1
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Biddie SC, Weykopf G, Hird EF, Friman ET, Bickmore WA. DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants. Genome Biol 2024; 25:208. [PMID: 39107801 PMCID: PMC11304670 DOI: 10.1186/s13059-024-03352-1] [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: 03/06/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have revealed a multitude of candidate genetic variants affecting the risk of developing complex traits and diseases. However, the highlighted regions are typically in the non-coding genome, and uncovering the functional causative single nucleotide variants (SNVs) is challenging. Prioritization of variants is commonly based on genomic annotation with markers of active regulatory elements, but current approaches still poorly predict functional variants. To address this, we systematically analyze six markers of active regulatory elements for their ability to identify functional variants. RESULTS We benchmark against molecular quantitative trait loci (molQTL) from assays of regulatory element activity that identify allelic effects on DNA-binding factor occupancy, reporter assay expression, and chromatin accessibility. We identify the combination of DNase footprints and divergent enhancer RNA (eRNA) as markers for functional variants. This signature provides high precision, but with a trade-off of low recall, thus substantially reducing candidate variant sets to prioritize variants for functional validation. We present this as a framework called FINDER-Functional SNV IdeNtification using DNase footprints and eRNA. CONCLUSIONS We demonstrate the utility to prioritize variants using leukocyte count trait and analyze variants in linkage disequilibrium with a lead variant to predict a functional variant in asthma. Our findings have implications for prioritizing variants from GWAS, in development of predictive scoring algorithms, and for functionally informed fine mapping approaches.
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Affiliation(s)
- Simon C Biddie
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- NHS Lothian, Edinburgh, UK.
| | - Giovanna Weykopf
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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2
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Lihanova Y, Nagel R, Jakob T, Sasso S. Characterization of activating cis-regulatory elements from the histone genes of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:525-539. [PMID: 38693717 DOI: 10.1111/tpj.16781] [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: 06/27/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Regulation of gene expression in eukaryotes is controlled by cis-regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis-regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii. To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii, and their activity was quantified by flow cytometry. Two tested candidates, Eupstr and Ehist cons, significantly upregulated gene expression and were characterized in detail. Eupstr, which originates from highly expressed genes of C. reinhardtii, is an orientation-independent CRE capable of activating both the RBCS2 and β2-tubulin promoters. Ehist cons, which is a CRM from histone genes of angiosperms, upregulates the β2-tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in Ehist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta, Chlamydomonas schloesseri, and Edaphochlamys debaryana, demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
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Affiliation(s)
- Yuliia Lihanova
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Torsten Jakob
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Severin Sasso
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
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3
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Park SJ, Nakai K. A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response. NAR Genom Bioinform 2024; 6:lqae050. [PMID: 38711859 PMCID: PMC11071120 DOI: 10.1093/nargab/lqae050] [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: 11/05/2023] [Revised: 04/15/2024] [Accepted: 04/27/2024] [Indexed: 05/08/2024] Open
Abstract
Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The present study aimed to develop a computational method for accurately modeling the spatial proximal and distal regulatory interactions. Our method combined regression-based models to identify key regulators through gene expression prediction and a graph-embedding approach to detect coregulated genes. This approach enabled a detailed investigation of the gene regulatory mechanisms for germinal center B cells, accompanied by dramatic rearrangements of the genome structure. We found that while the promoter-proximal regulatory elements were the principal regulators of gene expression, the distal regulators fine-tuned transcription. Moreover, our approach unveiled the presence of modular regulators, such as cofactors and proximal/distal transcription factors, which were co-expressed with their target genes. Some of these modules exhibited abnormal expression patterns in lymphoma. These findings suggest that the dysregulation of interactions between transcriptional and architectural factors is associated with chromatin reorganization failure, which may increase the risk of malignancy. Therefore, our computational approach helps decipher the transcriptional cis-regulatory code spatially interacting.
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Affiliation(s)
- Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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4
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Fletez-Brant K, Qiu Y, Gorkin DU, Hu M, Hansen KD. Removing unwanted variation between samples in Hi-C experiments. Brief Bioinform 2024; 25:bbae217. [PMID: 38711367 PMCID: PMC11074651 DOI: 10.1093/bib/bbae217] [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: 05/25/2023] [Revised: 01/26/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Hi-C data are commonly normalized using single sample processing methods, with focus on comparisons between regions within a given contact map. Here, we aim to compare contact maps across different samples. We demonstrate that unwanted variation, of likely technical origin, is present in Hi-C data with replicates from different individuals, and that properties of this unwanted variation change across the contact map. We present band-wise normalization and batch correction, a method for normalization and batch correction of Hi-C data and show that it substantially improves comparisons across samples, including in a quantitative trait loci analysis as well as differential enrichment across cell types.
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Affiliation(s)
- Kipper Fletez-Brant
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltmore, MD 21205, USA
| | - Yunjiang Qiu
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Ludwig Institute for Cancer Research, New York, NY 10016, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, New York, NY 10016, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Currently: Department of Biology. Emory University. Atlanta, GA 30322, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44196, USA
| | - Kasper D Hansen
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltmore, MD 21205, USA
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5
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Silver BD, Willett CG, Maher KA, Wang D, Deal RB. Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements. G3 (BETHESDA, MD.) 2024; 14:jkae016. [PMID: 38253712 PMCID: PMC10917500 DOI: 10.1093/g3journal/jkae016] [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: 11/10/2023] [Revised: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II often initiates transcription in both directions at the promoter transcription start site, but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements such as enhancers. These bidirectional RNA Polymerase II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the transcription start site or cis-regulatory elements. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant Arabidopsis thaliana accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both transcription start sites and cis-regulatory elements in A. thaliana, Drosophila melanogaster, and Homo sapiens. Our results provide evidence for mostly unidirectional RNA Polymerase II initiation at both promoters and gene-proximal cis-regulatory elements of A. thaliana, whereas bidirectional transcription initiation is observed widely at promoters in both D. melanogaster and H. sapiens, as well as cis-regulatory elements in Drosophila. Furthermore, the distribution of transcription-associated histone modifications around transcription start sites in the Oryza sativa (rice) and Glycine max (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.
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Affiliation(s)
- Brianna D Silver
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Courtney G Willett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Kelsey A Maher
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dongxue Wang
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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6
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Silver BD, Willett CG, Maher KA, Wang D, Deal RB. Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565513. [PMID: 37961418 PMCID: PMC10635121 DOI: 10.1101/2023.11.03.565513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II (Pol II) often initiates transcription in both directions at the promoter transcription start site (TSS), but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements (CREs) such as enhancers. These bidirectional Pol II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the TSS or CRE. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant Arabidopsis thaliana accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both TSSs and CREs in Arabidopsis thaliana, Drosophila melanogaster, and Homo sapiens. Our results provide evidence for mostly unidirectional Pol II initiation at both promoters and gene-proximal CREs of Arabidopsis thaliana, whereas bidirectional transcription initiation is observed widely at promoters in both Drosophila melanogaster and Homo sapiens, as well as CREs in Drosophila. Furthermore, the distribution of transcription-associated histone modifications around TSSs in the Oryza sativa (rice) and Glycine max (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.
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Affiliation(s)
- Brianna D. Silver
- Department of Biology, Emory University, Atlanta, GA 30322 USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322 USA
| | - Courtney G. Willett
- Department of Biology, Emory University, Atlanta, GA 30322 USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322 USA
| | - Kelsey A. Maher
- Department of Biology, Emory University, Atlanta, GA 30322 USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322 USA
| | - Dongxue Wang
- Department of Biology, Emory University, Atlanta, GA 30322 USA
| | - Roger B. Deal
- Department of Biology, Emory University, Atlanta, GA 30322 USA
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7
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Gao Z, Smith AL, Scott JF, Bevington S, Boyes J. Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation. Nucleic Acids Res 2023; 51:10344-10363. [PMID: 37702072 PMCID: PMC10602925 DOI: 10.1093/nar/gkad741] [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: 03/16/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Transcription enhancers are essential activators of V(D)J recombination that orchestrate non-coding transcription through complementary, unrearranged gene segments. How transcription is coordinately increased at spatially distinct promoters, however, remains poorly understood. Using the murine immunoglobulin lambda (Igλ) locus as model, we find that three enhancer-like elements in the 3' Igλ domain, Eλ3-1, HSCλ1 and HSE-1, show strikingly similar transcription factor binding dynamics and close spatial proximity, suggesting that they form an active enhancer hub. Temporal analyses show coordinate recruitment of complementary V and J gene segments to this hub, with comparable transcription factor binding dynamics to that at enhancers. We find further that E2A, p300, Mediator and Integrator bind to enhancers as early events, whereas YY1 recruitment and eRNA synthesis occur later, corresponding to transcription activation. Remarkably, the interplay between sense and antisense enhancer RNA is central to both active enhancer hub formation and coordinate Igλ transcription: Antisense Eλ3-1 eRNA represses Igλ activation whereas temporal analyses demonstrate that accumulating levels of sense eRNA boost YY1 recruitment to stabilise enhancer hub/promoter interactions and lead to coordinate transcription activation. These studies therefore demonstrate for the first time a critical role for threshold levels of sense versus antisense eRNA in locus activation.
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Affiliation(s)
- Zeqian Gao
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alastair L Smith
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - James N F Scott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah L Bevington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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8
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Wang R, Xu Q, Wang C, Tian K, Wang H, Ji X. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res 2023; 51:6784-6805. [PMID: 37264934 PMCID: PMC10359638 DOI: 10.1093/nar/gkad401] [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: 12/15/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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9
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Brückner DB, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science 2023; 380:1357-1362. [PMID: 37384691 PMCID: PMC10439308 DOI: 10.1126/science.adf5568] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.
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Affiliation(s)
- David B. Brückner
- Institute of Science and Technology, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Hongtao Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lev Barinov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin Zoller
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
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10
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Brückner DB, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524527. [PMID: 36711618 PMCID: PMC9882297 DOI: 10.1101/2023.01.18.524527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the 3D pair-wise motion of distal chromosomal elements, such as enhancers and promoters, is essential and necessitates dynamic fluidity. Therefore, the interplay of chromosome organization and dynamics is crucial for gene regulation. Here, we use a live imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output in the developing fly embryo while systematically varying the genomic separation between these two DNA loci. Our analysis reveals a combination of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation and lead to long-ranged correlations compared to existing polymer models. This scaling implies that encounter times of DNA loci are much less dependent on genomic separation than predicted by existing polymer models, with potentially significant consequences for eukaryotic gene expression.
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Affiliation(s)
- David B. Brückner
- Institute of Science and Technology, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Hongtao Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lev Barinov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Benjamin Zoller
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology, CNRS UMR3738, Institut Pasteur, Paris, France
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology, CNRS UMR3738, Institut Pasteur, Paris, France
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11
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Wong GL, Manore SG, Doheny DL, Lo HW. STAT family of transcription factors in breast cancer: Pathogenesis and therapeutic opportunities and challenges. Semin Cancer Biol 2022; 86:84-106. [PMID: 35995341 PMCID: PMC9714692 DOI: 10.1016/j.semcancer.2022.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most commonly diagnosed cancer and second-leading cause of cancer deaths in women. Breast cancer stem cells (BCSCs) promote metastasis and therapeutic resistance contributing to tumor relapse. Through activating genes important for BCSCs, transcription factors contribute to breast cancer metastasis and therapeutic resistance, including the signal transducer and activator of transcription (STAT) family of transcription factors. The STAT family consists of six major isoforms, STAT1, STAT2, STAT3, STAT4, STAT5, and STAT6. Canonical STAT signaling is activated by the binding of an extracellular ligand to a cell-surface receptor followed by STAT phosphorylation, leading to STAT nuclear translocation and transactivation of target genes. It is important to note that STAT transcription factors exhibit diverse effects in breast cancer; some are either pro- or anti-tumorigenic while others maintain dual, context-dependent roles. Among the STAT transcription factors, STAT3 is the most widely studied STAT protein in breast cancer for its critical roles in promoting BCSCs, breast cancer cell proliferation, invasion, angiogenesis, metastasis, and immune evasion. Consequently, there have been substantial efforts in developing cancer therapeutics to target breast cancer with dysregulated STAT3 signaling. In this comprehensive review, we will summarize the diverse roles that each STAT family member plays in breast cancer pathobiology, as well as, the opportunities and challenges in pharmacologically targeting STAT proteins and their upstream activators in the context of breast cancer treatment.
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Affiliation(s)
- Grace L Wong
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Sara G Manore
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Daniel L Doheny
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Hui-Wen Lo
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA; Breast Cancer Center of Excellence, Wake Forest University School of Medicine, Winston-Salem, NC, USA; Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
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12
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Kim J, Lee C, Ko BJ, Yoo DA, Won S, Phillippy AM, Fedrigo O, Zhang G, Howe K, Wood J, Durbin R, Formenti G, Brown S, Cantin L, Mello CV, Cho S, Rhie A, Kim H, Jarvis ED. False gene and chromosome losses in genome assemblies caused by GC content variation and repeats. Genome Biol 2022; 23:204. [PMID: 36167554 PMCID: PMC9516821 DOI: 10.1186/s13059-022-02765-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements. RESULTS Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna's hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5'-proximal promoters and 5' exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies. CONCLUSIONS Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.
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Affiliation(s)
- Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong Ahn Yoo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Sohyoung Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York City, USA
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | | | | | - Richard Durbin
- Wellcome Sanger Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York City, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
| | - Samara Brown
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
| | - Lindsey Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Seoae Cho
- eGnome, Inc, Seoul, Republic of Korea
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- eGnome, Inc, Seoul, Republic of Korea.
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York City, USA.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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13
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Fragoso RR, Arraes FBM, Lourenço-Tessutti IT, Miranda VJ, Basso MF, Ferreira AVJ, Viana AAB, Lins CBJ, Lins PC, Moura SM, Batista JAN, Silva MCM, Engler G, Morgante CV, Lisei-de-Sa ME, Vasques RM, de Almeida-Engler J, Grossi-de-Sa MF. Functional characterization of the pUceS8.3 promoter and its potential use for ectopic gene overexpression. PLANTA 2022; 256:69. [PMID: 36066773 DOI: 10.1007/s00425-022-03980-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
The pUceS8.3 is a constitutive gene promoter with potential for ectopic and strong genes overexpression or active biomolecules in plant tissues attacked by pests, including nematode-induced giant cells or galls. Soybean (Glycine max) is one of the most important agricultural commodities worldwide and a major protein and oil source. Herein, we identified the soybean ubiquitin-conjugating (E2) enzyme gene (GmUBC4; Glyma.18G216000), which is significantly upregulated in response to Anticarsia gemmatalis attack and Meloidogyne incognita-induced galls during plant parasitism by plant nematode. The GmUBC4 promoter sequence and its different modules were functionally characterized in silico and in planta using transgenic Arabidopsis thaliana and G. max lines. Its full-length transcriptional regulatory region (promoter and 5´-UTR sequences, named pUceS8.3 promoter) was able to drive higher levels of uidA (β-glucuronidase) gene expression in different tissues of transgenic A. thaliana lines compared to its three shortened modules and the p35SdAMV promoter. Notably, higher β-glucuronidase (GUS) enzymatic activity was shown in M. incognita-induced giant cells when the full pUceS8.3 promoter drove the expression of this reporter gene. Furthermore, nematode-specific dsRNA molecules were successfully overexpressed under the control of the pUceS8.3 promoter in transgenic soybean lines. The RNAi gene construct used here was designed to post-transcriptionally downregulate the previously characterized pre-mRNA splicing factor genes from Heterodera glycines and M. incognita. A total of six transgenic soybean lines containing RNAi gene construct were selected for molecular characterization after infection with M. incognita pre-parasitic second-stage (ppJ2) nematodes. A strong reduction in the egg number produced by M. incognita after parasitism was observed in those transgenic soybean lines, ranging from 71 to 92% compared to wild-type control plants. The present data demonstrated that pUceS8.3 is a gene promoter capable of effectively driving dsRNA overexpression in nematode-induced giant cells of transgenic soybean lines and can be successfully applied as an important biotechnological asset to generate transgenic crops with improved resistance to root-knot nematodes as well as other pests.
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Affiliation(s)
- Rodrigo Rocha Fragoso
- Embrapa Savannah, Planaltina, DF, Brazil
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Fabricio Barbosa Monteiro Arraes
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Isabela Tristan Lourenço-Tessutti
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Vívian Jesus Miranda
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Marcos Fernando Basso
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | | | | | - Camila Barrozo Jesus Lins
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Philippe Castro Lins
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Stéfanie Menezes Moura
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - João Aguiar Nogueira Batista
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Federal University of Minas Gerais, Belo Horizonte-MG, Brazil
| | - Maria Cristina Mattar Silva
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Gilbert Engler
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- INRAE, Université Côte d'Azur, CNRS, Sophia-Antipolis, France
| | - Carolina Vianna Morgante
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Embrapa Semiarid, Petrolina-PE, Brazil
| | - Maria Eugênia Lisei-de-Sa
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
- Minas Gerais Agricultural Research Company (EPAMIG), Uberaba-MG, Brazil
| | - Raquel Medeiros Vasques
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil
| | - Janice de Almeida-Engler
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil
- INRAE, Université Côte d'Azur, CNRS, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- National Institute of Science and Technology, INCT PlantStress Biotech, Embrapa, Brazil.
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, Brasília DF, CEP 70.770-900, Brazil.
- Catholic University of Brasilia, Brasília-DF, Brazil.
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14
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Razin SV, Zhegalova IV, Kantidze OL. Domain Model of Eukaryotic Genome Organization: From DNA Loops Fixed on the Nuclear Matrix to TADs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:667-680. [PMID: 36154886 DOI: 10.1134/s0006297922070082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 06/16/2023]
Abstract
The article reviews the development of ideas on the domain organization of eukaryotic genome, with special attention on the studies of DNA loops anchored to the nuclear matrix and their role in the emergence of the modern model of eukaryotic genome spatial organization. Critical analysis of results demonstrating that topologically associated chromatin domains are structural-functional blocks of the genome supports the notion that these blocks are fundamentally different from domains whose existence was proposed by the domain hypothesis of eukaryotic genome organization formulated in the 1980s. Based on the discussed evidence, it is concluded that the model postulating that eukaryotic genome is built from uniformly organized structural-functional blocks has proven to be untenable.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Zhegalova
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Kharkevich Institute for Information Transmission Problems, Moscow, 127051, Russia
| | - Omar L Kantidze
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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15
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Lee DSW, Strom AR, Brangwynne CP. The mechanobiology of nuclear phase separation. APL Bioeng 2022; 6:021503. [PMID: 35540725 PMCID: PMC9054271 DOI: 10.1063/5.0083286] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/19/2022] [Indexed: 02/06/2023] Open
Abstract
The cell nucleus can be thought of as a complex, dynamic, living material, which functions to organize and protect the genome and coordinate gene expression. These functions are achieved via intricate mechanical and biochemical interactions among its myriad components, including the nuclear lamina, nuclear bodies, and the chromatin itself. While the biophysical organization of the nuclear lamina and chromatin have been thoroughly studied, the concept that liquid-liquid phase separation and related phase transitions play a role in establishing nuclear structure has emerged only recently. Phase transitions are likely to be intimately coupled to the mechanobiology of structural elements in the nucleus, but their interplay with one another is still not understood. Here, we review recent developments on the role of phase separation and mechanics in nuclear organization and discuss the functional implications in cell physiology and disease states.
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Affiliation(s)
- Daniel S. W. Lee
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Amy R. Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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16
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Mulero Hernández J, Fernández-Breis JT. Analysis of the landscape of human enhancer sequences in biological databases. Comput Struct Biotechnol J 2022; 20:2728-2744. [PMID: 35685360 PMCID: PMC9168495 DOI: 10.1016/j.csbj.2022.05.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/01/2022] Open
Abstract
The process of gene regulation extends as a network in which both genetic sequences and proteins are involved. The levels of regulation and the mechanisms involved are multiple. Transcription is the main control mechanism for most genes, being the downstream steps responsible for refining the transcription patterns. In turn, gene transcription is mainly controlled by regulatory events that occur at promoters and enhancers. Several studies are focused on analyzing the contribution of enhancers in the development of diseases and their possible use as therapeutic targets. The study of regulatory elements has advanced rapidly in recent years with the development and use of next generation sequencing techniques. All this information has generated a large volume of information that has been transferred to a growing number of public repositories that store this information. In this article, we analyze the content of those public repositories that contain information about human enhancers with the aim of detecting whether the knowledge generated by scientific research is contained in those databases in a way that could be computationally exploited. The analysis will be based on three main aspects identified in the literature: types of enhancers, type of evidence about the enhancers, and methods for detecting enhancer-promoter interactions. Our results show that no single database facilitates the optimal exploitation of enhancer data, most types of enhancers are not represented in the databases and there is need for a standardized model for enhancers. We have identified major gaps and challenges for the computational exploitation of enhancer data.
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Affiliation(s)
- Juan Mulero Hernández
- Dept. Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, IMIB-Arrixaca, Spain
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17
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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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18
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Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022; 15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
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Affiliation(s)
- Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Emily Martinsen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marit Ledsaak
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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19
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Zuin J, Roth G, Zhan Y, Cramard J, Redolfi J, Piskadlo E, Mach P, Kryzhanovska M, Tihanyi G, Kohler H, Eder M, Leemans C, van Steensel B, Meister P, Smallwood S, Giorgetti L. Nonlinear control of transcription through enhancer-promoter interactions. Nature 2022; 604:571-577. [PMID: 35418676 PMCID: PMC9021019 DOI: 10.1038/s41586-022-04570-y] [Citation(s) in RCA: 159] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs)1-4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer-promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.
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Affiliation(s)
- Jessica Zuin
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Julie Cramard
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Josef Redolfi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ewa Piskadlo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Pia Mach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Gergely Tihanyi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mathias Eder
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christ Leemans
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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20
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Al-Mousawi J, Boskovic A. Transcriptional and epigenetic control of early life cell fate decisions. Curr Opin Oncol 2022; 34:148-154. [PMID: 35025815 DOI: 10.1097/cco.0000000000000814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Global epigenetic reprogramming of the parental genomes after fertilization ensures the establishment of genome organization permissive for cell specialization and differentiation during development. In this review, we highlight selected, well-characterized relationships between epigenetic factors and transcriptional cell fate regulators during the initial stages of mouse development. RECENT FINDINGS Blastomeres of the mouse embryo are characterized by atypical and dynamic histone modification arrangements, noncoding RNAs and DNA methylation profiles. Moreover, asymmetries in epigenomic patterning between embryonic cells arise as early as the first cleavage, with potentially instructive roles during the first lineage allocations in the mouse embryo. Although it is widely appreciated that transcription factors and developmental signaling pathways play a crucial role in cell fate specification at the onset of development, it is increasingly clear that their function is tightly connected to the underlying epigenetic status of the embryonic cells in which they act. SUMMARY Findings on the interplay between genetic, epigenetic and environmental factors during reprogramming and differentiation in the embryo are crucial for understanding the molecular underpinnings of disease processes, particularly tumorigenesis, which is characterized by global epigenetic rewiring and progressive loss of cellular identity.
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Affiliation(s)
- Jasmina Al-Mousawi
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, Italy
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21
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Henley MJ, Koehler AN. Advances in targeting 'undruggable' transcription factors with small molecules. Nat Rev Drug Discov 2021; 20:669-688. [PMID: 34006959 DOI: 10.1038/s41573-021-00199-0] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) represent key biological players in diseases including cancer, autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors, TFs have traditionally been considered 'undruggable' by small-molecule ligands due to significant structural disorder and lack of defined small-molecule binding pockets. Renewed interest in the field has been ignited by significant progress in chemical biology approaches to ligand discovery and optimization, especially the advent of targeted protein degradation approaches, along with increasing appreciation of the critical role a limited number of collaborators play in the regulation of key TF effector genes. Here, we review current understanding of TF-mediated gene regulation, discuss successful targeting strategies and highlight ongoing challenges and emerging approaches to address them.
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Affiliation(s)
- Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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22
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Jiang JC, Rothnagel JA, Upton KR. Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. Sci Rep 2021; 11:8083. [PMID: 33850167 PMCID: PMC8044218 DOI: 10.1038/s41598-021-86395-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
While transposons are generally silenced in somatic tissues, many transposons escape epigenetic repression in epithelial cancers, become transcriptionally active and contribute to the regulation of human gene expression. We have developed a bioinformatic pipeline for the integrated analysis of transcription factor binding and transcriptomic data to identify transposon-derived promoters that are activated in specific diseases and developmental states. We applied this pipeline to a breast cancer model, and found that the L1PA2 transposon subfamily contributes abundant regulatory sequences to co-ordinated transcriptional regulation in breast cancer. Transcription factor profiling demonstrates that over 27% of L1PA2 transposons harbour co-localised binding sites of functionally interacting, cancer-associated transcription factors in MCF7 cells, a cell line used to model breast cancer. Transcriptomic analysis reveals that L1PA2 transposons also contribute transcription start sites to up-regulated transcripts in MCF7 cells, including some transcripts with established oncogenic properties. In addition, we verified the utility of our pipeline on other transposon subfamilies, as well as on leukemia and lung carcinoma cell lines. We demonstrate that the normally quiescent regulatory activities of transposons can be activated and alter the cancer transcriptome. In particular, the L1PA2 subfamily contributes abundant regulatory sequences, and likely plays a global role in modulating breast cancer transcriptional regulation. Understanding the regulatory impact of L1PA2 on breast cancer genomes provides additional insights into cancer genome regulation, and may provide novel biomarkers for disease diagnosis, prognosis and therapy.
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Affiliation(s)
- Jiayue-Clara Jiang
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Joseph A Rothnagel
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Kyle R Upton
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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23
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A proof-of-concept study for the pathogenetic role of enhancer hypomethylation of MYBPHL in multiple myeloma. Sci Rep 2021; 11:7009. [PMID: 33772052 PMCID: PMC7997988 DOI: 10.1038/s41598-021-86473-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Enhancer DNA methylation and expression of MYBPHL was studied in multiple myeloma (MM). By bisulfite genomic sequencing, among the three CpGs inside the MYBPHL enhancer, CpG1 was significantly hypomethylated in MM cell lines (6.7–50.0%) than normal plasma cells (37.5–75.0%) (P = 0.007), which was negatively correlated with qPCR-measured MYBPHL expression. In RPMI-8226 and WL-2 cells, bearing the highest CpG1 methylation, 5-azadC caused enhancer demethylation and expression of MYBPHL. In primary samples, higher CpG1 methylation was associated with lower MYBPHL expression. By luciferase assay, luciferase activity was enhanced by MYBPHL enhancer compared with empty vector control, but reduced by site-directed mutagenesis of each CpG. RNA-seq data of newly diagnosed MM patients showed that MYBPHL expression was associated with t(11;14). MOLP-8 cells carrying t(11;14) express the highest levels of MYBPHL, and its knockdown reduced cellular proliferation and increased cell death. Herein, as a proof-of-concept, our data demonstrated that the MYBPHL enhancer, particularly CpG1, was hypomethylated and associated with increased MYBPHL expression in MM, which was implicated in myelomagenesis.
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Hu M, Cebola I, Carrat G, Jiang S, Nawaz S, Khamis A, Canouil M, Froguel P, Schulte A, Solimena M, Ibberson M, Marchetti P, Cardenas-Diaz FL, Gadue PJ, Hastoy B, Almeida-Souza L, McMahon H, Rutter GA. Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a regulator of insulin secretion. Cell Rep 2021; 34:108703. [PMID: 33535042 PMCID: PMC7856552 DOI: 10.1016/j.celrep.2021.108703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
Using chromatin conformation capture, we show that an enhancer cluster in the STARD10 type 2 diabetes (T2D) locus forms a defined 3-dimensional (3D) chromatin domain. A 4.1-kb region within this locus, carrying 5 T2D-associated variants, physically interacts with CTCF-binding regions and with an enhancer possessing strong transcriptional activity. Analysis of human islet 3D chromatin interaction maps identifies the FCHSD2 gene as an additional target of the enhancer cluster. CRISPR-Cas9-mediated deletion of the variant region, or of the associated enhancer, from human pancreas-derived EndoC-βH1 cells impairs glucose-stimulated insulin secretion. Expression of both STARD10 and FCHSD2 is reduced in cells harboring CRISPR deletions, and lower expression of STARD10 and FCHSD2 is associated, the latter nominally, with the possession of risk variant alleles in human islets. Finally, CRISPR-Cas9-mediated loss of STARD10 or FCHSD2, but not ARAP1, impairs regulated insulin secretion. Thus, multiple genes at the STARD10 locus influence β cell function.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Gaelle Carrat
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Shuying Jiang
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Sameena Nawaz
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LE, UK
| | - Amna Khamis
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Mickaël Canouil
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Philippe Froguel
- Université de Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - EGID, 59000 Lille, France
| | - Anke Schulte
- Sanofi-Aventis Deutschland GmbH, 65926 Frankfurt am Main, Germany
| | - Michele Solimena
- Paul Langerhans Institute of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Piero Marchetti
- Department of Endocrinology and Metabolism, University of Pisa, 56126 Pisa, Italy
| | - Fabian L Cardenas-Diaz
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Centre for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Gadue
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Centre for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benoit Hastoy
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LE, UK
| | - Leonardo Almeida-Souza
- HiLIFE Institute of Biotechnology & Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Harvey McMahon
- MRC MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK; Lee Kong Chian School of Medicine, Nan Yang Technological University, Singapore, Singapore.
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Lidschreiber K, Jung LA, von der Emde H, Dave K, Taipale J, Cramer P, Lidschreiber M. Transcriptionally active enhancers in human cancer cells. Mol Syst Biol 2021; 17:e9873. [PMID: 33502116 PMCID: PMC7838827 DOI: 10.15252/msb.20209873] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. Here, we use transient transcriptome sequencing (TT-seq) to map thousands of transcriptionally active putative enhancers in fourteen human cancer cell lines covering seven types of cancer. These enhancers were associated with cell type-specific gene expression, enriched for genetic variants that predispose to cancer, and included functionally verified enhancers. Enhancer-promoter (E-P) pairing by correlation of transcription activity revealed ~ 40,000 putative E-P pairs, which were depleted for housekeeping genes and enriched for transcription factors, cancer-associated genes, and 3D conformational proximity. The cell type specificity and transcription activity of target genes increased with the number of paired putative enhancers. Our results represent a rich resource for future studies of gene regulation by enhancers and their role in driving cancerous cell growth.
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Affiliation(s)
- Katja Lidschreiber
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
| | - Lisa A Jung
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
- Department of Cell and Molecular BiologyKarolinska InstitutetBiomedicumSolnaSweden
| | - Henrik von der Emde
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Kashyap Dave
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetBiomedicumSolnaSweden
| | - Jussi Taipale
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetBiomedicumSolnaSweden
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Genome‐Scale Biology ProgramUniversity of HelsinkiHelsinkiFinland
| | - Patrick Cramer
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
| | - Michael Lidschreiber
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
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Zhao H, Liu X, Yu L, Lin S, Zhang C, Xu H, Leng Z, Huang W, Lei J, Li T, Li J, Yang F, Wang L. Comprehensive landscape of epigenetic-dysregulated lncRNAs reveals a profound role of enhancers in carcinogenesis in BC subtypes. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 23:667-681. [PMID: 33575113 PMCID: PMC7851425 DOI: 10.1016/j.omtn.2020.12.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 12/19/2020] [Indexed: 01/26/2023]
Abstract
Aberrant expression of long non-coding RNAs (lncRNA) is associated with altered DNA methylation and histone modifications during carcinogenesis. However, identifying epigenetically dysregulated lncRNAs and characterizing their functional mechanisms in different cancer subtypes are still major challenges for cancer studies. In this study, we systematically analyzed the epigenetic alterations of lncRNAs at important regulatory elements in three breast cancer subtypes. We identified 87, 691, and 1,197 epigenetically dysregulated lncRNAs in luminal, basal, and claudin-low subtypes of breast cancer, respectively. The landscape of epigenetically dysregulated lncRNAs at enhancer elements revealed that epigenetic changes of the majority of lncRNAs occurred in a subtype-specific manner and contributed to subtype-specific biological functions. We identified six acetylation of lysine 27 on histone H3 (H3K27ac)-dysregulated lncRNAs and three DNA methylation-dysregulated lncRNAs (CTC-303L1.2, RP11-738B7.1, and SLC26A4-AS1) as prognostic biomarkers of basal subtype. These lncRNAs were involved in immune response-related biological functions. Treatment of the basal breast cancer cell line MDA-MB-468 with CREBBP/EP300 bromodomain inhibitors downregulated H3K27 acetylation levels and caused a decrease in the expression of five H3K27ac-dysregulated lncRNAs (LINC00393, KB-1836B5.1, RP1-140K8.5, AC005162.1, and AC020916.2) and inhibition of the growth of breast cancer cells. One epigenetically dysregulated lncRNA (LINC01983) and four lncRNA regulators (UCA1, RP11-221J22.2, RP11-221J22.1, and RP1-212P9.3) were identified as prognostic biomarkers of the luminal molecular subtype of breast cancer by controlling the tumor necrosis factor (TNF) signaling pathway, T helper (Th)17 cell differentiation, and T cell migration. Finally, our results highlighted a profound role of enhancer-related H3K27ac-dysregulated lncRNAs, DNA methylation-dysregulated lncRNAs, and lncRNA regulators in breast cancer subtype carcinogenesis and their potential prognostic value.
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Affiliation(s)
- Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaoqin Liu
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Lei Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shihua Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Caiyu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Haotian Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zhijun Leng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Waidong Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Junjie Lei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tengyue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jing Li
- Department of Ultrasonic Medicine, The 1st Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Fan Yang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Gómez Acuña LI, Nazer E, Rodríguez-Seguí SA, Pozzi B, Buggiano V, Marasco LE, Agirre E, He C, Alló M, Kornblihtt AR. Nuclear role for human Argonaute-1 as an estrogen-dependent transcription coactivator. J Cell Biol 2020; 219:e201908097. [PMID: 32673398 PMCID: PMC7480116 DOI: 10.1083/jcb.201908097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/20/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
In mammals, argonaute (AGO) proteins have been characterized for their roles in small RNA-mediated posttranscriptional and also in transcriptional gene silencing. Here, we report a different role for AGO1 in estradiol-triggered transcriptional activation in human cells. We show that in MCF-7 mammary gland cells, AGO1 associates with transcriptional enhancers of estrogen receptor α (ERα) and that this association is up-regulated by treating the cells with estrogen (E2), displaying a positive correlation with the activation of these enhancers. Moreover, we show that AGO1 interacts with ERα and that this interaction is also increased by E2 treatment, but occurs in the absence of RNA. We show that AGO1 acts positively as a coactivator in estradiol-triggered transcription regulation by promoting ERα binding to its enhancers. Consistently, AGO1 depletion decreases long-range contacts between ERα enhancers and their target promoters. Our results point to a role of AGO1 in transcriptional regulation in human cells that is independent from small RNA binding.
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Affiliation(s)
- Luciana I Gómez Acuña
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Ezequiel Nazer
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Santiago A Rodríguez-Seguí
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Valeria Buggiano
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciano E Marasco
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | | | - Cody He
- Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Mariano Alló
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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28
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Li H, Wang Z, Han K, Guo M, Zou Y, Zhang W, Ma W, Hua H. Cloning and functional identification of a Chilo suppressalis-inducible promoter of rice gene, OsHPL2. PEST MANAGEMENT SCIENCE 2020; 76:3177-3187. [PMID: 32336018 DOI: 10.1002/ps.5872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/11/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Promoters play a key role in driving insect-resistant genes during breeding of transgenic plants. In current transgenic procedures for breeding rice resistance to striped stem borer (Chilo suppressalis Walker, SSB), the constitutive promoter is used to drive the insect-resistant gene. To reduce the burden of constitutive promoters on plant growth, isolation and identification of insect-inducible promoters are particularly important. However, few promoters are induced specifically by insect feeding. RESULTS We found rice hydroperoxide lyase gene (OsHPL2) (LOC_Os02g12680) was upregulated after feeding by SSB. We subsequently cloned the promoter of OsHPL2 and analysed its expression pattern using the β-glucuronidase (GUS) reporter gene. Histochemical assays and quantitative analyses of GUS activity confirmed that P HPL2 :GUS was activated by SSB, but did not respond to brown planthopper (Nilaparvata lugens Stål, BPH) infestation, mechanical wounding or phytohormone treatments. A series of 5' truncated assays were conducted and three positive regulatory regions (-1452 to -1213, -903 to -624, and -376 to -176) induced by SSB infestation were identified. P2R123-min 35S and P2TR2-min 35S promoters linked with cry1C of transgenic plants showed the highest levels of Cry1C protein expression and SSB larval mortality. CONCLUSION We identified an SSB-inducible promoter and three positive internal regions. Transgenic rice plants with the OsHPL2 promoter and its positive regions driving cry1C exhibited the expected larvicidal effect on SSB. Our study is the first report of an SSB-inducible promoter that could be used as a potential resource for breeding insect-resistant transgenic crops. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Hanpeng Li
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhengjie Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kehong Han
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mengjian Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yulan Zou
- College of Life Science, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhang
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongxia Hua
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Bylino OV, Ibragimov AN, Shidlovskii YV. Evolution of Regulated Transcription. Cells 2020; 9:E1675. [PMID: 32664620 PMCID: PMC7408454 DOI: 10.3390/cells9071675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.
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Affiliation(s)
- Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
| | - Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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Corless S, Höcker S, Erhardt S. Centromeric RNA and Its Function at and Beyond Centromeric Chromatin. J Mol Biol 2020; 432:4257-4269. [DOI: 10.1016/j.jmb.2020.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/21/2022]
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Di Stefano M, Stadhouders R, Farabella I, Castillo D, Serra F, Graf T, Marti-Renom MA. Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs. Nat Commun 2020; 11:2564. [PMID: 32444798 PMCID: PMC7244774 DOI: 10.1038/s41467-020-16396-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/01/2020] [Indexed: 12/22/2022] Open
Abstract
Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome conformation capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We apply TADdyn on in situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterize the structural rearrangements that take place upon changes in the transcriptional state of 21 genomic loci of diverse expression dynamics. By measuring various structural and dynamical properties, we find that during gene activation, the transcription starting site contacts with open and active regions in 3D chromatin domains. We propose that these 3D hubs of open and active chromatin may constitute a general feature to trigger and maintain gene transcription.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain. .,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Ralph Stadhouders
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Department of Pulmonary Medicine and Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - François Serra
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Computational Biology Group-Barcelona Supercomputing Center (BSC), 08034, Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain. .,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain. .,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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32
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UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize. PLoS Genet 2020; 16:e1008764. [PMID: 32330129 PMCID: PMC7202667 DOI: 10.1371/journal.pgen.1008764] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/06/2020] [Accepted: 04/07/2020] [Indexed: 12/22/2022] Open
Abstract
Enhancers are cis-acting DNA segments with the ability to increase target gene expression. They show high sensitivity to DNase and contain specific DNA elements in an open chromatin state that allows the binding of transcription factors (TFs). While numerous enhancers are annotated in the maize genome, few have been characterized genetically. KERNEL ROW NUMBER4 (KRN4), an intergenic quantitative trait locus for kernel row number, is assumed to be a cis-regulatory element of UNBRANCHED3 (UB3), a key inflorescence gene. However, the mechanism by which KRN4 controls UB3 expression remains unclear. Here, we found that KRN4 exhibits an open chromatin state, harboring sequences that showed high enhancer activity toward the 35S and UB3 promoters. KRN4 is bound by UB2-centered transcription complexes and interacts with the UB3 promoter by three duplex interactions to affect UB3 expression. Sequence variation at KRN4 enhances ub2 and ub3 mutant ear fasciation. Therefore, we suggest that KRN4 functions as a distal enhancer of the UB3 promoter via chromatin interactions and recruitment of UB2-centered transcription complexes for the fine-tuning of UB3 expression in meristems of ear inflorescences. These results provide evidence that an intergenic region helps to finely tune gene expression, providing a new perspective on the genetic control of quantitative traits.
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McCord RP, Kaplan N, Giorgetti L. Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function. Mol Cell 2020; 77:688-708. [PMID: 32001106 PMCID: PMC7134573 DOI: 10.1016/j.molcel.2019.12.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapidly developing technologies have recently fueled an exciting era of discovery in the field of chromosome structure and nuclear organization. In addition to chromosome conformation capture (3C) methods, new alternative techniques have emerged to study genome architecture and biological processes in the nucleus, often in single or living cells. This sets an unprecedented stage for exploring the mechanisms that link chromosome structure and biological function. Here we review popular as well as emerging approaches to study chromosome organization, focusing on the contribution of complementary methodologies to our understanding of structures revealed by 3C methods and their biological implications, and discuss the next technical and conceptual frontiers.
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Affiliation(s)
- Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Noam Kaplan
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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Zhou S, Hawley JR, Soares F, Grillo G, Teng M, Madani Tonekaboni SA, Hua JT, Kron KJ, Mazrooei P, Ahmed M, Arlidge C, Yun HY, Livingstone J, Huang V, Yamaguchi TN, Espiritu SMG, Zhu Y, Severson TM, Murison A, Cameron S, Zwart W, van der Kwast T, Pugh TJ, Fraser M, Boutros PC, Bristow RG, He HH, Lupien M. Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer. Nat Commun 2020; 11:441. [PMID: 31974375 PMCID: PMC6978390 DOI: 10.1038/s41467-020-14318-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 12/20/2019] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer is the second most commonly diagnosed malignancy among men worldwide. Recurrently mutated in primary and metastatic prostate tumors, FOXA1 encodes a pioneer transcription factor involved in disease onset and progression through both androgen receptor-dependent and androgen receptor-independent mechanisms. Despite its oncogenic properties however, the regulation of FOXA1 expression remains unknown. Here, we identify a set of six cis-regulatory elements in the FOXA1 regulatory plexus harboring somatic single-nucleotide variants in primary prostate tumors. We find that deletion and repression of these cis-regulatory elements significantly decreases FOXA1 expression and prostate cancer cell growth. Six of the ten single-nucleotide variants mapping to FOXA1 regulatory plexus significantly alter the transactivation potential of cis-regulatory elements by modulating the binding of transcription factors. Collectively, our results identify cis-regulatory elements within the FOXA1 plexus mutated in primary prostate tumors as potential targets for therapeutic intervention. FOXA1 pioneer transcription factor is recurrently mutated in primary and metastatic prostate tumors. Here, authors identify a set of six cis-regulatory elements in the FOXA1 regulatory plexus harboring somatic SNVs in primary prostate tumors and characterize their role in regulating FOXA1 expression and prostate cancer cell growth.
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Affiliation(s)
- Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - James R Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fraser Soares
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Giacomo Grillo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mona Teng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Seyed Ali Madani Tonekaboni
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Junjie Tony Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Ken J Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Hwa Young Yun
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | - Yanyun Zhu
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sarina Cameron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Theodorus van der Kwast
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Michael Fraser
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Ontario Institute for Cancer Research, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, CA, Canada.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Department of Urology, University of California, Los Angeles, CA, USA.,Institute for Precision Health, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada.,CRUK Manchester Institute and Manchester Cancer Research Centre, Manchester, UK.,Division of Cancer Sciences, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, UK.,The Christie NHS Foundation Trust, Manchester, UK
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,Ontario Institute for Cancer Research, Toronto, ON, Canada.
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Matkarimov BT, Zharkov DO, Saparbaev MK. Mechanistic insight into the role of Poly(ADP-ribosyl)ation in DNA topology modulation and response to DNA damage. Mutagenesis 2019; 35:107-118. [DOI: 10.1093/mutage/gez045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
AbstractGenotoxic stress generates single- and double-strand DNA breaks either through direct damage by reactive oxygen species or as intermediates of DNA repair. Failure to detect and repair DNA strand breaks leads to deleterious consequences such as chromosomal aberrations, genomic instability and cell death. DNA strand breaks disrupt the superhelical state of cellular DNA, which further disturbs the chromatin architecture and gene activity regulation. Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyse the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are regarded as DNA damage sensors that, upon activation by strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. Noteworthy, the regularly branched structure of poly(ADP-ribose) polymer suggests that the mechanism of its synthesis may involve circular movement of PARP1 around the DNA helix, with a branching point in PAR corresponding to one complete 360° turn. We propose that PARP1 stays bound to a DNA strand break end, but rotates around the helix displaced by the growing poly(ADP-ribose) chain, and that this rotation could introduce positive supercoils into damaged chromosomal DNA. This topology modulation would enable nucleosome displacement and chromatin decondensation around the lesion site, facilitating the access of DNA repair proteins or transcription factors. PARP1-mediated DNA supercoiling can be transmitted over long distances, resulting in changes in the high-order chromatin structures. The available structures of PARP1 are consistent with the strand break-induced PAR synthesis as a driving force for PARP1 rotation around the DNA axis.
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Affiliation(s)
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Murat K Saparbaev
- Groupe «Réparation de l’ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université Paris-Sud, Gustave Roussy Cancer Campus, Villejuif Cedex, France
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36
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Abstract
The search for oncogenic mutations in haematological malignancies has largely focused on coding sequence variants. These variants have been critical in understanding these complex cancers in greater detail, ultimately leading to better disease monitoring, subtyping and prognostication. In contrast, the search for oncogenic variants in the noncoding genome has proven to be challenging given the vastness of the search space, the intrinsic difficulty in assessing the impact of variants that do not code for functional proteins, and our still primitive understanding of the function harboured by large parts of the noncoding genome. Recent studies have broken ground on this quest, identifying somatically acquired and recurrent mutations in the noncoding genome that activate the expression of proto-oncogenes. In this Review, we explore some of the best-characterised examples of noncoding mutations in haematological malignancies, and highlight how a significant majority of these variants impinge on gene regulation through the formation of aberrant enhancers and promoters. We delve into the challenges faced by those that embark on a search for noncoding driver mutations, and provide a framework distilled from studies that have successfully identified such variants to overcome some of the most salient hurdles. Finally, we discuss the current therapeutic strategies being explored to target the oncogenic mechanism supported by recurrent noncoding variants. We postulate that the continued discovery and functional characterisation of somatic variants in the noncoding genome will not only advance our understanding of haematological malignancies, but offer novel therapeutic avenues and provide important insights into transcriptional regulation on a broader scale. Summary: This Review highlights the challenging but rewarding search for somatic mutations in the noncoding genome, and how such variants nucleate aberrant enhancers and promoters that drive the expression of proto-oncogenes.
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Affiliation(s)
- Sunniyat Rahman
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Marc R Mansour
- Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
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37
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Higgins GA, Williams AM, Ade AS, Alam HB, Athey BD. Druggable Transcriptional Networks in the Human Neurogenic Epigenome. Pharmacol Rev 2019; 71:520-538. [PMID: 31530573 PMCID: PMC6750186 DOI: 10.1124/pr.119.017681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromosome conformation capture methods have revealed the dynamics of genome architecture which is spatially organized into topologically associated domains, with gene regulation mediated by enhancer-promoter pairs in chromatin space. New evidence shows that endogenous hormones and several xenobiotics act within circumscribed topological domains of the spatial genome, impacting subsets of the chromatin contacts of enhancer-gene promoter pairs in cis and trans Results from the National Institutes of Health-funded PsychENCODE project and the study of chromatin remodeling complexes have converged to provide a clearer understanding of the organization of the neurogenic epigenome in humans. Neuropsychiatric diseases, including schizophrenia, bipolar spectrum disorder, autism spectrum disorder, attention deficit hyperactivity disorder, and other neuropsychiatric disorders are significantly associated with mutations in neurogenic transcriptional networks. In this review, we have reanalyzed the results from publications of the PsychENCODE Consortium using pharmacoinformatics network analysis to better understand druggable targets that control neurogenic transcriptional networks. We found that valproic acid and other psychotropic drugs directly alter these networks, including chromatin remodeling complexes, transcription factors, and other epigenetic modifiers. We envision a new generation of CNS therapeutics targeted at neurogenic transcriptional control networks, including druggable parts of chromatin remodeling complexes and master transcription factor-controlled pharmacogenomic networks. This may provide a route to the modification of interconnected gene pathways impacted by disease in patients with neuropsychiatric and neurodegenerative disorders. Direct and indirect therapeutic strategies to modify the master regulators of neurogenic transcriptional control networks may ultimately help extend the life span of CNS neurons impacted by disease.
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Affiliation(s)
- Gerald A Higgins
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Aaron M Williams
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Alex S Ade
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Hasan B Alam
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Brian D Athey
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
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38
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Ghorbanpour E, Lillicrap D. Innovative Molecular Testing Strategies for Adjunctive Investigations in Hemostasis and Thrombosis. Semin Thromb Hemost 2019; 45:751-756. [PMID: 31404933 PMCID: PMC7594468 DOI: 10.1055/s-0039-1692977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Clinicians and scientists in the fields of hemostasis and thrombosis have been among those first to integrate new molecular strategies for the purpose of enhancing disease diagnosis and treatment. The molecular diagnosis and introduction of gene therapy approaches for hemophilia are obvious examples of this tendency. In this review, the authors summarize information concerning three molecular technologies that have reached various stages of translational potential for their incorporation into the clinical management of disorders of hemostasis. Chromatin conformation assays are now being used to capture structural knowledge of long-range genomic interactions that can alter patterns of gene expression and contribute to quantitative trait pathogenesis. Liquid biopsies in various forms are providing opportunities for early cancer detection, and in the context of tumor-educated platelets, as described here, can also characterize tumor type and the extent of tumor progression. This technology is already being trialed in patients with unprovoked venous thrombosis to assess the potential for occult malignancies. Lastly, advances in single cell transcriptome analysis, provide opportunities to definitively determine molecular events in rare cells, such as antigen-specific regulatory T cells, within the context of heterogeneous cell populations.
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Affiliation(s)
- Elham Ghorbanpour
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - David Lillicrap
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
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Pessina F, Giavazzi F, Yin Y, Gioia U, Vitelli V, Galbiati A, Barozzi S, Garre M, Oldani A, Flaus A, Cerbino R, Parazzoli D, Rothenberg E, d'Adda di Fagagna F. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat Cell Biol 2019; 21:1286-1299. [PMID: 31570834 PMCID: PMC6859070 DOI: 10.1038/s41556-019-0392-4] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/16/2019] [Indexed: 12/31/2022]
Abstract
Damage-induced long non-coding RNAs (dilncRNA) synthesized at DNA double-strand breaks (DSBs) by RNA polymerase II are necessary for DNA-damage-response (DDR) focus formation. We demonstrate that induction of DSBs results in the assembly of functional promoters that include a complete RNA polymerase II preinitiation complex, MED1 and CDK9. Absence or inactivation of these factors causes a reduction in DDR foci both in vivo and in an in vitro system that reconstitutes DDR events on nucleosomes. We also show that dilncRNAs drive molecular crowding of DDR proteins, such as 53BP1, into foci that exhibit liquid-liquid phase-separation condensate properties. We propose that the assembly of DSB-induced transcriptional promoters drives RNA synthesis, which stimulates phase separation of DDR factors in the shape of foci.
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Affiliation(s)
- Fabio Pessina
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Fabio Giavazzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Ubaldo Gioia
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Valerio Vitelli
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Sara Barozzi
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Amanda Oldani
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Andrew Flaus
- Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Roberto Cerbino
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, Italy
| | - Dario Parazzoli
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Fabrizio d'Adda di Fagagna
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.
- Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia, Italy.
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40
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An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana. Sci Rep 2019; 9:13777. [PMID: 31551463 PMCID: PMC6760150 DOI: 10.1038/s41598-019-50389-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/10/2019] [Indexed: 12/29/2022] Open
Abstract
Certain introns significantly increase mRNA accumulation by a poorly understood mechanism. These introns have no effect when located upstream, or more than ~1 Kb downstream, of the start of transcription. We tested the ability of a formerly non-stimulating intron containing 11 copies of the sequence TTNGATYTG, which is over-represented in promoter-proximal introns in Arabidopsis thaliana, to affect expression from various positions. The activity profile of this intron at different locations was similar to that of a natural intron from the UBQ10 gene, suggesting that the motif increases mRNA accumulation by the same mechanism. A series of introns with different numbers of this motif revealed that the effect on expression is linearly dependent on motif copy number up to at least 20, with each copy adding another 1.5-fold increase in mRNA accumulation. Furthermore, 6 copies of the motif stimulated mRNA accumulation to a similar degree from within an intron or when introduced into the 5'-UTR and coding sequences of an intronless construct, demonstrating that splicing is not required for this sequence to boost expression. The ability of this motif to substantially elevate expression from several hundred nucleotides downstream of the transcription start site reveals a novel type of eukaryotic gene regulation.
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Bicoid-Dependent Activation of the Target Gene hunchback Requires a Two-Motif Sequence Code in a Specific Basal Promoter. Mol Cell 2019; 75:1178-1187.e4. [PMID: 31402096 DOI: 10.1016/j.molcel.2019.06.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/14/2019] [Accepted: 06/25/2019] [Indexed: 01/08/2023]
Abstract
In complex genetic loci, individual enhancers interact most often with specific basal promoters. Here we investigate the activation of the Bicoid target gene hunchback (hb), which contains two basal promoters (P1 and P2). Early in embryogenesis, P1 is silent, while P2 is strongly activated. In vivo deletion of P2 does not cause activation of P1, suggesting that P2 contains intrinsic sequence motifs required for activation. We show that a two-motif code (a Zelda binding site plus TATA) is required and sufficient for P2 activation. Zelda sites are present in the promoters of many embryonically expressed genes, but the combination of Zelda plus TATA does not seem to be a general code for early activation or Bicoid-specific activation per se. Because Zelda sites are also found in Bicoid-dependent enhancers, we propose that simultaneous binding to both enhancers and promoters independently synchronizes chromatin accessibility and facilitates correct enhancer-promoter interactions.
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Benabdallah NS, Williamson I, Illingworth RS, Kane L, Boyle S, Sengupta D, Grimes GR, Therizols P, Bickmore WA. Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation. Mol Cell 2019; 76:473-484.e7. [PMID: 31494034 PMCID: PMC6838673 DOI: 10.1016/j.molcel.2019.07.038] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 05/08/2019] [Accepted: 07/29/2019] [Indexed: 12/29/2022]
Abstract
Enhancers can regulate the promoters of their target genes over very large genomic distances. It is widely assumed that mechanisms of enhancer action involve the reorganization of three-dimensional chromatin architecture, but this is poorly understood. The predominant model involves physical enhancer-promoter interaction by looping out the intervening chromatin. However, studying the enhancer-driven activation of the Sonic hedgehog gene (Shh), we have identified a change in chromosome conformation that is incompatible with this simple looping model. Using super-resolution 3D-FISH and chromosome conformation capture, we observe a decreased spatial proximity between Shh and its enhancers during the differentiation of embryonic stem cells to neural progenitors. We show that this can be recapitulated by synthetic enhancer activation, is impeded by chromatin-bound proteins located between the enhancer and the promoter, and appears to involve the catalytic activity of poly (ADP-ribose) polymerase. Our data suggest that models of enhancer-promoter communication need to encompass chromatin conformations other than looping. Super-resolution microscopy reveals increased enhancer-promoter separation upon activation Synthetic enhancer activation supports decreased enhancer-promoter proximity Enhancer-promoter separation can be driven by poly(ADP-ribose) polymerase 1
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Affiliation(s)
- Nezha S Benabdallah
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK; Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Robert S Illingworth
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Lauren Kane
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Dipta Sengupta
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Pierre Therizols
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK; UMR INSERM 944, CNRS 7212, Bâtiment Jean Bernard, Hôpital Saint Louis, Paris, France
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
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43
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Genetic Variation in Long-Range Enhancers. Curr Top Behav Neurosci 2019; 42:35-50. [PMID: 31396896 DOI: 10.1007/7854_2019_110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Cis-regulatory elements (CREs), including insulators, promoters, and enhancers, play critical roles in the establishment and maintenance of normal cellular function. Within each cell, the 3D structure of chromatin is arranged in specific patterns to expose the CREs required for optimal spatiotemporal regulation of gene expression. CREs can act over large distances along the linear genome, facilitated by looping of the intervening chromatin to allow direct interaction between distal regulatory elements and their target genes. A number of pathologies are associated with dysregulation of CRE function, including developmental disorders, cancers, and neuropsychiatric disease. A majority of known neuropsychiatric disease risk loci are noncoding, and increasing evidence suggests that they contribute to disease through disruption of CREs. As such, rather than directly altering the amino acid content of proteins, these variants are instead thought to affect where, when, and to what extent a given gene is expressed. The distances over which CREs can operate often render their target genes difficult to identify. Furthermore, as many risk loci contain multiple variants in high linkage disequilibrium, identification of the causative single nucleotide polymorphism(s) therein is not straightforward. Thus, deciphering the genetic etiology of complex neuropsychiatric disorders presents a significant challenge.
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44
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Landscape of Enhancer-Enhancer Cooperative Regulation during Human Cardiac Commitment. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:840-851. [PMID: 31465963 PMCID: PMC6717080 DOI: 10.1016/j.omtn.2019.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/20/2019] [Accepted: 07/17/2019] [Indexed: 01/22/2023]
Abstract
Although accumulating evidence has demonstrated the key roles of enhancers in gene expression regulation, the contribution of genome-wide enhancer-enhancer interactions to developmental decisions remains unclear. Here we explored the cooperative regulation patterns among enhancers to understand their regulatory mechanism. We first filtered robust enhancers in embryonic stem cells (ESCs) through integrating bidirectional transcription, genomic location, and epigenetic modification. Genome-wide enhancer-enhancer interactions were then identified based on enhancer-promoter relationships that were derived from Hi-C data. We further explored the interacting principles of the identified enhancer-enhancer interactions. The results revealed that the observed cooperativity occurred mainly between enhancers distributed within a 1-kb to 10-Mb distance across the genome. In addition, enhancer-enhancer pairs had higher expression correlations than non-interacting pairs. Finally, we identified robust enhancers during human cardiac commitment, and we found that enhancers exhibited strong stage-specific expression patterns. We further inferred the enhancer-enhancer interactions based on RNA sequencing (RNA-seq) data in heart development, according to the regulatory principles characterized from Hi-C data. The identified enhancer-enhancer interaction networks (EEINs) presented highly dynamic linkages. Moreover, enhancers cooperatively targeted many marker genes in each developmental stage to regulate stage-specific functions, which contribute to the organization of cell identity in heart development. Our work will increase the understanding of enhancer regulation in human heart development.
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Novo CL, Javierre BM, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJ. Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition. Cell Rep 2019. [PMID: 29514091 PMCID: PMC5863031 DOI: 10.1016/j.celrep.2018.02.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs). We found that SEs form complex, spatial networks in which individual SEs contact multiple promoters, and a rewiring of promoter-SE interactions occurs between pluripotent states. We also show that long-range promoter-SE interactions are more prevalent in ESCs than in epiblast stem cells (EpiSCs) or Nanog-deficient ESCs. We conclude that SEs form cell-type-specific interaction networks that are partly dependent on core transcription factors, thereby providing insights into the gene regulatory organization of pluripotent cells. Promoter-capture Hi-C identifies 3D interactions in mouse pluripotent cells Super-enhancers (SEs) form complex spatial networks contacting multiple promoters Rewiring of promoter-SE interactions between ESC and EpiSC pluripotent states Long-range SE interactions are a hallmark of mouse ESCs
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Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Steven W Wingett
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | | | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
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Hojo MA, Masuda K, Hojo H, Nagahata Y, Yasuda K, Ohara D, Takeuchi Y, Hirota K, Suzuki Y, Kawamoto H, Kawaoka S. Identification of a genomic enhancer that enforces proper apoptosis induction in thymic negative selection. Nat Commun 2019; 10:2603. [PMID: 31197149 PMCID: PMC6565714 DOI: 10.1038/s41467-019-10525-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/19/2019] [Indexed: 12/23/2022] Open
Abstract
During thymic negative selection, autoreactive thymocytes carrying T cell receptor (TCR) with overtly strong affinity to self-MHC/self-peptide are removed by Bim-dependent apoptosis, but how Bim is specifically regulated to link TCR activation and apoptosis induction is unclear. Here we identify a murine T cell-specific genomic enhancer EBAB (Bub1-Acoxl-Bim), whose deletion leads to accumulation of thymocytes expressing high affinity TCRs. Consistently, EBAB knockout mice have defective negative selection and fail to delete autoreactive thymocytes in various settings, with this defect accompanied by reduced Bim expression and apoptosis induction. By contrast, EBAB is dispensable for maintaining peripheral T cell homeostasis via Bim-dependent pathways. Our data thus implicate EBAB as an important, developmental stage-specific regulator of Bim expression and apoptosis induction to enforce thymic negative selection and suppress autoimmunity. Our study unravels a part of genomic enhancer codes that underlie complex and context-dependent gene regulation in TCR signaling.
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Affiliation(s)
- Miki Arai Hojo
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa-shi, Chiba, 277-8562, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Soraku-gun, Kyoto, 619-0237, Japan
| | - Kyoko Masuda
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Hiroaki Hojo
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Soraku-gun, Kyoto, 619-0237, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
- ERATO Sato Live Bio-forecasting Project, Japan Science and Technology Agency (JST), Soraku-gun, Kyoto, 619-0237, Japan
| | - Yosuke Nagahata
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Keiko Yasuda
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Daiya Ohara
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Yusuke Takeuchi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Keiji Hirota
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Hiroshi Kawamoto
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Shinpei Kawaoka
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Soraku-gun, Kyoto, 619-0237, Japan.
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan.
- ERATO Sato Live Bio-forecasting Project, Japan Science and Technology Agency (JST), Soraku-gun, Kyoto, 619-0237, Japan.
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Fields BD, Nguyen SC, Nir G, Kennedy S. A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans. eLife 2019; 8:42823. [PMID: 31084706 PMCID: PMC6516958 DOI: 10.7554/elife.42823] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/02/2019] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic DNA is highly organized within nuclei and this organization is important for genome function. Fluorescent in situ hybridization (FISH) approaches allow 3D architectures of genomes to be visualized. Scalable FISH technologies, which can be applied to whole animals, are needed to help unravel how genomic architecture regulates, or is regulated by, gene expression during development, growth, reproduction, and aging. Here, we describe a multiplexed DNA FISH Oligopaint library that targets the entire Caenorhabditis elegans genome at chromosome, three megabase, and 500 kb scales. We describe a hybridization strategy that provides flexibility to DNA FISH experiments by coupling a single primary probe synthesis reaction to dye conjugated detection oligos via bridge oligos, eliminating the time and cost typically associated with labeling probe sets for individual experiments. The approach allows visualization of genome organization at varying scales in all/most cells across all stages of development in an intact animal model system. DNA contains the instructions needed to build and maintain a living organism. How DNA is physically arranged inside a cell is not random, and DNA organization is important because it can affect, for example, which genes are active, and which are not. Researchers often use a technique called “fluorescence in situ hybridization” (or FISH for short) to study how DNA is organized in cells. FISH tethers fluorescent molecules to defined sections of DNA, making those sections glow under the right wavelength of light. It is possible to collect images of the fluorescent DNA regions under a microscope to see where they are in relation to each other and to the rest of the cell. Fields, Nguyen et al. have now created a new library of FISH molecules that can be used to analyze the DNA of a microscopic worm known as Caenorhabditis elegans – a model organism that is widely used to study genetics, animal development, and cell biology. The library can be used to visualize the worm’s whole genome at different scales. The library enables accurate and reliable investigations of how DNA is organized inside C. elegans, including in intact worms, meaning it also offers the first chance to study DNA organization in a whole organism through all stages of its life cycle. This new resource could help to reveal the relationships between DNA organization, cell specialization and gene activity in different cells at different stages of development. This could help to clarify the relationships between physical DNA organization and biological change. This design strategy behind this whole genome library should also be adaptable for similar studies in other animal species.
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Affiliation(s)
- Brandon D Fields
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Scott Kennedy
- Department of Genetics, Harvard Medical School, Boston, United States
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Ho EYK, Cao Q, Gu M, Chan RWL, Wu Q, Gerstein M, Yip KY. Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Brief Bioinform 2019; 21:836-850. [PMID: 30895290 DOI: 10.1093/bib/bbz030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 01/22/2023] Open
Abstract
Since the 1st discovery of transcriptional enhancers in 1981, their textbook definition has remained largely unchanged in the past 37 years. With the emergence of high-throughput assays and genome editing, which are switching the paradigm from bottom-up discovery and testing of individual enhancers to top-down profiling of enhancer activities genome-wide, it has become increasingly evidenced that this classical definition has left substantial gray areas in different aspects. Here we survey a representative set of recent research articles and report the definitions of enhancers they have adopted. The results reveal that a wide spectrum of definitions is used usually without the definition stated explicitly, which could lead to difficulties in data interpretation and downstream analyses. Based on these findings, we discuss the practical implications and suggestions for future studies.
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Affiliation(s)
| | - Qin Cao
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Mengting Gu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ricky Wai-Lun Chan
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Qiong Wu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.,Program in Computational Biology and Bioinformatics.,Department of Computer Science, Yale University, New Haven, Connecticut, USA
| | - Kevin Y Yip
- Department of Biomedical Engineering.,Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre.,CUHK-BGI Innovation Institute of Trans-omics.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong
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Cremer M, Cremer T. Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences. Genes Chromosomes Cancer 2019; 58:427-436. [DOI: 10.1002/gcc.22714] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marion Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
| | - Thomas Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
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Abstract
Although the number of sequenced insect genomes numbers in the hundreds, little is known about gene regulatory sequences in any species other than the well-studied Drosophila melanogaster. We provide here a detailed protocol for using SCRMshaw, a computational method for predicting cis-regulatory modules (CRMs, also "enhancers") in sequenced insect genomes. SCRMshaw is effective for CRM discovery throughout the range of holometabolous insects and potentially in even more diverged species, with true-positive prediction rates of 75% or better. Minimal requirements for using SCRMshaw are a genome sequence and training data in the form of known Drosophila CRMs; a comprehensive set of the latter can be obtained from the SCRMshaw download site. For basic applications, a user with only modest computational know-how can run SCRMshaw on a desktop computer. SCRMshaw can be run with a single, narrow set of training data to predict CRMs regulating a specific pattern of gene expression, or with multiple sets of training data covering a broad range of CRM activities to provide an initial rough regulatory annotation of a complete, newly-sequenced genome.
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Affiliation(s)
- Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA.
| | - Marc S Halfon
- Departments of Biochemistry, Biomedical Informatics, and Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY, USA.
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.
- Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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