A.C.)
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65
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Grillo G, Keshavarzian T, Linder S, Arlidge C, Mout L, Nand A, Teng M, Qamra A, Zhou S, Kron KJ, Murison A, Hawley JR, Fraser M, van der Kwast TH, Raj GV, He HH, Zwart W, Lupien M. Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer. Cancer Discov 2023; 13:2470-2487. [PMID: 37694973 PMCID: PMC10618745 DOI: 10.1158/2159-8290.cd-23-0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/30/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023]
Abstract
Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac chromatin immunoprecipitation sequencing data from 32 normal cell states, we report pluripotent/stem and mature cell state-specific "regulatory transposable elements." Pluripotent/stem elements are binding sites for pluripotency factors (e.g., NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements. SIGNIFICANCE We show that oncogenesis relies on co-opting transposable elements from pluripotent stem cells as regulatory elements altering the recruitment of lineage-specific transcription factors. We further discover how co-option is dependent on active chromatin states with important implications for developing treatment options against drivers of oncogenesis across the repetitive DNA. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
- Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tina Keshavarzian
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisanne Mout
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ankita Nand
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mona Teng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aditi Qamra
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ken J. Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James R. Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Theodorus H. van der Kwast
- Laboratory Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ganesh V. Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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66
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Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet 2023; 24:739-754. [PMID: 37365273 DOI: 10.1038/s41576-023-00618-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
The interplay between chromatin, transcription factors and genes generates complex regulatory circuits that can be represented as gene regulatory networks (GRNs). The study of GRNs is useful to understand how cellular identity is established, maintained and disrupted in disease. GRNs can be inferred from experimental data - historically, bulk omics data - and/or from the literature. The advent of single-cell multi-omics technologies has led to the development of novel computational methods that leverage genomic, transcriptomic and chromatin accessibility information to infer GRNs at an unprecedented resolution. Here, we review the key principles of inferring GRNs that encompass transcription factor-gene interactions from transcriptomics and chromatin accessibility data. We focus on the comparison and classification of methods that use single-cell multimodal data. We highlight challenges in GRN inference, in particular with respect to benchmarking, and potential further developments using additional data modalities.
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Affiliation(s)
- Pau Badia-I-Mompel
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Lorna Wessels
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience, Medical Faculty, MannHeim Heidelberg University, Mannheim, Germany
| | - Sophia Müller-Dott
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Rémi Trimbour
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, Paris, France
| | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
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67
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Feng M, Wang J, Li K, Nakamura F. UBE2A/B is the trans-acting factor mediating mechanotransduction and contact inhibition. Biochem J 2023; 480:1659-1674. [PMID: 37818922 DOI: 10.1042/bcj20230208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
Mechanotransduction and contact inhibition (CI) control gene expression to regulate proliferation, differentiation, and even tumorigenesis of cells. However, their downstream trans-acting factors (TAFs) are not well known due to a lack of a high-throughput method to quantitatively detect them. Here, we developed a method to identify TAFs on the cis-acting sequences that reside in open chromatin or DNaseI-hypersensitive sites (DHSs) and to detect nucleocytoplasmic shuttling TAFs using computational and experimental screening. The DHS-proteomics revealed over 1000 potential mechanosensing TAFs and UBE2A/B (Ubiquitin-conjugating enzyme E2 A) was experimentally identified as a force- and CI-dependent nucleocytoplasmic shuttling TAF. We found that translocation of YAP/TAZ and UBE2A/B are distinctively regulated by inhibition of myosin contraction, actin-polymerization, and CI depending on cell types. Next-generation sequence analysis revealed many downstream genes including YAP are transcriptionally regulated by ubiquitination of histone by UBE2A/B. Our results suggested a YAP-independent mechanotransduction and CI pathway mediated by UBE2A/B.
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Affiliation(s)
- Mingwei Feng
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiale Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Kangjing Li
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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68
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Umarov R, Hon CC. Enhancer target prediction: state-of-the-art approaches and future prospects. Biochem Soc Trans 2023; 51:1975-1988. [PMID: 37830459 DOI: 10.1042/bst20230917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023]
Abstract
Enhancers are genomic regions that regulate gene transcription and are located far away from the transcription start sites of their target genes. Enhancers are highly enriched in disease-associated variants and thus deciphering the interactions between enhancers and genes is crucial to understanding the molecular basis of genetic predispositions to diseases. Experimental validations of enhancer targets can be laborious. Computational methods have thus emerged as a valuable alternative for studying enhancer-gene interactions. A variety of computational methods have been developed to predict enhancer targets by incorporating genomic features (e.g. conservation, distance, and sequence), epigenomic features (e.g. histone marks and chromatin contacts) and activity measurements (e.g. covariations of enhancer activity and gene expression). With the recent advances in genome perturbation and chromatin conformation capture technologies, data on experimentally validated enhancer targets are becoming available for supervised training of these methods and evaluation of their performance. In this review, we categorize enhancer target prediction methods based on their rationales and approaches. Then we discuss their merits and limitations and highlight the future directions for enhancer targets prediction.
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Affiliation(s)
- Ramzan Umarov
- RIKEN Centre for Integrative Medical Sciences, Yokohama RIKEN Institute, Yokohama, Japan
| | - Chung-Chau Hon
- RIKEN Centre for Integrative Medical Sciences, Yokohama RIKEN Institute, Yokohama, Japan
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69
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Gao G, Chen M, Mo R, Li N, Xu Y, Lu Y. Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice. Genes (Basel) 2023; 14:2027. [PMID: 38002970 PMCID: PMC10671530 DOI: 10.3390/genes14112027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.
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Affiliation(s)
- Guangtong Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoxian Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Mo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Abatti LE, Lado-Fernández P, Huynh L, Collado M, Hoffman M, Mitchell J. Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. Nucleic Acids Res 2023; 51:10109-10131. [PMID: 37738673 PMCID: PMC10602899 DOI: 10.1093/nar/gkad734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023] Open
Abstract
Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung adenocarcinoma. Deletion of the SRR124-134 cluster disrupts expression of the SOX2 oncogene, dysregulates genome-wide transcription and chromatin accessibility and reduces the ability of cancer cells to form colonies in vitro. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124-134 activity and SOX2 transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.
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Affiliation(s)
- Luis E Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Lado-Fernández
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
- Department of Physiology and Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Linh Huynh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Manuel Collado
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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71
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Li M, Feng Y, Han Q, Yang Y, Shi Y, Zheng D, Zhang W. Genomic variations combined with epigenetic modifications rewire open chromatin in rice. PLANT PHYSIOLOGY 2023; 193:1880-1896. [PMID: 37539937 DOI: 10.1093/plphys/kiad440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
Cis-regulatory elements (CREs) fine-tune gene transcription in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global sequence and structural variations (SVs) are responsible for multilevel changes between indica and japonica rice (Oryza sativa) is still not fully elucidated. To address this, we conducted multiomic studies using MNase hypersensitivity sequencing (MH-seq) in combination with RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and bisulfite sequencing (BS-seq) between the japonica rice variety Nipponbare (NIP) and indica rice variety 93-11. We found that differential MNase hypersensitive sites (MHSs) exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Notably, through MHS-genome-wide association studies (GWAS) integration, we found that key sequence variations may be associated with differences of agronomic traits between NIP and 93-11, which is partly achieved by MHSs harboring CREs. In addition, SV-derived differential MHSs caused by transposable element (TE) insertion, especially by noncommon TEs among rice varieties, were associated with genes with distinct functions, indicating that TE-driven gene neo- or subfunctionalization is mediated by changes of chromatin openness. This study thus provides insights into how sequence and genomic SVs control agronomic traits of NIP and 93-11; it also provides genome-editing targets for molecular breeding aiming at improving favorable agronomic properties.
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Affiliation(s)
- Mengqi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yilong Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Qi Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Ying Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yining Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Dongyang Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
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Wang H, Sun H, Liang B, Zhang F, Yang F, Cui B, Ding L, Wang X, Wang R, Cai J, Tang Y, Rao J, Hu W, Zhao S, Wu W, Chen X, Wu K, Lai J, Xie Y, Li B, Tang J, Shen S, Liu Y. Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia. Nat Commun 2023; 14:6792. [PMID: 37880218 PMCID: PMC10600232 DOI: 10.1038/s41467-023-42565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
For around half of the pediatric B-lineage acute lymphoblastic leukemia (B-ALL) patients, the molecular mechanism of relapse remains unclear. To fill this gap in knowledge, here we characterize the chromatin accessibility landscape in pediatric relapsed B-ALL. We observe rewired accessible chromatin regions (ACRs) associated with transcription dysregulation in leukemia cells as compared with normal B-cell progenitors. We show that over a quarter of the ACRs in B-ALL are in quiescent regions with high heterogeneity among B-ALLs. We identify subtype-specific and allele-imbalanced chromatin accessibility by integrating multi-omics data. By characterizing the differential ACRs between diagnosis and relapse in B-ALL, we identify alterations in chromatin accessibility during drug treatment. Further analysis of ACRs associated with relapse free survival leads to the identification of a subgroup of B-ALL which show early relapse. These data provide an advanced and integrative portrait of the importance of chromatin accessibility alterations in tumorigenesis and drug responses.
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Affiliation(s)
- Han Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bilin Liang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Zhang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Wang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ronghua Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaoyang Cai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjing Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianan Rao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Hu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuang Zhao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Wu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxiao Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kefei Wu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junchen Lai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangyang Xie
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyan Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
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73
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Khodursky S, Zheng EB, Svetec N, Durkin SM, Benjamin S, Gadau A, Wu X, Zhao L. The evolution and mutational robustness of chromatin accessibility in Drosophila. Genome Biol 2023; 24:232. [PMID: 37845780 PMCID: PMC10578003 DOI: 10.1186/s13059-023-03079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates the understanding of the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different species and tissues of Drosophila. RESULTS We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that our models generalize well across substantially evolutionarily diverged species of insects, implying that the sequence determinants of accessibility are highly conserved. Using our model to examine species-specific gains in accessibility, we find evidence suggesting that these regions may be ancestrally poised for evolution. Using in silico mutagenesis, we show that accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that accessibility is mutationally robust. Subsequently, we show that accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. Conversely, simulations under strong selection demonstrate that accessibility can be extremely malleable despite its robustness. Finally, we identify motifs predictive of accessibility, recovering both novel and previously known motifs. CONCLUSIONS These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks to explore fundamental questions in regulatory genomics and evolution.
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Affiliation(s)
- Samuel Khodursky
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Eric B Zheng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Sylvia M Durkin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
- Present Address: Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Sigi Benjamin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Alice Gadau
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Xia Wu
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA.
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Pan J, Chang Z, Zhang X, Dong Q, Zhao H, Shi J, Wang G. Research progress of single-cell sequencing in tuberculosis. Front Immunol 2023; 14:1276194. [PMID: 37901241 PMCID: PMC10611525 DOI: 10.3389/fimmu.2023.1276194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Tuberculosis is a major infectious disease caused by Mycobacterium tuberculosis infection. The pathogenesis and immune mechanism of tuberculosis are not clear, and it is urgent to find new drugs, diagnosis, and treatment targets. A useful tool in the quest to reveal the enigmas related to Mycobacterium tuberculosis infection and disease is the single-cell sequencing technique. By clarifying cell heterogeneity, identifying pathogenic cell groups, and finding key gene targets, the map at the single cell level enables people to better understand the cell diversity of complex organisms and the immune state of hosts during infection. Here, we briefly reviewed the development of single-cell sequencing, and emphasized the different applications and limitations of various technologies. Single-cell sequencing has been widely used in the study of the pathogenesis and immune response of tuberculosis. We review these works summarizing the most influential findings. Combined with the multi-molecular level and multi-dimensional analysis, we aim to deeply understand the blank and potential future development of the research on Mycobacterium tuberculosis infection using single-cell sequencing technology.
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Affiliation(s)
| | | | | | | | | | - Jingwei Shi
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
| | - Guoqing Wang
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
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75
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McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H. Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants. CELL GENOMICS 2023; 3:100404. [PMID: 37868037 PMCID: PMC10589626 DOI: 10.1016/j.xgen.2023.100404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 02/23/2023] [Accepted: 08/21/2023] [Indexed: 10/24/2023]
Abstract
Genome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel reporter assay (MPRA) on 5,173 fine-mapped schizophrenia GWAS variants in primary human neural progenitors and identified 439 variants with allelic regulatory effects (MPRA-positive variants). Transcription factor binding had modest predictive power, while fine-map posterior probability, enhancer overlap, and evolutionary conservation failed to predict MPRA-positive variants. Furthermore, 64% of MPRA-positive variants did not exhibit expressive quantitative trait loci signature, suggesting that MPRA could identify yet unexplored variants with regulatory potentials. To predict the combinatorial effect of MPRA-positive variants on gene regulation, we propose an accessibility-by-contact model that combines MPRA-measured allelic activity with neuronal chromatin architecture.
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Affiliation(s)
- Jessica C. McAfee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sool Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jiseok Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica L. Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kimberly Insigne
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marielle L. Bond
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nanxiang Zhao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P. Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Douglas H. Phanstiel
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - W. Brad Ruzicka
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02141, USA
- Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Quantitative and Computational Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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76
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Arenas-Mena C, Akin S. Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus. Genetics 2023; 225:iyad145. [PMID: 37551428 PMCID: PMC10789315 DOI: 10.1093/genetics/iyad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
Transcriptional regulatory elements (TREs) are the primary nodes that control developmental gene regulatory networks. In embryo stages, larvae, and adult differentiated red spherule cells of the sea urchin Strongylocentrotus purpuratus, transcriptionally engaged TREs are detected by Precision Run-On Sequencing (PRO-seq), which maps genome-wide at base pair resolution the location of paused or elongating RNA polymerase II (Pol II). In parallel, TRE accessibility is estimated by the Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq). Our analysis identifies surprisingly early and widespread TRE accessibility in 4-cell cleavage embryos that is not necessarily followed by concurrent or subsequent transcription. TRE transcriptional differences identified by PRO-seq provide more contrast among embryonic stages than ATAC-seq accessibility differences, in agreement with the apparent excess of accessible but inactive TREs during embryogenesis. Global TRE accessibility reaches a maximum around the 20-hour late blastula stage, which coincides with the consolidation of major embryo regionalizations and peak histone variant H2A.Z expression. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during embryogenesis. However, our results would not reconcile well with labile nucleosome models based on simple A/T sequence enrichment. In addition, a large number of distal TREs become transcriptionally disengaged during developmental progression, in support of an early Pol II paused model for developmental gene regulation that eventually resolves in transcriptional activation or silencing. Thus, developmental potency in early embryos may be facilitated by incipient accessibility and transcriptional pause at TREs.
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Affiliation(s)
- Cesar Arenas-Mena
- Department of Biology, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY, 10314, USA
- PhD Programs in Biology and Biochemistry at the City University of New York (CUNY), Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA
| | - Serhat Akin
- Department of Biology, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY, 10314, USA
- PhD Program in Biology at the City University of New York (CUNY), Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA
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77
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Örd T, Örd D, Adler P, Örd T. Genome-wide census of ATF4 binding sites and functional profiling of trait-associated genetic variants overlapping ATF4 binding motifs. PLoS Genet 2023; 19:e1011014. [PMID: 37906604 PMCID: PMC10637723 DOI: 10.1371/journal.pgen.1011014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/10/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023] Open
Abstract
Activating Transcription Factor 4 (ATF4) is an important regulator of gene expression in stress responses and developmental processes in many cell types. Here, we catalogued ATF4 binding sites in the human genome and identified overlaps with trait-associated genetic variants. We probed these genetic variants for allelic regulatory activity using a massively parallel reporter assay (MPRA) in HepG2 hepatoma cells exposed to tunicamycin to induce endoplasmic reticulum stress and ATF4 upregulation. The results revealed that in the majority of cases, the MPRA allelic activity of these SNPs was in agreement with the nucleotide preference seen in the ATF4 binding motif from ChIP-Seq. Luciferase and electrophoretic mobility shift assays in additional cellular models further confirmed ATF4-dependent regulatory effects for the SNPs rs532446 (GADD45A intronic; linked to hematological parameters), rs7011846 (LPL upstream; myocardial infarction), rs2718215 (diastolic blood pressure), rs281758 (psychiatric disorders) and rs6491544 (educational attainment). CRISPR-Cas9 disruption and/or deletion of the regulatory elements harboring rs532446 and rs7011846 led to the downregulation of GADD45A and LPL, respectively. Thus, these SNPs could represent examples of GWAS genetic variants that affect gene expression by altering ATF4-mediated transcriptional activation.
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Affiliation(s)
- Tiit Örd
- Institute of Genomics, University of Tartu, Tartu, Estonia
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Daima Örd
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Priit Adler
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Tõnis Örd
- Institute of Genomics, University of Tartu, Tartu, Estonia
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78
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Li X, Li Y, Jin Y, Zhang Y, Wu J, Xu Z, Huang Y, Cai L, Gao S, Liu T, Zeng F, Wang Y, Wang W, Yuan TF, Tian H, Shu Y, Guo F, Lu W, Mao Y, Mei X, Rao Y, Peng B. Transcriptional and epigenetic decoding of the microglial aging process. NATURE AGING 2023; 3:1288-1311. [PMID: 37697166 PMCID: PMC10570141 DOI: 10.1038/s43587-023-00479-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/03/2023] [Indexed: 09/13/2023]
Abstract
As important immune cells, microglia undergo a series of alterations during aging that increase the susceptibility to brain dysfunctions. However, the longitudinal characteristics of microglia remain poorly understood. In this study, we mapped the transcriptional and epigenetic profiles of microglia from 3- to 24-month-old mice. We first discovered unexpected sex differences and identified age-dependent microglia (ADEM) genes during the aging process. We then compared the features of aging and reactivity in female microglia at single-cell resolution and epigenetic level. To dissect functions of aged microglia excluding the influence from other aged brain cells, we established an accelerated microglial turnover model without directly affecting other brain cells. By this model, we achieved aged-like microglia in non-aged brains and confirmed that aged-like microglia per se contribute to cognitive decline. Collectively, our work provides a comprehensive resource for decoding the aging process of microglia, shedding light on how microglia maintain brain functions.
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Affiliation(s)
- Xiaoyu Li
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Yuxin Li
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Yuxiao Jin
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Yuheng Zhang
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Jingchuan Wu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhen Xu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yubin Huang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lin Cai
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuai Gao
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Taohui Liu
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Fanzhuo Zeng
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yafei Wang
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Wenxu Wang
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Ti-Fei Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hengli Tian
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yousheng Shu
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Feifan Guo
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Wei Lu
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xifan Mei
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yanxia Rao
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
| | - Bo Peng
- Department of Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, China.
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
- Co-Innovation Center of Neurodegeneration, Nantong University, Nantong, China.
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79
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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80
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Robert S, Rada-Iglesias A. The interaction between enhancer variants and environmental factors as an overlooked aetiological paradigm in human complex disease. Bioessays 2023; 45:e2300038. [PMID: 37170707 DOI: 10.1002/bies.202300038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
The interactions between genetic and environmental risk factors contribute to the aetiology of complex human diseases. Genome-wide association studies (GWAS) have revealed that most of the genetic variants associated with complex diseases are located in the non-coding part of the genome, preferentially within enhancers. Enhancers are distal cis-regulatory elements composed of clusters of transcription factors binding sites that positively regulate the expression of their target genes. The generation of genome-wide maps for histone marks (e.g., H3K27ac), chromatin accessibility and transcription factor and coactivator (e.g., p300) binding profiles have enabled the identification of enhancers across many human cell types and tissues. Nonetheless, the functional and pathological consequences of the majority of disease-associated genetic variants located within enhancers seem to be rather minor under normal conditions, thus questioning their medical relevance. Here we propose that, due to the prevalence of enhancer redundancy, the pathological effects of many disease-associated non-coding genetic variants might be preferentially (or even only) manifested under environmental stress.
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Affiliation(s)
- Sarah Robert
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de, Santander, Cantabria, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de, Santander, Cantabria, Spain
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81
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Gonçalves TM, Stewart CL, Baxley SD, Xu J, Li D, Gabel HW, Wang T, Avraham O, Zhao G. Towards a comprehensive regulatory map of Mammalian Genomes. RESEARCH SQUARE 2023:rs.3.rs-3294408. [PMID: 37841836 PMCID: PMC10571623 DOI: 10.21203/rs.3.rs-3294408/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Genome mapping studies have generated a nearly complete collection of genes for the human genome, but we still lack an equivalently vetted inventory of human regulatory sequences. Cis-regulatory modules (CRMs) play important roles in controlling when, where, and how much a gene is expressed. We developed a training data-free CRM-prediction algorithm, the Mammalian Regulatory MOdule Detector (MrMOD) for accurate CRM prediction in mammalian genomes. MrMOD provides genome position-fixed CRM models similar to the fixed gene models for the mouse and human genomes using only genomic sequences as the inputs with one adjustable parameter - the significance p-value. Importantly, MrMOD predicts a comprehensive set of high-resolution CRMs in the mouse and human genomes including all types of regulatory modules not limited to any tissue, cell type, developmental stage, or condition. We computationally validated MrMOD predictions used a compendium of 21 orthogonal experimental data sets including thousands of experimentally defined CRMs and millions of putative regulatory elements derived from hundreds of different tissues, cell types, and stimulus conditions obtained from multiple databases. In ovo transgenic reporter assay demonstrates the power of our prediction in guiding experimental design. We analyzed CRMs located in the chromosome 17 using unsupervised machine learning and identified groups of CRMs with multiple lines of evidence supporting their functionality, linking CRMs with upstream binding transcription factors and downstream target genes. Our work provides a comprehensive base pair resolution annotation of the functional regulatory elements and non-functional regions in the mammalian genomes.
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Affiliation(s)
| | | | | | - Jason Xu
- Missouri University of Science & Technology
| | - Daofeng Li
- Washington University School of Medicine
| | | | - Ting Wang
- Washington University School of Medicine
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82
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Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J. Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development. Nat Commun 2023; 14:5862. [PMID: 37735176 PMCID: PMC10514308 DOI: 10.1038/s41467-023-41408-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
While the accessibility of enhancers is dynamically regulated during development, promoters tend to be constitutively accessible and poised for activation by paused Pol II. By studying Lola-I, a Drosophila zinc finger transcription factor, we show here that the promoter state can also be subject to developmental regulation independently of gene activation. Lola-I is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers and reveal a mechanism for the de novo establishment of paused Pol II at promoters.
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Affiliation(s)
- Vivekanandan Ramalingam
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center----, Kansas City, KS, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Xinyang Yu
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Michael Buck
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biomedical Informatics, Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center----, Kansas City, KS, USA.
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83
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Cerda-Smith CG, Hutchinson HM, Liu A, Goel VY, Sept C, Kim H, Casaní-Galdón S, Burkman KG, Bassil CF, Hansen AS, Aryee MJ, Johnstone SE, Eyler CE, Wood KC. Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558459. [PMID: 37786671 PMCID: PMC10541578 DOI: 10.1101/2023.09.20.558459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Enhancers possess both structural elements mediating promoter looping and functional elements mediating gene expression. Traditional models of enhancer-mediated gene regulation imply genomic overlap or immediate adjacency of these elements. We test this model by combining densely-tiled CRISPRa screening with nucleosome-resolution Region Capture Micro-C topology analysis. Using this integrated approach, we comprehensively define the cis-regulatory landscape for the tumor suppressor PTEN, identifying and validating 10 distinct enhancers and defining their 3D spatial organization. Unexpectedly, we identify several long-range functional enhancers whose promoter proximity is facilitated by chromatin loop anchors several kilobases away, and demonstrate that accounting for this spatial separation improves the computational prediction of validated enhancers. Thus, we propose a new model of enhancer organization incorporating spatial separation of essential functional and structural components.
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Affiliation(s)
- Christian G. Cerda-Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Haley M. Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Annie Liu
- Department of Surgery, Duke University School of Medicine; Durham, NC 27710, USA
| | - Viraat Y. Goel
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, 02139, USA
- Broad Institute; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Corriene Sept
- Broad Institute; Cambridge, MA 02139, USA
- Department of Biostatistics, Harvard School of Public Health; Boston, MA 02215, USA
| | - Holly Kim
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Salvador Casaní-Galdón
- Broad Institute; Cambridge, MA 02139, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute; Boston, MA 02215, USA
- Departments of Cell Biology and Pathology, Harvard Medical School; Boston, MA 02114, USA
| | - Katherine G. Burkman
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Christopher F. Bassil
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, 02139, USA
- Broad Institute; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Martin J. Aryee
- Broad Institute; Cambridge, MA 02139, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02114, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA 02215, USA
| | - Sarah E. Johnstone
- Broad Institute; Cambridge, MA 02139, USA
- Department of Pathology, Dana-Farber Cancer Institute; Boston, MA 02215, USA
| | - Christine E. Eyler
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine; Durham, NC 27710, USA
| | - Kris C. Wood
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine; Durham, NC 27710, USA
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84
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Huang Y, Zhang J, Li X, Wu Z, Xie G, Wang Y, Liu Z, Jiao M, Zhang H, Shi B, Wang Y, Zhang Y. Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development. FASEB J 2023; 37:e23111. [PMID: 37531300 DOI: 10.1096/fj.202300131rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The post-transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC- and ChIP-seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down-regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.
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Affiliation(s)
- Yuemeng Huang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Zhengqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
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85
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Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.
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86
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Kleinschmidt H, Xu C, Bai L. Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation. Chromosoma 2023; 132:167-189. [PMID: 37184694 PMCID: PMC10542970 DOI: 10.1007/s00412-023-00796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
Abstract
Despite the recent explosion in genome-wide studies in chromatin and gene regulation, we are still far from extracting a set of genetic rules that can predict the function of the regulatory genome. One major reason for this deficiency is that gene regulation is a multi-layered process that involves an enormous variable space, which cannot be fully explored using native genomes. This problem can be partially solved by introducing synthetic DNA libraries into cells, a method that can test the regulatory roles of thousands to millions of sequences with limited variables. Here, we review recent applications of this method to study transcription factor (TF) binding, nucleosome positioning, and transcriptional activity. We discuss the design principles, experimental procedures, and major findings from these studies and compare the pros and cons of different approaches.
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Affiliation(s)
- Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA.
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87
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Cai C, Wan P, Wang H, Cai X, Wang J, Chai Z, Wang J, Wang H, Zhang M, Yang N, Wu Z, Zhu J, Yang X, Li Y, Yue B, Dang R, Zhong J. Transcriptional and open chromatin analysis of bovine skeletal muscle development by single-cell sequencing. Cell Prolif 2023; 56:e13430. [PMID: 36855961 PMCID: PMC10472525 DOI: 10.1111/cpr.13430] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Skeletal muscle is a complex heterogeneous tissue and characterizing its cellular heterogeneity and transcriptional and epigenetic signatures are important for understanding the details of its ontogeny. In our study, we applied scRNA-seq and scATAC-seq to investigate the cell types, molecular features, transcriptional and epigenetic regulation, and patterns of developing bovine skeletal muscle from gestational, lactational and adult stages. Detailed molecular analyses were used to dissect cellular heterogeneity, and we deduced the differentiation trajectory of myogenic cells and uncovered their dynamic gene expression profiles. SCENIC analysis was performed to demonstrate key regulons during cell fate decisions. We explored the future expression states of these heterogeneous cells by RNA velocity analysis and found extensive networks of intercellular communication using the toolkit CellChat. Moreover, the transcriptomic and chromatin accessibility modalities were confirmed to be highly concordant, and integrative analysis of chromatin accessibility and gene expression revealed key transcriptional regulators acting during myogenesis. In bovine skeletal muscle, by scRNA-seq and scATAC-seq analysis, different cell types such as adipocytes, endothelial cells, fibroblasts, lymphocytes, monocytes, pericyte cells and eight skeletal myogenic subpopulations were identified at the three developmental stages. The pseudotime trajectory exhibited a distinct sequential ordering for these myogenic subpopulations and eight distinct gene clusters were observed according to their expression pattern. Moreover, specifically expressed TFs (such as MSC, MYF5, MYOD1, FOXP3, ESRRA, BACH1, SIX2 and ATF4) associated with muscle development were predicted, and likely future transcriptional states of individual cells and the developmental dynamics of differentiation among neighbouring cells were predicted. CellChat analysis on the scRNA-seq data set then classified many ligand-receptor pairs among these cell clusters, which were further categorized into significant signalling pathways, including BMP, IGF, WNT, MSTN, ANGPTL, TGFB, TNF, VEGF and FGF. Finally, scRNA-seq and scATAC-seq results were successfully integrated to reveal a series of specifically expressed TFs that are likely to be candidates for the promotion of cell fate transition during bovine skeletal muscle development. Overall, our results outline a single-cell dynamic chromatin/transcriptional landscape for normal bovine skeletal muscle development; these provide an important resource for understanding the structure and function of mammalian skeletal muscle, which will promote research into its biology.
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Affiliation(s)
- Cuicui Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
- Guyuan BranchNingxia Academy of Agriculture and Forestry SciencesGuyuanChina
| | - Peng Wan
- Guyuan BranchNingxia Academy of Agriculture and Forestry SciencesGuyuanChina
| | - Hui Wang
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Xin Cai
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Jiabo Wang
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Zhixin Chai
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Jikun Wang
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Haibo Wang
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Ming Zhang
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Nan Yang
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Zhijuan Wu
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Xueyao Yang
- Guyuan BranchNingxia Academy of Agriculture and Forestry SciencesGuyuanChina
| | - Yulian Li
- Guyuan BranchNingxia Academy of Agriculture and Forestry SciencesGuyuanChina
| | - Binglin Yue
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Jincheng Zhong
- Key Laboratory of Qinghai‐Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduChina
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88
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Choudalakis M, Kungulovski G, Mauser R, Bashtrykov P, Jeltsch A. Refined read-out: The hUHRF1 Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3. Protein Sci 2023; 32:e4760. [PMID: 37593997 PMCID: PMC10464304 DOI: 10.1002/pro.4760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/19/2023]
Abstract
UHRF1 is an essential chromatin protein required for DNA methylation maintenance, mammalian development, and gene regulation. We investigated the Tandem-Tudor domain (TTD) of human UHRF1 that is known to bind H3K9me2/3 histones and is a major driver of UHRF1 localization in cells. We verified binding to H3K9me2/3 but unexpectedly discovered stronger binding to H3 peptides and mononucleosomes containing K9me2/3 with additional K4me1. We investigated the combined binding of TTD to H3K4me1-K9me2/3 versus H3K9me2/3 alone, engineered mutants with specific and differential changes of binding, and discovered a novel read-out mechanism for H3K4me1 in an H3K9me2/3 context that is based on the interaction of R207 with the H3K4me1 methyl group and on counting the H-bond capacity of H3K4. Individual TTD mutants showed up to a 10,000-fold preference for the double-modified peptides, suggesting that after a conformational change, WT TTD could exhibit similar effects. The frequent appearance of H3K4me1-K9me2 regions in human chromatin demonstrated in our TTD chromatin pull-down and ChIP-western blot data suggests that it has specific biological roles. Chromatin pull-down of TTD from HepG2 cells and full-length murine UHRF1 ChIP-seq data correlate with H3K4me1 profiles indicating that the H3K4me1-K9me2/3 interaction of TTD influences chromatin binding of full-length UHRF1. We demonstrate the H3K4me1-K9me2/3 specific binding of UHRF1-TTD to enhancers and promoters of cell-type-specific genes at the flanks of cell-type-specific transcription factor binding sites, and provided evidence supporting an H3K4me1-K9me2/3 dependent and TTD mediated downregulation of these genes by UHRF1. All these findings illustrate the important physiological function of UHRF1-TTD binding to H3K4me1-K9me2/3 double marks in a cellular context.
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Affiliation(s)
- Michel Choudalakis
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Goran Kungulovski
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Rebekka Mauser
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Pavel Bashtrykov
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Albert Jeltsch
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
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89
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Favaro P, Glass DR, Borges L, Baskar R, Reynolds W, Ho D, Bruce T, Tebaykin D, Scanlon VM, Shestopalov I, Bendall SC. Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555623. [PMID: 37693547 PMCID: PMC10491219 DOI: 10.1101/2023.08.30.555623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine, lower-risk application. To deeply phenotype HSPCs, following a screen of 328 antigens, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary human hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and provide new, detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model were validated with corresponding epigenetic analysis and in vitro clonal differentiation assays. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.
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Affiliation(s)
- Patricia Favaro
- Department of Pathology, Stanford University
- These authors contributed equally
| | - David R. Glass
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Present address: Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Luciene Borges
- Department of Pathology, Stanford University
- Present address: Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
- These authors contributed equally
| | - Reema Baskar
- Department of Pathology, Stanford University
- Present address: Genome Institute of Singapore
| | | | - Daniel Ho
- Department of Pathology, Stanford University
| | | | | | - Vanessa M. Scanlon
- Department of Laboratory Medicine, Yale School of Medicine
- Present address: Center for Regenerative Medicine and Skeletal Biology, University of Connecticut Health
| | | | - Sean C. Bendall
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Lead author
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90
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Sackerson C, Garcia V, Medina N, Maldonado J, Daly J, Cartwright R. Comparative analysis of the myoglobin gene in whales and humans reveals evolutionary changes in regulatory elements and expression levels. PLoS One 2023; 18:e0284834. [PMID: 37643191 PMCID: PMC10464968 DOI: 10.1371/journal.pone.0284834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Cetacea and other diving mammals have undergone numerous adaptations to their aquatic environment, among them high levels of the oxygen-carrying intracellular hemoprotein myoglobin in skeletal muscles. Hypotheses regarding the mechanisms leading to these high myoglobin levels often invoke the induction of gene expression by exercise, hypoxia, and other physiological gene regulatory pathways. Here we explore an alternative hypothesis: that cetacean myoglobin genes have evolved high levels of transcription driven by the intrinsic developmental mechanisms that drive muscle cell differentiation. We have used luciferase assays in differentiated C2C12 cells to test this hypothesis. Contrary to our hypothesis, we find that the myoglobin gene from the minke whale, Balaenoptera acutorostrata, shows a low level of expression, only about 8% that of humans. This low expression level is broadly shared among cetaceans and artiodactylans. Previous work on regulation of the human gene has identified a core muscle-specific enhancer comprised of two regions, the "AT element" and a C-rich sequence 5' of the AT element termed the "CCAC-box". Analysis of the minke whale gene supports the importance of the AT element, but the minke whale CCAC-box ortholog has little effect. Instead, critical positive input has been identified in a G-rich region 3' of the AT element. Also, a conserved E-box in exon 1 positively affects expression, despite having been assigned a repressive role in the human gene. Last, a novel region 5' of the core enhancer has been identified, which we hypothesize may function as a boundary element. These results illustrate regulatory flexibility during evolution. We discuss the possibility that low transcription levels are actually beneficial, and that evolution of the myoglobin protein toward enhanced stability is a critical factor in the accumulation of high myoglobin levels in adult cetacean muscle tissue.
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Affiliation(s)
- Charles Sackerson
- Biology Department, California State University Channel Islands, Camarillo, California, United States of America
| | - Vivian Garcia
- Biology Department, California State University Channel Islands, Camarillo, California, United States of America
| | - Nicole Medina
- Biology Department, California State University Channel Islands, Camarillo, California, United States of America
| | - Jessica Maldonado
- Biology Department, California State University Channel Islands, Camarillo, California, United States of America
| | - John Daly
- Biology Department, California State University Channel Islands, Camarillo, California, United States of America
| | - Rachel Cartwright
- Biology Department, California State University Channel Islands, Camarillo, California, United States of America
- The Keiki Kohola Project, Lahaina, Hawaii, United States of America
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91
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Guzman C, Duttke S, Zhu Y, De Arruda Saldanha C, Downes N, Benner C, Heinz S. Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation. Nucleic Acids Res 2023; 51:e80. [PMID: 37403796 PMCID: PMC10450201 DOI: 10.1093/nar/gkad562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Cis-regulatory elements (CREs) can be classified by the shapes of their transcription start site (TSS) profiles, which are indicative of distinct regulatory mechanisms. Massively parallel reporter assays (MPRAs) are increasingly being used to study CRE regulatory mechanisms, yet the degree to which MPRAs replicate individual endogenous TSS profiles has not been determined. Here, we present a new low-input MPRA protocol (TSS-MPRA) that enables measuring TSS profiles of episomal reporters as well as after lentiviral reporter chromatinization. To sensitively compare MPRA and endogenous TSS profiles, we developed a novel dissimilarity scoring algorithm (WIP score) that outperforms the frequently used earth mover's distance on experimental data. Using TSS-MPRA and WIP scoring on 500 unique reporter inserts, we found that short (153 bp) MPRA promoter inserts replicate the endogenous TSS patterns of ∼60% of promoters. Lentiviral reporter chromatinization did not improve fidelity of TSS-MPRA initiation patterns, and increasing insert size frequently led to activation of extraneous TSS in the MPRA that are not active in vivo. We discuss the implications of our findings, which highlight important caveats when using MPRAs to study transcription mechanisms. Finally, we illustrate how TSS-MPRA and WIP scoring can provide novel insights into the impact of transcription factor motif mutations and genetic variants on TSS patterns and transcription levels.
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Affiliation(s)
- Carlos Guzman
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
- Department of Bioengineering, Graduate Program in Bioinformatics & Systems Biology, U.C. San Diego, La Jolla, CA 92093, USA
| | - Sascha Duttke
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Yixin Zhu
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Camila De Arruda Saldanha
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Nicholas L Downes
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Christopher Benner
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Sven Heinz
- Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
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92
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Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun 2023; 14:4999. [PMID: 37591828 PMCID: PMC10435551 DOI: 10.1038/s41467-023-40505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have linked hundreds of loci to cardiac diseases. However, in most loci the causal variants and their target genes remain unknown. We developed a combined experimental and analytical approach that integrates single cell epigenomics with GWAS to prioritize risk variants and genes. We profiled accessible chromatin in single cells obtained from human hearts and leveraged the data to study genetics of Atrial Fibrillation (AF), the most common cardiac arrhythmia. Enrichment analysis of AF risk variants using cell-type-resolved open chromatin regions (OCRs) implicated cardiomyocytes as the main mediator of AF risk. We then performed statistical fine-mapping, leveraging the information in OCRs, and identified putative causal variants in 122 AF-associated loci. Taking advantage of the fine-mapping results, our novel statistical procedure for gene discovery prioritized 46 high-confidence risk genes, highlighting transcription factors and signal transduction pathways important for heart development. In summary, our analysis provides a comprehensive map of AF risk variants and genes, and a general framework to integrate single-cell genomics with genetic studies of complex traits.
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Affiliation(s)
- Alan Selewa
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Kaixuan Luo
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael Wasney
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Linsin Smith
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaotong Sun
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chenwei Tang
- The College, The University of Chicago, Chicago, IL, 60637, USA
| | - Heather Eckart
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ivan P Moskowitz
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA
| | - Anindita Basu
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Sebastian Pott
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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93
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Yuan Y, Chen Q, Brovkina M, Clowney EJ, Yadlapalli S. Clock-dependent chromatin accessibility rhythms regulate circadian transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553315. [PMID: 37645872 PMCID: PMC10462003 DOI: 10.1101/2023.08.15.553315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility over the circadian cycle. We observed significant circadian oscillations in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible throughout the circadian cycle, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons.
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Affiliation(s)
- Ye Yuan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qianqian Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Margarita Brovkina
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - E Josephine Clowney
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA
| | - Swathi Yadlapalli
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA
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94
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Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, Ahituv N, Abyzov A, Vaccarino FM. Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553170. [PMID: 37645832 PMCID: PMC10461976 DOI: 10.1101/2023.08.14.553170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Regulation of gene expression through enhancers is one of the major processes shaping the structure and function of the human brain during development. High-throughput assays have predicted thousands of enhancers involved in neurodevelopment, and confirming their activity through orthogonal functional assays is crucial. Here, we utilized Massively Parallel Reporter Assays (MPRAs) in stem cells and forebrain organoids to evaluate the activity of ~7,000 gene-linked enhancers previously identified in human fetal tissues and brain organoids. We used a Gaussian mixture model to evaluate the contribution of background noise in the measured activity signal to confirm the activity of ~35% of the tested enhancers, with most showing temporal-specific activity, suggesting their evolving role in neurodevelopment. The temporal specificity was further supported by the correlation of activity with gene expression. Our findings provide a valuable gene regulatory resource to the scientific community.
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Affiliation(s)
- Davide Capauto
- Child Study Center, Yale University, New Haven, CT 06520
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT 06520
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520
| | | | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University; Kyoto, Japan
| | | | | | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Flora M. Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
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95
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Gosai SJ, Castro RI, Fuentes N, Butts JC, Kales S, Noche RR, Mouri K, Sabeti PC, Reilly SK, Tewhey R. Machine-guided design of synthetic cell type-specific cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552077. [PMID: 37609287 PMCID: PMC10441439 DOI: 10.1101/2023.08.08.552077] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in the body. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for an intended purpose has arisen naturally through evolution. Here, we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell type specificity. We leverage innovations in deep neural network modeling of CRE activity across three cell types, efficient in silico optimization, and massively parallel reporter assays (MPRAs) to design and empirically test thousands of CREs. Through in vitro and in vivo validation, we show that synthetic sequences outperform natural sequences from the human genome in driving cell type-specific expression. Synthetic sequences leverage unique sequence syntax to promote activity in the on-target cell type and simultaneously reduce activity in off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs and demonstrate the required literacy to write regulatory code that is fit-for-purpose in vivo across vertebrates.
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Affiliation(s)
- SJ Gosai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston MA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - RI Castro
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - N Fuentes
- The Jackson Laboratory, Bar Harbor, ME, USA
- Harvard College, Harvard University, Cambridge, MA, USA
| | - JC Butts
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
| | - S Kales
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - RR Noche
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Zebrafish Research Core, Yale School of Medicine, New Haven, CT, USA
| | - K Mouri
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - PC Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - SK Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
| | - R Tewhey
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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96
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Klein DC, Lardo SM, McCannell KN, Hainer SJ. FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells. BMC Biol 2023; 21:167. [PMID: 37542287 PMCID: PMC10403911 DOI: 10.1186/s12915-023-01669-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND The FACT complex is a conserved histone chaperone with critical roles in transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or inhibition can block induction of pluripotent stem cells, yet the mechanism through which FACT regulates cell fate decisions remains unclear. RESULTS To explore the mechanism for FACT function, we generated AID-tagged murine embryonic cell lines for FACT subunit SPT16 and paired depletion with nascent transcription and chromatin accessibility analyses. We also analyzed SPT16 occupancy using CUT&RUN and found that SPT16 localizes to both promoter and enhancer elements, with a strong overlap in binding with OCT4, SOX2, and NANOG. Over a timecourse of SPT16 depletion, nucleosomes invade new loci, including promoters, regions bound by SPT16, OCT4, SOX2, and NANOG, and TSS-distal DNaseI hypersensitive sites. Simultaneously, transcription of Pou5f1 (encoding OCT4), Sox2, Nanog, and enhancer RNAs produced from these genes' associated enhancers are downregulated. CONCLUSIONS We propose that FACT maintains cellular pluripotency through a precise nucleosome-based regulatory mechanism for appropriate expression of both coding and non-coding transcripts associated with pluripotency.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Santana M Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Kurtis N McCannell
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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97
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Medina TS, Murison A, Smith M, Kinker GS, Chakravarthy A, Vitiello GAF, Turpin W, Shen SY, Yau HL, Sarmento OF, Faubion W, Lupien M, Silverberg MS, Arrowsmith CH, De Carvalho DD. The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population. Front Immunol 2023; 14:1161901. [PMID: 37600767 PMCID: PMC10436103 DOI: 10.3389/fimmu.2023.1161901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The imbalance between Th17 and regulatory T cells in inflammatory bowel diseases (IBD) promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate or repress gene expression. Methods Here, we characterized the chromatin landscape and heterogeneity of intestinal and peripheral CD4 T cellsfrom IBD patients using in house ATAC-Seq and single cell RNA-Seq libraries. Results We show that chromatin accessibility profiles of CD4 T cells from inflamed intestinal biopsies relate to genes associated with a network of inflammatory processes. After integrating the chromatin profiles of tissue-derived CD4 T cells and in-vitro polarized CD4 T cell subpopulations, we found that the chromatin accessibility changes of CD4 T cells were associated with a higher predominance of pathogenic Th17 cells (pTh17 cells) in inflamed biopsies. In addition, IBD risk loci in CD4 T cells were colocalized with accessible chromatin changes near pTh17-related genes, as shown in intronic STAT3 and IL23R regions enriched in areas of active intestinal inflammation. Moreover, single cell RNA-Seq analysis revealed a population of pTh17 cells that co-expresses Th1 and cytotoxic transcriptional programs associated with IBD severity. Discussion Altogether, we show that cytotoxic pTh17 cells were specifically associated with IBD genetic variants and linked to intestinal inflammation of IBD patients.
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Affiliation(s)
- Tiago S. Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle Smith
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Gabriela S. Kinker
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Williams Turpin
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen L. Yau
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Olga F. Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - William Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mark S. Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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98
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Baker BH, Zhang S, Simon JM, McLarnan SM, Chung WK, Pearson BL. Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Front Neurosci 2023; 17:1106573. [PMID: 37599994 PMCID: PMC10435087 DOI: 10.3389/fnins.2023.1106573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction De novo mutations contribute to a large proportion of sporadic psychiatric and developmental disorders, yet the potential role of environmental carcinogens as drivers of causal de novo mutations in neurodevelopmental disorders is poorly studied. Methods To explore environmental mutation vulnerability of disease-associated gene sets, we analyzed publicly available whole genome sequencing datasets of mutations in human induced pluripotent stem cell clonal lines exposed to 12 classes of environmental carcinogens, and human lung cancers from individuals living in highly polluted regions. We compared observed rates of exposure-induced mutations in disease-related gene sets with the expected rates of mutations based on control genes randomly sampled from the genome using exact binomial tests. To explore the role of sequence characteristics in mutation vulnerability, we modeled the effects of sequence length, gene expression, and percent GC content on mutation rates of entire genes and gene coding sequences using multivariate Quasi-Poisson regressions. Results We demonstrate that several mutagens, including radiation and polycyclic aromatic hydrocarbons, disproportionately mutate genes related to neurodevelopmental disorders including autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder. Other disease genes including amyotrophic lateral sclerosis, Alzheimer's disease, congenital heart disease, orofacial clefts, and coronary artery disease were generally not mutated more than expected. Longer sequence length was more strongly associated with elevated mutations in entire genes compared with mutations in coding sequences. Increased expression was associated with decreased coding sequence mutation rate, but not with the mutability of entire genes. Increased GC content was associated with increased coding sequence mutation rates but decreased mutation rates in entire genes. Discussion Our findings support the possibility that neurodevelopmental disorder genetic etiology is partially driven by a contribution of environment-induced germ line and somatic mutations.
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Affiliation(s)
- Brennan H. Baker
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shaoyi Zhang
- Master of Public Health Program, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeremy M. Simon
- Department of Genetics and Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah M. McLarnan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Brandon L. Pearson
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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99
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Yankee TN, Oh S, Winchester EW, Wilderman A, Robinson K, Gordon T, Rosenfeld JA, VanOudenhove J, Scott DA, Leslie EJ, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nat Commun 2023; 14:4623. [PMID: 37532691 PMCID: PMC10397224 DOI: 10.1038/s41467-023-40363-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Craniofacial disorders arise in early pregnancy and are one of the most common congenital defects. To fully understand how craniofacial disorders arise, it is essential to characterize gene expression during the patterning of the craniofacial region. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from 4-8 weeks post conception. Comparisons to dozens of other human tissues revealed 239 genes most strongly expressed during craniofacial development. Craniofacial-biased developmental enhancers were enriched +/- 400 kb surrounding these craniofacial-biased genes. Gene co-expression analysis revealed that regulatory hubs are enriched for known disease causing genes and are resistant to mutation in the normal healthy population. Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. While most have not been previously implicated in craniofacial disorders, we demonstrate this set of genes has increased levels of de novo mutations in orofacial clefting patients warranting further study.
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Affiliation(s)
- Tara N Yankee
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Sungryong Oh
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | | | - Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tia Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Jennifer VanOudenhove
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Justin Cotney
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, Wang E, Sakellaropoulos T, Boccalatte F, Thandapani P, Skok J, Aifantis I, Fenyö D, Xia B, Tsirigos A. Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nat Biotechnol 2023; 41:1140-1150. [PMID: 36624151 PMCID: PMC10329734 DOI: 10.1038/s41587-022-01612-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/14/2022] [Indexed: 01/11/2023]
Abstract
Investigating how chromatin organization determines cell-type-specific gene expression remains challenging. Experimental methods for measuring three-dimensional chromatin organization, such as Hi-C, are costly and have technical limitations, restricting their broad application particularly in high-throughput genetic perturbations. We present C.Origami, a multimodal deep neural network that performs de novo prediction of cell-type-specific chromatin organization using DNA sequence and two cell-type-specific genomic features-CTCF binding and chromatin accessibility. C.Origami enables in silico experiments to examine the impact of genetic changes on chromatin interactions. We further developed an in silico genetic screening approach to assess how individual DNA elements may contribute to chromatin organization and to identify putative cell-type-specific trans-acting regulators that collectively determine chromatin architecture. Applying this approach to leukemia cells and normal T cells, we demonstrate that cell-type-specific in silico genetic screening, enabled by C.Origami, can be used to systematically discover novel chromatin regulation circuits in both normal and disease-related biological systems.
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Affiliation(s)
- Jimin Tan
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
| | - Nina Shenker-Tauris
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- The Jackson Laboratory for Genomics Medicine, Farmington, CT, USA
| | | | - Francesco Boccalatte
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Palaniraja Thandapani
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Jane Skok
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Bo Xia
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY, USA.
- Society of Fellows, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, USA.
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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