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Mulet-Lazaro R, Delwel R. Oncogenic Enhancers in Leukemia. Blood Cancer Discov 2024; 5:303-317. [PMID: 39093124 PMCID: PMC11369600 DOI: 10.1158/2643-3230.bcd-23-0211] [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: 03/01/2024] [Revised: 06/06/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
Although the study of leukemogenesis has traditionally focused on protein-coding genes, the role of enhancer dysregulation is becoming increasingly recognized. The advent of high-throughput sequencing, together with a better understanding of enhancer biology, has revealed how various genetic and epigenetic lesions produce oncogenic enhancers that drive transformation. These aberrations include translocations that lead to enhancer hijacking, point mutations that modulate enhancer activity, and copy number alterations that modify enhancer dosage. In this review, we describe these mechanisms in the context of leukemia and discuss potential therapeutic avenues to target these regulatory elements. Significance: Large-scale sequencing projects have uncovered recurrent gene mutations in leukemia, but the picture remains incomplete: some patients harbor no such aberrations, whereas others carry only a few that are insufficient to bring about transformation on their own. One of the missing pieces is enhancer dysfunction, which only recently has emerged as a critical driver of leukemogenesis. Knowledge of the various mechanisms of enhancer dysregulation is thus key for a complete understanding of leukemia and its causes, as well as the development of targeted therapies in the era of precision medicine.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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2
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Kimura Y, Ono Y, Katayama K, Imoto S. IVEA: an integrative variational Bayesian inference method for predicting enhancer-gene regulatory interactions. BIOINFORMATICS ADVANCES 2024; 4:vbae118. [PMID: 39193566 PMCID: PMC11349192 DOI: 10.1093/bioadv/vbae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/26/2024] [Accepted: 08/18/2024] [Indexed: 08/29/2024]
Abstract
Motivation Enhancers play critical roles in cell-type-specific transcriptional control. Despite the identification of thousands of candidate enhancers, unravelling their regulatory relationships with their target genes remains challenging. Therefore, computational approaches are needed to accurately infer enhancer-gene regulatory relationships. Results In this study, we propose a new method, IVEA, that predicts enhancer-gene regulatory interactions by estimating promoter and enhancer activities. Its statistical model is based on the gene regulatory mechanism of transcriptional bursting, which is characterized by burst size and frequency controlled by promoters and enhancers, respectively. Using transcriptional readouts, chromatin accessibility, and chromatin contact data as inputs, promoter and enhancer activities were estimated using variational Bayesian inference, and the contribution of each enhancer-promoter pair to target gene transcription was calculated. Our analysis demonstrates that the proposed method can achieve high prediction accuracy and provide biologically relevant enhancer-gene regulatory interactions. Availability and implementation The IVEA code is available on GitHub at https://github.com/yasumasak/ivea. The publicly available datasets used in this study are described in Supplementary Table S4.
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Affiliation(s)
- Yasumasa Kimura
- DX Drug Discovery Department, Daiichi Sankyo RD Novare Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Research Function Research Innovation Planning Department, Daiichi Sankyo Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan
| | - Yoshimasa Ono
- DX Drug Discovery Department, Daiichi Sankyo RD Novare Co., Ltd., Edogawa-ku, Tokyo 134-8630, Japan
| | - Kotoe Katayama
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
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3
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Zhao J, Zhou Y, Tzelepis I, Burget NG, Shi J, Faryabi RB. Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells. SCIENCE ADVANCES 2024; 10:eadl4043. [PMID: 39110799 PMCID: PMC11305386 DOI: 10.1126/sciadv.adl4043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Sequencing-based mapping of ensemble pairwise interactions among regulatory elements support the existence of topological assemblies known as promoter-enhancer hubs or cliques in cancer. Yet, prevalence, regulators, and functions of promoter-enhancer hubs in individual cancer cells remain unclear. Here, we systematically integrated functional genomics, transcription factor screening, and optical mapping of promoter-enhancer interactions to identify key promoter-enhancer hubs, examine heterogeneity of their assembly, determine their regulators, and elucidate their role in gene expression control in individual triple negative breast cancer (TNBC) cells. Optical mapping of individual SOX9 and MYC alleles revealed the existence of frequent multiway interactions among promoters and enhancers within spatial hubs. Our single-allele studies further demonstrated that lineage-determining SOX9 and signaling-dependent NOTCH1 transcription factors compact MYC and SOX9 hubs. Together, our findings suggest that promoter-enhancer hubs are dynamic and heterogeneous topological assemblies, which are controlled by oncogenic transcription factors and facilitate subtype-restricted gene expression in cancer.
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Affiliation(s)
- Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ilias Tzelepis
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Noah G. Burget
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert B. Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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4
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Naderi J, Magalhaes AP, Kibar G, Stik G, Zhang Y, Mackowiak SD, Wieler HM, Rossi F, Buschow R, Christou-Kent M, Alcoverro-Bertran M, Graf T, Vingron M, Hnisz D. An activity-specificity trade-off encoded in human transcription factors. Nat Cell Biol 2024; 26:1309-1321. [PMID: 38969762 PMCID: PMC11321997 DOI: 10.1038/s41556-024-01411-0] [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: 01/27/2023] [Accepted: 03/20/2024] [Indexed: 07/07/2024]
Abstract
Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and specificity in human TFs encoded as submaximal dispersion of aromatic residues in their intrinsically disordered protein regions. We identified approximately 500 human TFs that encode short periodic blocks of aromatic residues in their intrinsically disordered regions, resembling imperfect prion-like sequences. Mutation of periodic aromatic residues reduced transcriptional activity, whereas increasing the aromatic dispersion of multiple human TFs enhanced transcriptional activity and reprogramming efficiency, promoted liquid-liquid phase separation in vitro and more promiscuous DNA binding in cells. Together with recent work on enhancer elements, these results suggest an important evolutionary role of suboptimal features in transcriptional control. We propose that rational engineering of amino acid features that alter phase separation may be a strategy to optimize TF-dependent processes, including cellular reprogramming.
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Affiliation(s)
- Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Alexandre P Magalhaes
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gözde Kibar
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gregoire Stik
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Yaotian Zhang
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hannah M Wieler
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Francesca Rossi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rene Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marie Christou-Kent
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Alcoverro-Bertran
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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5
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Ichiyama-Kobayashi S, Hata K, Wakamori K, Takahata Y, Murakami T, Yamanaka H, Takano H, Yao R, Uzawa N, Nishimura R. Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development. JCI Insight 2024; 9:e175486. [PMID: 38855864 DOI: 10.1172/jci.insight.175486] [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: 09/06/2023] [Accepted: 05/01/2024] [Indexed: 06/11/2024] Open
Abstract
The transcription factor SRY-related HMG box 9 (Sox9) is essential for chondrogenesis. Mutations in and around SOX9 cause campomelic dysplasia (CD) characterized by skeletal malformations. Although the function of Sox9 in this context is well studied, the mechanisms that regulate Sox9 expression in chondrocytes remain to be elucidated. Here, we have used genome-wide profiling to identify 2 Sox9 enhancers located in a proximal breakpoint cluster responsible for CD. Enhancer activity of E308 (located 308 kb 5' upstream) and E160 (located 160 kb 5' upstream) correlated with Sox9 expression levels, and both enhancers showed a synergistic effect in vitro. While single deletions in mice had no apparent effect, simultaneous deletion of both E308 and E160 caused a dwarf phenotype, concomitant with a reduction of Sox9 expression in chondrocytes. Moreover, bone morphogenetic protein 2-dependent chondrocyte differentiation of limb bud mesenchymal cells was severely attenuated in E308/E160 deletion mice. Finally, we found that an open chromatin region upstream of the Sox9 gene was reorganized in the E308/E160 deletion mice to partially compensate for the loss of E308 and E160. In conclusion, our findings reveal a mechanism of Sox9 gene regulation in chondrocytes that might aid in our understanding of the pathophysiology of skeletal disorders.
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Affiliation(s)
- Sachi Ichiyama-Kobayashi
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry
| | - Kanta Wakamori
- Department of Molecular and Cellular Biochemistry
- Department of Oral and Maxillofacial Oncology and Surgery, and
| | - Yoshifumi Takahata
- Department of Molecular and Cellular Biochemistry
- Genome Editing Research and Development Unit, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | | | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Hiroshi Takano
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Narikazu Uzawa
- Department of Oral and Maxillofacial Oncology and Surgery, and
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6
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Wu C, Huang J. Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns. BMC Genomics 2024; 25:483. [PMID: 38750461 PMCID: PMC11097474 DOI: 10.1186/s12864-024-10408-w] [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: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Multiple enhancers co-regulating the same gene is prevalent and plays a crucial role during development and disease. However, how multiple enhancers coordinate the same gene expression across various cell types remains largely unexplored at genome scale. RESULTS We develop a computational approach that enables the quantitative assessment of enhancer specificity and selectivity across diverse cell types, leveraging enhancer-promoter (E-P) interactions data. We observe two well-known gene regulation patterns controlled by enhancer clusters, which regulate the same gene either in a limited number of cell types (Specific pattern, Spe) or in the majority of cell types (Conserved pattern, Con), both of which are enriched for super-enhancers (SEs). We identify a previously overlooked pattern (Variable pattern, Var) that multiple enhancers link to the same gene, but rarely coexist in the same cell type. These three patterns control the genes associating with distinct biological function and exhibit unique epigenetic features. Specifically, we discover a subset of Var patterns contains Shared enhancers with stable enhancer-promoter interactions in the majority of cell types, which might contribute to maintaining gene expression by recruiting abundant CTCF. CONCLUSIONS Together, our findings reveal three distinct E-P regulation patterns across different cell types, providing insights into deciphering the complexity of gene transcriptional regulation.
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Affiliation(s)
- Chengyi Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, Fujian, China.
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7
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Ling Z, Li J, Jiang T, Zhang Z, Zhu Y, Zhou Z, Yang J, Tong X, Yang B, Huang L. Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits. Commun Biol 2024; 7:381. [PMID: 38553586 PMCID: PMC10980749 DOI: 10.1038/s42003-024-06050-7] [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: 09/09/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that affect the activity of regulatory elements in pigs are largely unknown, and the extent to which these variants influence gene expression and contribute to the understanding of complex phenotypes remains unclear. Here, we annotate 90,991 high-quality regulatory elements using acetylation of histone H3 on lysine 27 (H3K27ac) ChIP-seq of 292 pig livers. Combined with genome resequencing and RNA-seq data, we identify 28,425 H3K27ac quantitative trait loci (acQTLs) and 12,250 expression quantitative trait loci (eQTLs). Through the allelic imbalance analysis, we validate two causative acQTL variants in independent datasets. We observe substantial sharing of genetic controls between gene expression and H3K27ac, particularly within promoters. We infer that 46% of H3K27ac exhibit a concomitant rather than causative relationship with gene expression. By integrating GWAS, eQTLs, acQTLs, and transcription factor binding prediction, we further demonstrate their application, through metabolites dulcitol, phosphatidylcholine (PC) (16:0/16:0) and published phenotypes, in identifying likely causal variants and genes, and discovering sub-threshold GWAS loci. We provide insight into the relationship between regulatory elements and gene expression, and the genetic foundation for dissecting the molecular mechanism of phenotypes.
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Affiliation(s)
- Ziqi Ling
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Jing Li
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Tao Jiang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhen Zhang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Yaling Zhu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhimin Zhou
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Jiawen Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Xinkai Tong
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Bin Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Lusheng Huang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
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8
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Patel A, Dharap A. An Emerging Role for Enhancer RNAs in Brain Disorders. Neuromolecular Med 2024; 26:7. [PMID: 38546891 PMCID: PMC11263973 DOI: 10.1007/s12017-024-08776-3] [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: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Noncoding DNA undergoes widespread context-dependent transcription to produce noncoding RNAs. In recent decades, tremendous advances in genomics and transcriptomics have revealed important regulatory roles for noncoding DNA elements and the RNAs that they produce. Enhancers are one such element that are well-established drivers of gene expression changes in response to a variety of factors such as external stimuli, cellular responses, developmental cues, and disease states. They are known to act at long distances, interact with multiple target gene loci simultaneously, synergize with other enhancers, and associate with dynamic chromatin architectures to form a complex regulatory network. Recent advances in enhancer biology have revealed that upon activation, enhancers transcribe long noncoding RNAs, known as enhancer RNAs (eRNAs), that have been shown to play important roles in enhancer-mediated gene regulation and chromatin-modifying activities. In the brain, enhancer dysregulation and eRNA transcription has been reported in numerous disorders from acute injuries to chronic neurodegeneration. Because this is an emerging area, a comprehensive understanding of eRNA function has not yet been achieved in brain disorders; however, the findings to date have illuminated a role for eRNAs in activity-driven gene expression and phenotypic outcomes. In this review, we highlight the breadth of the current literature on eRNA biology in brain health and disease and discuss the challenges as well as focus areas and strategies for future in-depth research on eRNAs in brain health and disease.
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Affiliation(s)
- Ankit Patel
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA
| | - Ashutosh Dharap
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA.
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA.
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9
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Basurto-Cayuela L, Guerrero-Martínez JA, Gómez-Marín E, Sánchez-Escabias E, Escaño-Maestre M, Ceballos-Chávez M, Reyes JC. SWI/SNF-dependent genes are defined by their chromatin landscape. Cell Rep 2024; 43:113855. [PMID: 38427563 DOI: 10.1016/j.celrep.2024.113855] [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: 03/31/2023] [Revised: 11/23/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024] Open
Abstract
SWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014, an inhibitor of the ATPase activity of the complexes. We find that SWI/SNF activity is required to maintain chromatin accessibility and nucleosome occupancy for most enhancers but not for most promoters. SWI/SNF activity is needed for expression of genes with low to medium levels of expression that have promoters with (1) low chromatin accessibility, (2) low levels of active histone marks, (3) high H3K4me1/H3K4me3 ratio, (4) low nucleosomal phasing, and (5) enrichment in TATA-box motifs. These promoters are mostly occupied by the canonical Brahma-related gene 1/Brahma-associated factor (BAF) complex. These genes are surrounded by SWI/SNF-dependent enhancers and mainly encode signal transduction, developmental, and cell identity genes (with almost no housekeeping genes). Machine-learning models trained with different chromatin characteristics of promoters and their surrounding regulatory regions indicate that the chromatin landscape is a determinant for establishing SWI/SNF dependency.
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Affiliation(s)
- Laura Basurto-Cayuela
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José A Guerrero-Martínez
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Elena Gómez-Marín
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Elena Sánchez-Escabias
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Escaño-Maestre
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Ceballos-Chávez
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José C Reyes
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain.
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10
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Toneyan S, Koo PK. Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.03.547592. [PMID: 37461616 PMCID: PMC10349992 DOI: 10.1101/2023.07.03.547592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The rise of large-scale, sequence-based deep neural networks (DNNs) for predicting gene expression has introduced challenges in their evaluation and interpretation. Current evaluations align DNN predictions with experimental perturbation assays, which provides insights into the generalization capabilities within the studied loci but offers a limited perspective of what drives their predictions. Moreover, existing model explainability tools focus mainly on motif analysis, which becomes complex when interpreting longer sequences. Here we introduce CREME, an in silico perturbation toolkit that interrogates large-scale DNNs to uncover rules of gene regulation that it learns. Using CREME, we investigate Enformer, a prominent DNN in gene expression prediction, revealing cis-regulatory elements (CREs) that directly enhance or silence target genes. We explore the intricate complexity of higher-order CRE interactions, the relationship between CRE distance from transcription start sites on gene expression, as well as the biochemical features of enhancers and silencers learned by Enformer. Moreover, we demonstrate the flexibility of CREME to efficiently uncover a higher-resolution view of functional sequence elements within CREs. This work demonstrates how CREME can be employed to translate the powerful predictions of large-scale DNNs to study open questions in gene regulation.
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11
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Zhu X, Zhang Y, Yin Z, Ye Z, Qin Y, Cheng Z, Shen Y, Yin Z, Ma J, Tang Y, Ding H, Guo Y, Hou G, Shen N. Three-Dimensional Chromosomal Landscape Revealing miR-146a Dysfunctional Enhancer in Lupus and Establishing a CRISPR-Mediated Approach to Inhibit the Interferon Pathway. Arthritis Rheumatol 2024; 76:384-395. [PMID: 37728419 DOI: 10.1002/art.42703] [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: 02/05/2023] [Revised: 08/28/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVE The diminished expression of microRNA-146a (miR-146a) in systemic lupus erythematosus (SLE) contributes to the aberrant activation of the interferon pathway. Despite its significance, the underlying mechanism driving this reduced expression remains elusive. Considering the integral role of enhancers in steering gene expression, our study seeks to pinpoint the SLE-affected enhancers responsible for modulating miR-146a expression. Additionally, we aim to elucidate the mechanisms by which these enhancers influence the contribution of miR-146a to the activation of the interferon pathway. METHODS Circular chromosome conformation capture sequencing and epigenomic profiles were applied to identify candidate enhancers of miR-146a. CRISPR activation was performed to screen functional enhancers. Differential analysis of chromatin accessibility was used to identify SLE-dysregulated enhancers, and the mechanism underlying enhancer dysfunction was investigated by analyzing transcription factor binding. The therapeutic value of a lupus-related enhancer was further evaluated by targeting it in the peripheral blood mononuclear cells (PBMCs) of patients with SLE through a CRISPR activation approach. RESULTS We identified shared and cell-specific enhancers of miR-146a in distinct immune cells. An enhancer 32.5 kb downstream of miR-146a possesses less accessibility in SLE, and its chromatin openness was negatively correlated with SLE disease activity. Moreover, CCAAT/enhancer binding protein α, a down-regulated transcription factor in patients with SLE, binds to the 32.5-kb enhancer and induces the epigenomic change of this locus. Furthermore, CRISPR-based activation of this enhancer in SLE PBMCs could inhibit the activity of interferon pathway. CONCLUSION Our work defines a promising target for SLE intervention. We adopted integrative approaches to define cell-specific and functional enhancers of the SLE critical gene and investigated the mechanism underlying its dysregulation mediated by a lupus-related enhancer.
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Affiliation(s)
- Xinyi Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Yutong Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zihang Yin
- Sheng Yushou Center of Cell Biology and Immunology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Yuting Qin
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaorui Cheng
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiwei Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ya Guo
- Sheng Yushou Center of Cell Biology and Immunology, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China, and Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
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12
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. G3 (BETHESDA, MD.) 2024; 14:jkad269. [PMID: 38124496 PMCID: PMC11090500 DOI: 10.1093/g3journal/jkad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of Cebpa during macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
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13
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Lack N, Altintas UB, Seo JH, Giambartolomei C, Ozturan D, Fortunato B, Nelson G, Goldman S, Adelman K, Hach F, Freedman M. Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription. RESEARCH SQUARE 2024:rs.3.rs-3854707. [PMID: 38352568 PMCID: PMC10862967 DOI: 10.21203/rs.3.rs-3854707/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Androgen receptor (AR)-mediated transcription plays a critical role in normal prostate development and prostate cancer growth. AR drives gene expression by binding to thousands of cis-regulatory elements (CRE) that loop to hundreds of target promoters. With multiple CREs interacting with a single promoter, it remains unclear how individual AR bound CREs contribute to gene expression. To characterize the involvement of these CREs, we investigated the AR-driven epigenetic and chromosomal chromatin looping changes. We collected a kinetic multi-omic dataset comprised of steady-state mRNA, chromatin accessibility, transcription factor binding, histone modifications, chromatin looping, and nascent RNA. Using an integrated regulatory network, we found that AR binding induces sequential changes in the epigenetic features at CREs, independent of gene expression. Further, we showed that binding of AR does not result in a substantial rewiring of chromatin loops, but instead increases the contact frequency of pre-existing loops to target promoters. Our results show that gene expression strongly correlates to the changes in contact frequency. We then proposed and experimentally validated an unbalanced multi-enhancer model where the impact on gene expression of AR-bound enhancers is heterogeneous, and is proportional to their contact frequency with target gene promoters. Overall, these findings provide new insight into AR-mediated gene expression upon acute androgen simulation and develop a mechanistic framework to investigate nuclear receptor mediated perturbations.
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14
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Mañes-García J, Marco-Ferreres R, Beccari L. Shaping gene expression and its evolution by chromatin architecture and enhancer activity. Curr Top Dev Biol 2024; 159:406-437. [PMID: 38729683 DOI: 10.1016/bs.ctdb.2024.01.001] [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] [Indexed: 05/12/2024]
Abstract
Transcriptional regulation plays a pivotal role in orchestrating the intricate genetic programs governing embryonic development. The expression of developmental genes relies on the combined activity of several cis-regulatory elements (CREs), such as enhancers and silencers, which can be located at long linear distances from the genes that they regulate and that interact with them through establishment of chromatin loops. Mutations affecting their activity or interaction with their target genes can lead to developmental disorders and are thought to have importantly contributed to the evolution of the animal body plan. The income of next-generation-sequencing approaches has allowed identifying over a million of sequences with putative regulatory potential in the human genome. Characterizing their function and establishing gene-CREs maps is essential to decode the logic governing developmental gene expression and is one of the major challenges of the post-genomic era. Chromatin 3D organization plays an essential role in determining how CREs specifically contact their target genes while avoiding deleterious off-target interactions. Our understanding of these aspects has greatly advanced with the income of chromatin conformation capture techniques and fluorescence microscopy approaches to visualize the organization of DNA elements in the nucleus. Here we will summarize relevant aspects of how the interplay between CRE activity and chromatin 3D organization regulates developmental gene expression and how it relates to pathological conditions and the evolution of animal body plan.
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Affiliation(s)
| | | | - Leonardo Beccari
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.
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15
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Wilderman A, D'haene E, Baetens M, Yankee TN, Winchester EW, Glidden N, Roets E, Van Dorpe J, Janssens S, Miller DE, Galey M, Brown KM, Stottmann RW, Vergult S, Weaver KN, Brugmann SA, Cox TC, Cotney J. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development. Nat Commun 2024; 15:136. [PMID: 38167838 PMCID: PMC10762089 DOI: 10.1038/s41467-023-44506-2] [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: 03/24/2022] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Craniofacial abnormalities account for approximately one third of birth defects. The regulatory programs that build the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Clusters of coactivated enhancers and their target genes, known as superenhancers, are important in determining cell identity but have been largely unexplored in development. In this study we identified superenhancer regions unique to human embryonic craniofacial tissue. To demonstrate the importance of such regions in craniofacial development and disease, we focused on an ~600 kb noncoding region located between NPVF and NFE2L3. We identified long range interactions with this region in both human and mouse embryonic craniofacial tissue with the anterior portion of the HOXA gene cluster. Mice lacking this superenhancer exhibit perinatal lethality, and present with highly penetrant skull defects and orofacial clefts phenocopying Hoxa2-/- mice. Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.
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Affiliation(s)
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Emma Wentworth Winchester
- Graduate Program UConn Health, Farmington, CT, USA
- University of Connecticut School of Dental Medicine, Farmington, CT, USA
| | - Nicole Glidden
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ellen Roets
- Department of Obstetrics, Women's Clinic, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Miranda Galey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Kari M Brown
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - K Nicole Weaver
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy C Cox
- Department of Oral & Craniofacial Sciences, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri Kansas City, Kansas City, MO, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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16
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Mann R, Notani D. Transcription factor condensates and signaling driven transcription. Nucleus 2023; 14:2205758. [PMID: 37129580 PMCID: PMC10155639 DOI: 10.1080/19491034.2023.2205758] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023] Open
Abstract
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.
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Affiliation(s)
- Rajat Mann
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, TIFR, Bangalore, India
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17
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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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18
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Makrodimitris S, Pronk B, Abdelaal T, Reinders M. An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics. Brief Bioinform 2023; 25:bbad416. [PMID: 38018908 PMCID: PMC10685331 DOI: 10.1093/bib/bbad416] [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] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Multi-omic analyses are necessary to understand the complex biological processes taking place at the tissue and cell level, but also to make reliable predictions about, for example, disease outcome. Several linear methods exist that create a joint embedding using paired information per sample, but recently there has been a rise in the popularity of neural architectures that embed paired -omics into the same non-linear manifold. This work describes a head-to-head comparison of linear and non-linear joint embedding methods using both bulk and single-cell multi-modal datasets. We found that non-linear methods have a clear advantage with respect to linear ones for missing modality imputation. Performance comparisons in the downstream tasks of survival analysis for bulk tumor data and cell type classification for single-cell data lead to the following insights: First, concatenating the principal components of each modality is a competitive baseline and hard to beat if all modalities are available at test time. However, if we only have one modality available at test time, training a predictive model on the joint space of that modality can lead to performance improvements with respect to just using the unimodal principal components. Second, -omic profiles imputed by neural joint embedding methods are realistic enough to be used by a classifier trained on real data with limited performance drops. Taken together, our comparisons give hints to which joint embedding to use for which downstream task. Overall, product-of-experts performed well in most tasks and was reasonably fast, while early integration (concatenation) of modalities did quite poorly.
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Affiliation(s)
- Stavros Makrodimitris
- Delft Bioinformatics Lab, Delft University of Technology, Street, Postcode, State, Country
- Department of Medical Oncology, Erasmus University Medical Center, Street, Postcode, State, Country
- Department of Clinical Genetics, Erasmus University Medical Center, Street, Postcode, State, Country
| | - Bram Pronk
- Delft Bioinformatics Lab, Delft University of Technology, Street, Postcode, State, Country
| | - Tamim Abdelaal
- Delft Bioinformatics Lab, Delft University of Technology, Street, Postcode, State, Country
- Department of Radiology, Leiden University Medical Center, Street, Postcode, State, Country
- Leiden Computational Biology Center, Leiden University Medical Center, Street, Postcode, State, Country
| | - Marcel Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Street, Postcode, State, Country
- Leiden Computational Biology Center, Leiden University Medical Center, Street, Postcode, State, Country
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19
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Mulet-Lazaro R, Delwel R. From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis. Hemasphere 2023; 7:e969. [PMID: 37953829 PMCID: PMC10635615 DOI: 10.1097/hs9.0000000000000969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/11/2023] [Indexed: 11/14/2023] Open
Abstract
Blood comprises a wide array of specialized cells, all of which share the same genetic information and ultimately derive from the same precursor, the hematopoietic stem cell (HSC). This diversity of phenotypes is underpinned by unique transcriptional programs gradually acquired in the process known as hematopoiesis. Spatiotemporal regulation of gene expression depends on many factors, but critical among them are enhancers-sequences of DNA that bind transcription factors and increase transcription of genes under their control. Thus, hematopoiesis involves the activation of specific enhancer repertoires in HSCs and their progeny, driving the expression of sets of genes that collectively determine morphology and function. Disruption of this tightly regulated process can have catastrophic consequences: in hematopoietic malignancies, dysregulation of transcriptional control by enhancers leads to misexpression of oncogenes that ultimately drive transformation. This review attempts to provide a basic understanding of enhancers and their role in transcriptional regulation, with a focus on normal and malignant hematopoiesis. We present examples of enhancers controlling master regulators of hematopoiesis and discuss the main mechanisms leading to enhancer dysregulation in leukemia and lymphoma.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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20
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Nooti S, Naylor M, Long T, Groll B, Manu. LucFlow: A method to measure Luciferase reporter expression in single cells. PLoS One 2023; 18:e0292317. [PMID: 37792708 PMCID: PMC10550117 DOI: 10.1371/journal.pone.0292317] [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: 06/28/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Reporter assays, in which the expression of an inert protein is driven by gene regulatory elements such as promoters and enhancers, are a workhorse for investigating gene regulation. Techniques for measuring reporter gene expression vary from single-cell or single-molecule approaches having low throughput to bulk Luciferase assays that have high throughput. We developed a Luciferase Reporter Assay using Flow-Cytometry (LucFlow), which measures reporter expression in single cells immunostained for Luciferase. We optimized and tested LucFlow with a murine cell line that can be differentiated into neutrophils, into which promoter-reporter and enhancer-promoter-reporter constructs have been integrated in a site-specific manner. The single-cell measurements are comparable to bulk ones but we found that dead cells have no detectable Luciferase protein, so that bulk assays underestimate reporter expression. LucFlow is able to achieve a higher accuracy than bulk methods by excluding dead cells during flow cytometry. Prior to fixation and staining, the samples are spiked with stained cells that can be discriminated during flow cytometry and control for tube-to-tube variation in experimental conditions. Computing fold change relative to control cells allows LucFlow to achieve a high level of precision. LucFlow, therefore, enables the accurate and precise measurement of reporter expression in a high throughput manner.
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Affiliation(s)
- Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Brayden Groll
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
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21
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Romero A, Heidenreich AC, Román CL, Algañarás M, Nazer E, Gagliardino JJ, Maiztegui B, Flores LE, Rodríguez-Seguí SA. Transcriptional signature of islet neogenesis-associated protein peptide-treated rat pancreatic islets reveals induction of novel long non-coding RNAs. Front Endocrinol (Lausanne) 2023; 14:1226615. [PMID: 37842306 PMCID: PMC10570750 DOI: 10.3389/fendo.2023.1226615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Background Diabetes mellitus is characterized by chronic hyperglycemia with loss of β-cell function and mass. An attractive therapeutic approach to treat patients with diabetes in a non-invasive way is to harness the innate regenerative potential of the pancreas. The Islet Neogenesis-Associated Protein pentadecapeptide (INGAP-PP) has been shown to induce β-cell regeneration and improve their function in rodents. To investigate its possible mechanism of action, we report here the global transcriptional effects induced by the short-term INGAP-PP in vitro treatment of adult rat pancreatic islets. Methods and findings Rat pancreatic islets were cultured in vitro in the presence of INGAP-PP for 4 days, and RNA-seq was generated from triplicate treated and control islet samples. We performed a de novo rat gene annotation based on the alignment of RNA-seq reads. The list of INGAP-PP-regulated genes was integrated with epigenomic data. Using the new gene annotation generated in this work, we quantified RNA-seq data profiled in INS-1 cells treated with IL1β, IL1β+Calcipotriol (a vitamin D agonist) or vehicle, and single-cell RNA-seq data profiled in rat pancreatic islets. We found 1,669 differentially expressed genes by INGAP-PP treatment, including dozens of previously unannotated rat transcripts. Genes differentially expressed by the INGAP-PP treatment included a subset of upregulated transcripts that are associated with vitamin D receptor activation. Supported by epigenomic and single-cell RNA-seq data, we identified 9 previously unannotated long noncoding RNAs (lncRNAs) upregulated by INGAP-PP, some of which are also differentially regulated by IL1β and vitamin D in β-cells. These include Ri-lnc1, which is enriched in mature β-cells. Conclusions Our results reveal the transcriptional program that could explain the enhancement of INGAP-PP-mediated physiological effects on β-cell mass and function. We identified novel lncRNAs that are induced by INGAP-PP in rat islets, some of which are selectively expressed in pancreatic β-cells and downregulated by IL1β treatment of INS-1 cells. Our results suggest a relevant function for Ri-lnc1 in β-cells. These findings are expected to provide the basis for a deeper understanding of islet translational results from rodents to humans, with the ultimate goal of designing new therapies for people with diabetes.
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Affiliation(s)
- Agustín Romero
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana C. Heidenreich
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Carolina L. Román
- Centro de Endocrinología Experimental y Aplicada (CENEXA) - Universidad Nacional de La Plata (UNLP) - CONICET- Centro Asociado a la Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CeAs CICPBA), Facultad de Ciencias Médicas UNLP, La Plata, Argentina
| | - Macarena Algañarás
- Centro de Endocrinología Experimental y Aplicada (CENEXA) - Universidad Nacional de La Plata (UNLP) - CONICET- Centro Asociado a la Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CeAs CICPBA), Facultad de Ciencias Médicas UNLP, La Plata, Argentina
| | - Ezequiel Nazer
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Juan J. Gagliardino
- Centro de Endocrinología Experimental y Aplicada (CENEXA) - Universidad Nacional de La Plata (UNLP) - CONICET- Centro Asociado a la Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CeAs CICPBA), Facultad de Ciencias Médicas UNLP, La Plata, Argentina
| | - Bárbara Maiztegui
- Centro de Endocrinología Experimental y Aplicada (CENEXA) - Universidad Nacional de La Plata (UNLP) - CONICET- Centro Asociado a la Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CeAs CICPBA), Facultad de Ciencias Médicas UNLP, La Plata, Argentina
| | - Luis E. Flores
- Centro de Endocrinología Experimental y Aplicada (CENEXA) - Universidad Nacional de La Plata (UNLP) - CONICET- Centro Asociado a la Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CeAs CICPBA), Facultad de Ciencias Médicas UNLP, La Plata, Argentina
| | - Santiago A. Rodríguez-Seguí
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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22
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Miao B, Xing X, Bazylianska V, Madden P, Moszczynska A, Zhang B. Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats. Commun Biol 2023; 6:991. [PMID: 37758941 PMCID: PMC10533900 DOI: 10.1038/s42003-023-05355-3] [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: 07/13/2022] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Psychostimulant methamphetamine (METH) is neurotoxic to the brain and, therefore, its misuse leads to neurological and psychiatric disorders. The gene regulatory network (GRN) response to neurotoxic METH binge remains unclear in most brain regions. Here we examined the effects of binge METH on the GRN in the nucleus accumbens, dentate gyrus, Ammon's horn, and subventricular zone in male rats. At 24 h after METH, ~16% of genes displayed altered expression and over a quarter of previously open chromatin regions - parts of the genome where genes are typically active - showed shifts in their accessibility. Intriguingly, most changes were unique to each area studied, and independent regulation between transcriptome and chromatin accessibility was observed. Unexpectedly, METH differentially impacted gene activity and chromatin accessibility within the dentate gyrus and Ammon's horn. Around 70% of the affected chromatin-accessible regions in the rat brain have conserved DNA sequences in the human genome. These regions frequently act as enhancers, ramping up the activity of nearby genes, and contain mutations linked to various neurological conditions. By sketching out the gene regulatory networks associated with binge METH in specific brain regions, our study offers fresh insights into how METH can trigger profound, region-specific molecular shifts.
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Affiliation(s)
- Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Viktoriia Bazylianska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Pamela Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anna Moszczynska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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23
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Christou-Kent M, Cuartero S, Garcia-Cabau C, Ruehle J, Naderi J, Erber J, Neguembor MV, Plana-Carmona M, Alcoverro-Bertran M, De Andres-Aguayo L, Klonizakis A, Julià-Vilella E, Lynch C, Serrano M, Hnisz D, Salvatella X, Graf T, Stik G. CEBPA phase separation links transcriptional activity and 3D chromatin hubs. Cell Rep 2023; 42:112897. [PMID: 37516962 DOI: 10.1016/j.celrep.2023.112897] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Cell identity is orchestrated through an interplay between transcription factor (TF) action and genome architecture. The mechanisms used by TFs to shape three-dimensional (3D) genome organization remain incompletely understood. Here we present evidence that the lineage-instructive TF CEBPA drives extensive chromatin compartment switching and promotes the formation of long-range chromatin hubs during induced B cell-to-macrophage transdifferentiation. Mechanistically, we find that the intrinsically disordered region (IDR) of CEBPA undergoes in vitro phase separation (PS) dependent on aromatic residues. Both overexpressing B cells and native CEBPA-expressing cell types such as primary granulocyte-macrophage progenitors, liver cells, and trophectoderm cells reveal nuclear CEBPA foci and long-range 3D chromatin hubs at CEBPA-bound regions. In short, we show that CEBPA can undergo PS through its IDR, which may underlie in vivo foci formation and suggest a potential role of PS in regulating CEBPA function.
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Affiliation(s)
- Marie Christou-Kent
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Germans Trias I Pujol Research Institute (IGTP), Badalona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Julia Ruehle
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Julia Erber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marcos Plana-Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Luisa De Andres-Aguayo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Antonios Klonizakis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Cian Lynch
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Grégoire Stik
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.
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24
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Brown JL, Price JD, Erokhin M, Kassis JA. Context-dependent role of Pho binding sites in Polycomb complex recruitment in Drosophila. Genetics 2023; 224:iyad096. [PMID: 37216193 PMCID: PMC10411561 DOI: 10.1093/genetics/iyad096] [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: 03/09/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
Polycomb group (PcG) proteins maintain the silenced state of key developmental genes, but how these proteins are recruited to specific regions of the genome is still not completely understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) comprised of a flexible array of sites for sequence-specific DNA binding proteins, "PcG recruiters," including Pho, Spps, Cg, and GAF. Pho is thought to play a central role in PcG recruitment. Early data showed that mutation of Pho binding sites in PREs in transgenes abrogated the ability of those PREs to repress gene expression. In contrast, genome-wide experiments in pho mutants or by Pho knockdown showed that PcG proteins can bind to PREs in the absence of Pho. Here, we directly addressed the importance of Pho binding sites in 2 engrailed (en) PREs at the endogenous locus and in transgenes. Our results show that Pho binding sites are required for PRE activity in transgenes with a single PRE. In a transgene, 2 PREs together lead to stronger, more stable repression and confer some resistance to the loss of Pho binding sites. Making the same mutation in Pho binding sites has little effect on PcG-protein binding at the endogenous en gene. Overall, our data support the model that Pho is important for PcG binding but emphasize how multiple PREs and chromatin environment increase the ability of PREs to function in the absence of Pho. This supports the view that multiple mechanisms contribute to PcG recruitment in Drosophila.
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Affiliation(s)
- Janet Lesley Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua D Price
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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25
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Baniulyte G, Durham SA, Merchant LE, Sammons MA. Shared Gene Targets of the ATF4 and p53 Transcriptional Networks. Mol Cell Biol 2023; 43:426-449. [PMID: 37533313 PMCID: PMC10448979 DOI: 10.1080/10985549.2023.2229225] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 08/04/2023] Open
Abstract
The master tumor suppressor p53 regulates multiple cell fate decisions, such as cell cycle arrest and apoptosis, via transcriptional control of a broad gene network. Dysfunction in the p53 network is common in cancer, often through mutations that inactivate p53 or other members of the pathway. Induction of tumor-specific cell death by restoration of p53 activity without off-target effects has gained significant interest in the field. In this study, we explore the gene regulatory mechanisms underlying a putative anticancer strategy involving stimulation of the p53-independent integrated stress response (ISR). Our data demonstrate the p53 and ISR pathways converge to independently regulate common metabolic and proapoptotic genes. We investigated the architecture of multiple gene regulatory elements bound by p53 and the ISR effector ATF4 controlling this shared regulation. We identified additional key transcription factors that control basal and stress-induced regulation of these shared p53 and ATF4 target genes. Thus, our results provide significant new molecular and genetic insight into gene regulatory networks and transcription factors that are the target of numerous antitumor therapies.
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Affiliation(s)
- Gabriele Baniulyte
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Serene A. Durham
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Lauren E. Merchant
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Morgan A. Sammons
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
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26
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Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
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Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
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27
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Ober-Reynolds B, Wang C, Ko JM, Rios EJ, Aasi SZ, Davis MM, Oro AE, Greenleaf WJ. Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. Nat Genet 2023; 55:1288-1300. [PMID: 37500727 PMCID: PMC11190942 DOI: 10.1038/s41588-023-01445-4] [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: 09/01/2022] [Accepted: 06/17/2023] [Indexed: 07/29/2023]
Abstract
Genome-wide association studies have identified many loci associated with hair and skin disease, but identification of causal variants requires deciphering of gene-regulatory networks in relevant cell types. We generated matched single-cell chromatin profiles and transcriptomes from scalp tissue from healthy controls and patients with alopecia areata, identifying diverse cell types of the hair follicle niche. By interrogating these datasets at multiple levels of cellular resolution, we infer 50-100% more enhancer-gene links than previous approaches and show that aggregate enhancer accessibility for highly regulated genes predicts expression. We use these gene-regulatory maps to prioritize cell types, genes and causal variants implicated in the pathobiology of androgenetic alopecia (AGA), eczema and other complex traits. AGA genome-wide association studies signals are enriched in dermal papilla regulatory regions, supporting the role of these cells as drivers of AGA pathogenesis. Finally, we train machine learning models to nominate single-nucleotide polymorphisms that affect gene expression through disruption of transcription factor binding, predicting candidate functional single-nucleotide polymorphism for AGA and eczema.
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Affiliation(s)
| | - Chen Wang
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Justin M Ko
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Eon J Rios
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Dermatology, Department of Medicine, Santa Clara Valley Medical Center, San Jose, CA, USA
| | - Sumaira Z Aasi
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anthony E Oro
- Department of Dermatology, School of Medicine, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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28
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Chong-Morrison V, Mayes S, Simões FC, Senanayake U, Carroll DS, Riley PR, Wilson SW, Sauka-Spengler T. Ac/Ds transposition for CRISPR/dCas9-SID4x epigenome modulation in zebrafish. Biol Open 2023; 12:bio059995. [PMID: 37367831 PMCID: PMC10320716 DOI: 10.1242/bio.059995] [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: 05/03/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Due to its genetic amenability coupled with advances in genome editing, zebrafish is an excellent model to examine the function of (epi)genomic elements. Here, we repurposed the Ac/Ds maize transposition system to efficiently characterise zebrafish cis-regulated elements, also known as enhancers, in F0-microinjected embryos. We further used the system to stably express guide RNAs enabling CRISPR/dCas9-interference (CRISPRi) perturbation of enhancers without disrupting the underlying genetic sequence. In addition, we probed the phenomenon of antisense transcription at two neural crest gene loci. Our study highlights the utility of Ac/Ds transposition as a new tool for transient epigenome modulation in zebrafish.
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Affiliation(s)
- Vanessa Chong-Morrison
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Sarah Mayes
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Filipa C. Simões
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
- University of Oxford, Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, Oxford OX3 7DQ, UK
| | - Upeka Senanayake
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Dervla S. Carroll
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Paul R. Riley
- University of Oxford, Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, Oxford OX3 7DQ, UK
| | - Stephen W. Wilson
- University College London, Department of Cell & Developmental Biology, London WC1E 6BT, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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29
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Baniulyte G, Durham SA, Merchant LE, Sammons MA. Shared gene targets of the ATF4 and p53 transcriptional networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532778. [PMID: 36993734 PMCID: PMC10055071 DOI: 10.1101/2023.03.15.532778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The master tumor suppressor p53 regulates multiple cell fate decisions, like cell cycle arrest and apoptosis, via transcriptional control of a broad gene network. Dysfunction in the p53 network is common in cancer, often through mutations that inactivate p53 or other members of the pathway. Induction of tumor-specific cell death by restoration of p53 activity without off-target effects has gained significant interest in the field. In this study, we explore the gene regulatory mechanisms underlying a putative anti-cancer strategy involving stimulation of the p53-independent Integrated Stress Response (ISR). Our data demonstrate the p53 and ISR pathways converge to independently regulate common metabolic and pro-apoptotic genes. We investigated the architecture of multiple gene regulatory elements bound by p53 and the ISR effector ATF4 controlling this shared regulation. We identified additional key transcription factors that control basal and stress-induced regulation of these shared p53 and ATF4 target genes. Thus, our results provide significant new molecular and genetic insight into gene regulatory networks and transcription factors that are the target of numerous antitumor therapies.
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Affiliation(s)
- Gabriele Baniulyte
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Serene A. Durham
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Lauren E. Merchant
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Morgan A. Sammons
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
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30
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Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023; 150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [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: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in the specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here, we optimized a single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild-type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate that each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies that rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the retinoic acid response.
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Affiliation(s)
- Zainab Afzal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
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31
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Uyehara CM, Apostolou E. 3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles. Cell Rep 2023; 42:112068. [PMID: 37059094 PMCID: PMC10556201 DOI: 10.1016/j.celrep.2023.112068] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/25/2022] [Accepted: 01/20/2023] [Indexed: 04/16/2023] Open
Abstract
The spatiotemporal control of gene expression is dependent on the activity of cis-acting regulatory sequences, called enhancers, which regulate target genes over variable genomic distances and, often, by skipping intermediate promoters, suggesting mechanisms that control enhancer-promoter communication. Recent genomics and imaging technologies have revealed highly complex enhancer-promoter interaction networks, whereas advanced functional studies have started interrogating the forces behind the physical and functional communication among multiple enhancers and promoters. In this review, we first summarize our current understanding of the factors involved in enhancer-promoter communication, with a particular focus on recent papers that have revealed new layers of complexities to old questions. In the second part of the review, we focus on a subset of highly connected enhancer-promoter "hubs" and discuss their potential functions in signal integration and gene regulation, as well as the putative factors that might determine their dynamics and assembly.
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Affiliation(s)
- Christopher M Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
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32
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529579. [PMID: 37090616 PMCID: PMC10120690 DOI: 10.1101/2023.02.22.529579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene, Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophages in vitro by activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation-consistent with its role as a pioneer-but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of accessibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did increase significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
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33
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Liu TT, Ou F, Belk JA, Bagadia P, Anderson DA, Durai V, Yao W, Satpathy AT, Murphy TL, Murphy KM. Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation. Genes Dev 2023; 37:291-302. [PMID: 36990511 PMCID: PMC10153461 DOI: 10.1101/gad.350339.122] [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: 12/06/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
Abstract
Individual elements within a superenhancer can act in a cooperative or temporal manner, but the underlying mechanisms remain obscure. We recently identified an Irf8 superenhancer, within which different elements act at distinct stages of type 1 classical dendritic cell (cDC1) development. The +41-kb Irf8 enhancer is required for pre-cDC1 specification, while the +32-kb Irf8 enhancer acts to support subsequent cDC1 maturation. Here, we found that compound heterozygous Δ32/Δ41 mice, lacking the +32- and +41-kb enhancers on different chromosomes, show normal pre-cDC1 specification but, surprisingly, completely lack mature cDC1 development, suggesting cis dependence of the +32-kb enhancer on the +41-kb enhancer. Transcription of the +32-kb Irf8 enhancer-associated long noncoding RNA (lncRNA) Gm39266 is also dependent on the +41-kb enhancer. However, cDC1 development in mice remained intact when Gm39266 transcripts were eliminated by CRISPR/Cas9-mediated deletion of lncRNA promoters and when transcription across the +32-kb enhancer was blocked by premature polyadenylation. We showed that chromatin accessibility and BATF3 binding at the +32-kb enhancer were dependent on a functional +41-kb enhancer located in cis Thus, the +41-kb Irf8 enhancer controls the subsequent activation of the +32-kb Irf8 enhancer in a manner that is independent of associated lncRNA transcription.
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Affiliation(s)
- Tian-Tian Liu
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Feiya Ou
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - David A Anderson
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Winnie Yao
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA;
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Zhang Q, Brand M. The winding road toward transcriptional repression. Mol Cell 2023; 83:653-654. [PMID: 36868186 PMCID: PMC11018038 DOI: 10.1016/j.molcel.2023.02.005] [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: 02/02/2023] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 03/05/2023]
Abstract
Enhancers are known for their role in mediating transcriptional activation. In this issue, Vermunt et al.1 report the unexpected finding that genes can undergo a sequential transition between distinct enhancers to mediate progressive downregulation of expression.
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Affiliation(s)
- Qingzhou Zhang
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada; UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI, USA.
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35
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Kim S, Wysocka J. Deciphering the multi-scale, quantitative cis-regulatory code. Mol Cell 2023; 83:373-392. [PMID: 36693380 PMCID: PMC9898153 DOI: 10.1016/j.molcel.2022.12.032] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/24/2023]
Abstract
Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.
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Affiliation(s)
- Seungsoo Kim
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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36
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Idriss S, Hallal M, El-Kurdi A, Zalzali H, El-Rassi I, Ehli EA, Davis CM, Chung PED, Gendoo DMA, Zacksenhaus E, Saab R, Khoueiry P. A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements. Genome Res 2023; 33:269-282. [PMID: 36650051 PMCID: PMC10069464 DOI: 10.1101/gr.277037.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Pediatric pineoblastomas (PBs) are rare and aggressive tumors of grade IV histology. Although some oncogenic drivers are characterized, including germline mutations in RB1 and DICER1, the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated genome-wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time points of PB initiation and progression from pineal tissues of a mouse model of CCND1-driven PB. We identified PB-specific enhancers and super-enhancers, and found that in some cases, the accessible genome dynamics precede transcriptomic changes, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac signal become enriched for repressive state elements and harbor motifs of repressor transcription factors like HINFP, GLI2, and YY1. Copy number variant analysis identified deletion events specific to the tumorigenic stage, affecting, among others, the histone gene cluster and Gas1, the growth arrest specific gene. Gene set enrichment analysis and gene expression signatures positioned the model used here close to human PB samples, showing the potential of our findings for exploring new avenues in PB management and therapy. Overall, this study reports the first temporal and in vivo cis-regulatory, expression, and accessibility maps in PB.
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Affiliation(s)
- Salam Idriss
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Mohammad Hallal
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Abdullah El-Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Hasan Zalzali
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Inaam El-Rassi
- Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Christel M Davis
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Philip E D Chung
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deena M A Gendoo
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, United Kingdom
| | - Eldad Zacksenhaus
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Raya Saab
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; .,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
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37
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Attou A, Zülske T, Wedemann G. Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions. Biophys J 2022; 121:4788-4799. [PMID: 36325618 PMCID: PMC9811664 DOI: 10.1016/j.bpj.2022.10.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/12/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
The spatial organization of the eukaryotic genome plays an important role in regulating transcriptional activity. In the nucleus, chromatin forms loops that assemble into fundamental units called topologically associating domains that facilitate or inhibit long-range contacts. These loops are formed and held together by the ring-shaped cohesin protein complex, and this can involve binding of CCCTC-binding factor (CTCF). High-resolution conformation capture experiments provide the frequency at which two DNA fragments physically associate in three-dimensional space. However, technical limitations of this approach, such as low throughput, low resolution, or noise in contact maps, make data interpretation and identification of chromatin intraloop contacts, e.g., between distal regulatory elements and their target genes, challenging. Herein, an existing coarse-grained model of chromatin at single-nucleosome resolution was extended by integrating potentials describing CTCF and cohesin. We performed replica-exchange Monte Carlo simulations with regularly spaced nucleosomes and experimentally determined nucleosome positions in the presence of cohesin-CTCF, as well as depleted systems as controls. In fully extruded loops caused by the presence of cohesin and CTCF, the number of contacts within the formed loops was increased. The number and types of these contacts were impacted by the nucleosome distribution and loop size. Microloops were observed within cohesin-mediated loops due to thermal fluctuations without additional influence of other factors, and the number, size, and shape of microloops were determined by nucleosome distribution and loop size. Nucleosome positions directly affect the spatial structure and contact probability within a loop, with presumed consequences for transcriptional activity.
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Affiliation(s)
- Aymen Attou
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
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38
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Kneppers J, Severson TM, Siefert JC, Schol P, Joosten SEP, Yu IPL, Huang CCF, Morova T, Altıntaş UB, Giambartolomei C, Seo JH, Baca SC, Carneiro I, Emberly E, Pasaniuc B, Jerónimo C, Henrique R, Freedman ML, Wessels LFA, Lack NA, Bergman AM, Zwart W. Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential. Nat Commun 2022; 13:7367. [PMID: 36450752 PMCID: PMC9712620 DOI: 10.1038/s41467-022-35135-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Androgen receptor (AR) drives prostate cancer (PCa) development and progression. AR chromatin binding profiles are highly plastic and form recurrent programmatic changes that differentiate disease stages, subtypes and patient outcomes. While prior studies focused on concordance between patient subgroups, inter-tumor heterogeneity of AR enhancer selectivity remains unexplored. Here we report high levels of AR chromatin binding heterogeneity in human primary prostate tumors, that overlap with heterogeneity observed in healthy prostate epithelium. Such heterogeneity has functional consequences, as somatic mutations converge on commonly-shared AR sites in primary over metastatic tissues. In contrast, less-frequently shared AR sites associate strongly with AR-driven gene expression, while such heterogeneous AR enhancer usage also distinguishes patients' outcome. These findings indicate that epigenetic heterogeneity in primary disease is directly informative for risk of biochemical relapse. Cumulatively, our results illustrate a high level of AR enhancer heterogeneity in primary PCa driving differential expression and clinical impact.
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Affiliation(s)
- Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joseph C Siefert
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pieter Schol
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stacey E P Joosten
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ivan Pak Lok Yu
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | | | - Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Ji-Heui Seo
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Sylvan C Baca
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Isa Carneiro
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Carmen Jerónimo
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Matthew L Freedman
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, USA
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
- School of Medicine, Koç University, Istanbul, Turkey
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, 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.
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39
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Klonizakis A, Nikolaou C, Graf T. SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data. Bioinformatics 2022; 39:6832039. [PMID: 36394233 PMCID: PMC9805567 DOI: 10.1093/bioinformatics/btac742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/19/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
MOTIVATION The compartmentalization of biochemical reactions, involved in the activation of gene expression in the eukaryotic nucleus, leads to the formation of membraneless bodies through liquid-liquid phase separation. These formations, called transcriptional condensates, appear to play important roles in gene regulation as they are assembled through the association of multiple enhancer regions in 3D genomic space. To date, we are still lacking efficient computational methodologies to identify the regions responsible for the formation of such condensates, based on genomic and conformational data. RESULTS In this work, we present SEGCOND, a computational framework aiming to highlight genomic regions involved in the formation of transcriptional condensates. SEGCOND is flexible in combining multiple genomic datasets related to enhancer activity and chromatin accessibility, to perform a genome segmentation. It then uses this segmentation for the detection of highly transcriptionally active regions of the genome. At a final step, and through the integration of Hi-C data, it identifies regions of putative transcriptional condensates (PTCs) as genomic domains where multiple enhancer elements coalesce in 3D space. SEGCOND identifies a subset of enhancer segments with increased transcriptional activity. PTCs are also found to significantly overlap highly interconnected enhancer elements and super enhancers obtained through two independent approaches. Application of SEGCOND on data from a well-defined system of B-cell to macrophage transdifferentiation leads to the identification of previously unreported genes with a likely role in the process. AVAILABILITY AND IMPLEMENTATION Source code and details for the implementation of SEGCOND is available at https://github.com/AntonisK95/SEGCOND. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Antonios Klonizakis
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), C/ del Dr. Aiguader 88, Barcelona 08003, Spain,Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona 08003, Spain
| | | | - Thomas Graf
- To whom correspondence should be addressed. or
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40
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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41
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Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022; 31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [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: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Every cell in the human body inherits a copy of the same genetic information. The three billion base pairs of DNA in the human genome, and the roughly 50 000 coding and non-coding genes they contain, must thus encode all the complexity of human development and cell and tissue type diversity. Differences in gene regulation, or the modulation of gene expression, enable individual cells to interpret the genome differently to carry out their specific functions. Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize the regulatory roles of all sequences in a genome. Many researchers and consortia have identified such regulatory elements using functional assays and evolutionary analyses; we discuss the results, strengths and shortcomings of their approaches. We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness.
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Affiliation(s)
- Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
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Xiong L, Tolen EA, Choi J, Velychko S, Caizzi L, Velychko T, Adachi K, MacCarthy CM, Lidschreiber M, Cramer P, Schöler HR. Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells. eLife 2022; 11:71533. [PMID: 35621159 PMCID: PMC9142147 DOI: 10.7554/elife.71533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 05/17/2022] [Indexed: 12/21/2022] Open
Abstract
The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells (ESCs) and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2.
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Affiliation(s)
- Le Xiong
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Erik A Tolen
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Jinmi Choi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Livia Caizzi
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Kenjiro Adachi
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Caitlin M MacCarthy
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Münster, Germany
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43
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Wang J, Zhang S, Lu H, Xu H. Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction. Nat Commun 2022; 13:2714. [PMID: 35581264 PMCID: PMC9114328 DOI: 10.1038/s41467-022-30315-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Many eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the kinetic mechanisms of complex eukaryotic gene regulation. Alternative promoters differ in their expression patterns, whose mechanisms are not well understood. Here the authors show that alternative promoters of a Drosophila embryonic gene hunchback are regulated by different action modes of two enhancers.
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Affiliation(s)
- Jingyao Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Shihe Zhang
- Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China. .,School of Physics and Astronomy, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Hongfang Lu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Heng Xu
- Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China. .,School of Physics and Astronomy, Shanghai Jiao Tong University, 200240, Shanghai, China.
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44
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Enhancer RNAs (eRNAs) in Cancer: The Jacks of All Trades. Cancers (Basel) 2022; 14:cancers14081978. [PMID: 35454885 PMCID: PMC9030334 DOI: 10.3390/cancers14081978] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary This review focuses on eRNAs and the several mechanisms by which they can regulate gene expression. In particular we describe here the most recent examples of eRNAs dysregulated in cancer or involved in the immune escape of tumor cells. Abstract Enhancer RNAs (eRNAs) are non-coding RNAs (ncRNAs) transcribed in enhancer regions. They play an important role in transcriptional regulation, mainly during cellular differentiation. eRNAs are tightly tissue- and cell-type specific and are induced by specific stimuli, activating promoters of target genes in turn. eRNAs usually have a very short half-life but in some cases, once activated, they can be stably expressed and acquire additional functions. Due to their critical role, eRNAs are often dysregulated in cancer and growing number of interactions with chromatin modifiers, transcription factors, and splicing machinery have been described. Enhancer activation and eRNA transcription have particular relevance also in inflammatory response, placing the eRNAs at the interplay between cancer and immune cells. Here, we summarize all the possible molecular mechanisms recently reported in association with eRNAs activity.
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45
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Zhou T, Zhu X, Ye Z, Wang YF, Yao C, Xu N, Zhou M, Ma J, Qin Y, Shen Y, Tang Y, Yin Z, Xu H, Zhang Y, Zang X, Ding H, Yang W, Guo Y, Harley JB, Namjou B, Kaufman KM, Kottyan LC, Weirauch MT, Hou G, Shen N. Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery. Nat Commun 2022; 13:1855. [PMID: 35388006 PMCID: PMC8987079 DOI: 10.1038/s41467-022-29514-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Despite strong evidence that human genetic variants affect the expression of many key transcription factors involved in autoimmune diseases, establishing biological links between non-coding risk variants and the gene targets they regulate remains a considerable challenge. Here, we combine genetic, epigenomic, and CRISPR activation approaches to screen for functional variants that regulate IRF8 expression. We demonstrate that the locus containing rs2280381 is a cell-type-specific enhancer for IRF8 that spatially interacts with the IRF8 promoter. Further, rs2280381 mediates IRF8 expression through enhancer RNA AC092723.1, which recruits TET1 to the IRF8 promoter regulating IRF8 expression by affecting methylation levels. The alleles of rs2280381 modulate PU.1 binding and chromatin state to regulate AC092723.1 and IRF8 expression differentially. Our work illustrates an integrative strategy to define functional genetic variants that regulate the expression of critical genes in autoimmune diseases and decipher the mechanisms underlying the dysregulation of IRF8 expression mediated by lupus risk variants.
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Affiliation(s)
- Tian Zhou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Xinyi Zhu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Yong-Fei Wang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Chao Yao
- grid.9227.e0000000119573309Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031 China
| | - Ning Xu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Mi Zhou
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - Jianyang Ma
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuting Qin
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yiwei Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuanjia Tang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Hong Xu
- grid.16821.3c0000 0004 0368 8293Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China ,grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China
| | - Yutong Zhang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Xiaoli Zang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Huihua Ding
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Wanling Yang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Ya Guo
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - John B. Harley
- grid.413848.20000 0004 0420 2128US Department of Veterans Affairs Medical Center, Cincinnati, OH 45229 USA
| | - Bahram Namjou
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Kenneth M. Kaufman
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Leah C. Kottyan
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Matthew T. Weirauch
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Guojun Hou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Nan Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China ,grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
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Herrmann JC, Beagrie RA, Hughes JR. Making connections: enhancers in cellular differentiation. Trends Genet 2022; 38:395-408. [PMID: 34753603 DOI: 10.1016/j.tig.2021.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 01/23/2023]
Abstract
Deciphering the process by which hundreds of distinct cell types emerge from a single zygote to form a complex multicellular organism remains one of the greatest challenges in biological research. Enhancers are known to be central to cell type-specific gene expression, yet many questions regarding how these genomic elements interact both temporally and spatially with other cis- and trans-acting factors to control transcriptional activity during differentiation and development remain unanswered. Here, we review our current understanding of the role of enhancers and their interactions in this context and highlight recent progress achieved with experimental methods of unprecedented resolution.
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Affiliation(s)
- Jennifer C Herrmann
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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47
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Cao Y, Xia Y, Balowski JJ, Ou J, Song L, Safi A, Curtis T, Crawford GE, Poss KD, Cao J. Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration. Development 2022; 149:dev200133. [PMID: 35179181 PMCID: PMC8918790 DOI: 10.1242/dev.200133] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022]
Abstract
The epicardium is a mesothelial tissue layer that envelops the heart. Cardiac injury activates dynamic gene expression programs in epicardial tissue, which in zebrafish enables subsequent regeneration through paracrine and vascularizing effects. To identify tissue regeneration enhancer elements (TREEs) that control injury-induced epicardial gene expression during heart regeneration, we profiled transcriptomes and chromatin accessibility in epicardial cells purified from regenerating zebrafish hearts. We identified hundreds of candidate TREEs, which are defined by increased chromatin accessibility of non-coding elements near genes with increased expression during regeneration. Several of these candidate TREEs were incorporated into stable transgenic lines, with five out of six elements directing injury-induced epicardial expression but not ontogenetic epicardial expression in larval hearts. Whereas two independent TREEs linked to the gene gnai3 showed similar functional features of gene regulation in transgenic lines, two independent ncam1a-linked TREEs directed distinct spatiotemporal domains of epicardial gene expression. Thus, multiple TREEs linked to a regeneration gene can possess either matching or complementary regulatory controls. Our study provides a new resource and principles for understanding the regulation of epicardial genetic programs during heart regeneration. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Yingxi Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
| | - Yu Xia
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
| | - Joseph J. Balowski
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Jianhong Ou
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Curtis
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Regeneration Center, Duke University, Durham, NC 27710, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, USA
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48
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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49
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Kneppers J, Bergman AM, Zwart W. Prostate Cancer Epigenetic Plasticity and Enhancer Heterogeneity: Molecular Causes, Consequences and Clinical Implications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:255-275. [DOI: 10.1007/978-3-031-11836-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
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50
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Shao R, Kumar B, Lidschreiber K, Lidschreiber M, Cramer P, Elsässer SJ. Distinct transcription kinetics of pluripotent cell states. Mol Syst Biol 2022; 18:e10407. [PMID: 35020268 PMCID: PMC8754154 DOI: 10.15252/msb.202110407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) can adopt naïve, ground, and paused pluripotent states that give rise to unique transcriptomes. Here, we use transient transcriptome sequencing (TT-seq) to define both coding and non-coding transcription units (TUs) in these three pluripotent states and combine TT-seq with RNA polymerase II occupancy profiling to unravel the kinetics of RNA metabolism genome-wide. Compared to the naïve state (serum), RNA synthesis and turnover rates are globally reduced in the ground state (2i) and the paused state (mTORi). The global reduction in RNA synthesis goes along with a genome-wide decrease of polymerase elongation velocity, which is related to epigenomic features and alterations in the Pol II termination window. Our data suggest that transcription activity is the main determinant of steady state mRNA levels in the naïve state and that genome-wide changes in transcription kinetics invoke ground and paused pluripotent states.
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Affiliation(s)
- Rui Shao
- Science for Life LaboratoryDepartment of Medical Biochemistry and BiophysicsDivision of Genome BiologyKarolinska InstitutetStockholmSweden
- Ming Wai Lau Centre for Reparative MedicineStockholm nodeKarolinska InstitutetStockholmSweden
| | - Banushree Kumar
- Science for Life LaboratoryDepartment of Medical Biochemistry and BiophysicsDivision of Genome BiologyKarolinska InstitutetStockholmSweden
- Ming Wai Lau Centre for Reparative MedicineStockholm nodeKarolinska InstitutetStockholmSweden
| | - Katja Lidschreiber
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Michael Lidschreiber
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Patrick Cramer
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Simon J Elsässer
- Science for Life LaboratoryDepartment of Medical Biochemistry and BiophysicsDivision of Genome BiologyKarolinska InstitutetStockholmSweden
- Ming Wai Lau Centre for Reparative MedicineStockholm nodeKarolinska InstitutetStockholmSweden
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