151
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Büchel G, Carstensen A, Mak KY, Roeschert I, Leen E, Sumara O, Hofstetter J, Herold S, Kalb J, Baluapuri A, Poon E, Kwok C, Chesler L, Maric HM, Rickman DS, Wolf E, Bayliss R, Walz S, Eilers M. Association with Aurora-A Controls N-MYC-Dependent Promoter Escape and Pause Release of RNA Polymerase II during the Cell Cycle. Cell Rep 2017; 21:3483-3497. [PMID: 29262328 PMCID: PMC5746598 DOI: 10.1016/j.celrep.2017.11.090] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/12/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
MYC proteins bind globally to active promoters and promote transcriptional elongation by RNA polymerase II (Pol II). To identify effector proteins that mediate this function, we performed mass spectrometry on N-MYC complexes in neuroblastoma cells. The analysis shows that N-MYC forms complexes with TFIIIC, TOP2A, and RAD21, a subunit of cohesin. N-MYC and TFIIIC bind to overlapping sites in thousands of Pol II promoters and intergenic regions. TFIIIC promotes association of RAD21 with N-MYC target sites and is required for N-MYC-dependent promoter escape and pause release of Pol II. Aurora-A competes with binding of TFIIIC and RAD21 to N-MYC in vitro and antagonizes association of TOP2A, TFIIIC, and RAD21 with N-MYC during S phase, blocking N-MYC-dependent release of Pol II from the promoter. Inhibition of Aurora-A in S phase restores RAD21 and TFIIIC binding to chromatin and partially restores N-MYC-dependent transcriptional elongation. We propose that complex formation with Aurora-A controls N-MYC function during the cell cycle.
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Affiliation(s)
- Gabriele Büchel
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Anne Carstensen
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ka-Yan Mak
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Isabelle Roeschert
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Eoin Leen
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; University of Leicester, Leicester LE1 9HN, UK
| | - Olga Sumara
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Steffi Herold
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jacqueline Kalb
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Evon Poon
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Colin Kwok
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Louis Chesler
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Hans Michael Maric
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - David S Rickman
- Weill Cornell Medicine, Sandra and Edward Meyer Cancer Center, 413 E. 69(th) Street, New York, NY 10021, USA
| | - Elmar Wolf
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Richard Bayliss
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; University of Leicester, Leicester LE1 9HN, UK
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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152
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Sarkar K, Han SS, Wen KK, Ochs HD, Dupré L, Seidman MM, Vyas YM. R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome. J Allergy Clin Immunol 2017; 142:219-234. [PMID: 29248492 DOI: 10.1016/j.jaci.2017.11.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/07/2017] [Accepted: 11/10/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. OBJECTIVE We sought to define how dysfunctional gene transcription is causally linked to the degree of TH cell deficiency and genomic instability in the XLT/WAS clinical spectrum. METHODS In human TH1- or TH2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. RESULTS WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in TH1 cells relative to TH2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (TH1 genes) in TH1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (TH2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. CONCLUSION Transcriptional R-loop imbalance is a novel molecular defect causative in TH1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum and could be targeted therapeutically.
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Affiliation(s)
- Koustav Sarkar
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md
| | - Seong-Su Han
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md
| | - Kuo-Kuang Wen
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md
| | - Hans D Ochs
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, University of Washington, Seattle, Md
| | - Loïc Dupré
- INSERM, UMR1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, Md; Université Toulouse III Paul-Sabatier, Toulouse, Md; CNRS, UMR5282, Toulouse, Md; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Md; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Md
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health (NIH), NIH Biomedical Research Center, Baltimore, Md
| | - Yatin M Vyas
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md.
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153
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154
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Mariezcurrena A, Uhlmann F. Observation of DNA intertwining along authentic budding yeast chromosomes. Genes Dev 2017; 31:2151-2161. [PMID: 29208645 PMCID: PMC5749163 DOI: 10.1101/gad.305557.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
Abstract
DNA replication of circular genomes generates physically interlinked or catenated sister DNAs. These are resolved through transient DNA fracture by type II topoisomerases to permit chromosome segregation during cell division. Topoisomerase II is similarly required for linear chromosome segregation, suggesting that linear chromosomes also remain intertwined following DNA replication. Indeed, chromosome resolution defects are a frequent cause of chromosome segregation failure and consequent aneuploidies. When and where intertwines arise and persist along linear chromosomes are not known, owing to the difficulty of demonstrating intertwining of linear DNAs. Here, we used excision of chromosomal regions as circular "loop outs" to convert sister chromatid intertwines into catenated circles. This revealed intertwining at replication termination and cohesin-binding sites, where intertwines are thought to arise and persist but not to a greater extent than elsewhere in the genome. Intertwining appears to spread evenly along chromosomes but is excluded from heterochromatin. We found that intertwines arise before replication termination, suggesting that replication forks rotate during replication elongation to dissipate torsion ahead of the forks. Our approach provides previously inaccessible insight into the topology of eukaryotic chromosomes and illuminates a process critical for successful chromosome segregation.
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Affiliation(s)
- Ainhoa Mariezcurrena
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
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155
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Zheng KW, He YD, Liu HH, Li XM, Hao YH, Tan Z. Superhelicity Constrains a Localized and R-Loop-Dependent Formation of G-Quadruplexes at the Upstream Region of Transcription. ACS Chem Biol 2017; 12:2609-2618. [PMID: 28846373 DOI: 10.1021/acschembio.7b00435] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcription induces formation of intramolecular G-quadruplex structures at the upstream region of a DNA duplex by an upward transmission of negative supercoiling through the DNA. Currently the regulation of such G-quadruplex formation remains unclear. Using plasmid as a model, we demonstrate that while it is the dynamic negative supercoiling generated by a moving RNA polymerase that triggers a formation of a G-quadruplex, the constitutional superhelicity determines the potential and range of the formation of a G-quadruplex by constraining the propagation of the negative supercoiling. G-quadruplex formation is maximal in negatively supercoiled and nearly abolished in relaxed plasmids while being moderate in nicked and linear ones. The formation of a G-quadruplex strongly correlates with the presence of an R-loop. Preventing R-loop formation virtually abolished G-quadruplex formation even in the negatively supercoiled plasmid. Enzymatic action and protein binding that manipulate supercoiling or its propagation all impact the formation of G-quadruplexes. Because chromosomes and plasmids in cells in their natural form are maintained in a supercoiled state, our findings reveal a physical basis that justifies the formation and regulation of G-quadruplexes in vivo. The structural features involved in G-quadruplex formation may all serve as potential targets in clinical and therapeutic applications.
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Affiliation(s)
- Ke-wei Zheng
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yi-de He
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hong-he Liu
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xin-min Li
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yu-hua Hao
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Zheng Tan
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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156
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Vitelli V, Galbiati A, Iannelli F, Pessina F, Sharma S, d'Adda di Fagagna F. Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks. Annu Rev Genomics Hum Genet 2017; 18:87-113. [PMID: 28859573 DOI: 10.1146/annurev-genom-091416-035314] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.
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Affiliation(s)
- Valerio Vitelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | | | - Fabio Iannelli
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabio Pessina
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Sheetal Sharma
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy;
| | - Fabrizio d'Adda di Fagagna
- FIRC Institute of Molecular Oncology (IFOM), Milan 20139, Italy; .,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia 27100, Italy
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157
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Benedetti F, Racko D, Dorier J, Burnier Y, Stasiak A. Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe. Nucleic Acids Res 2017; 45:9850-9859. [PMID: 28973473 PMCID: PMC5622301 DOI: 10.1093/nar/gkx716] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/04/2017] [Indexed: 12/12/2022] Open
Abstract
The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the validity of various models of chromosome organization. Experimental contact maps can be compared with simulated contact maps and thus verify how good is the model. With increasing resolution of experimental contact maps, it became apparent though that active processes need to be introduced into models to recapitulate the experimental data. Since transcribing RNA polymerases are very strong molecular motors that induce axial rotation of transcribed DNA, we present here models that include such rotational motors. We also include into our models swivels and sites for intersegmental passages that account for action of DNA topoisomerases releasing torsional stress. Using these elements in our models, we show that transcription-induced supercoiling generated in the regions with divergent-transcription and supercoiling relaxation occurring between these regions are sufficient to explain formation of self-interacting chromatin domains in chromosomes of fission yeast (S. pombe).
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Affiliation(s)
- Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Yannis Burnier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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158
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Gressel S, Schwalb B, Decker TM, Qin W, Leonhardt H, Eick D, Cramer P. CDK9-dependent RNA polymerase II pausing controls transcription initiation. eLife 2017; 6:29736. [PMID: 28994650 PMCID: PMC5669633 DOI: 10.7554/elife.29736] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/06/2017] [Indexed: 12/11/2022] Open
Abstract
Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a 'multi-omics' approach to demonstrate that the duration of polymerase pausing generally limits the productive frequency of transcription initiation in human cells ('pause-initiation limit'). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. CDK9 activity decreases the pause duration but also increases the productive initiation frequency. This shows that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and thus the amount of mRNA synthesized per time. CDK9 activity is also associated with long-range chromatin interactions, suggesting that enhancers can influence the pause-initiation limit to regulate transcription.
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Affiliation(s)
- Saskia Gressel
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tim Michael Decker
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Weihua Qin
- Department of Biology II, Ludwig-Maximilians-Universität München, Center of Integrated Protein Science, Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, Center of Integrated Protein Science, Martinsried, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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159
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Canela A, Maman Y, Jung S, Wong N, Callen E, Day A, Kieffer-Kwon KR, Pekowska A, Zhang H, Rao SSP, Huang SC, Mckinnon PJ, Aplan PD, Pommier Y, Aiden EL, Casellas R, Nussenzweig A. Genome Organization Drives Chromosome Fragility. Cell 2017; 170:507-521.e18. [PMID: 28735753 PMCID: PMC6133249 DOI: 10.1016/j.cell.2017.06.034] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/22/2017] [Accepted: 06/21/2017] [Indexed: 01/06/2023]
Abstract
In this study, we show that evolutionarily conserved chromosome loop anchors bound by CCCTC-binding factor (CTCF) and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy rewire DNA cleavage sites to novel loop anchors. While transcription- and replication-coupled genomic rearrangements have been well documented, we demonstrate that DSBs formed at loop anchors are largely transcription-, replication-, and cell-type-independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in cancer. Thus, loop anchors serve as fragile sites that generate DSBs and chromosomal rearrangements. VIDEO ABSTRACT.
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Affiliation(s)
- Andres Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Seolkyoung Jung
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amanda Day
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kyong-Rim Kieffer-Kwon
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Aleksandra Pekowska
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, NIH, Bethesda, MD, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Peter J Mckinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter D Aplan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, NIH, Bethesda, MD, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Rafael Casellas
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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160
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Abstract
Topoisomerases manage the torsional stress associated with the separation of DNA strands during transcription and DNA replication. Eukaryotic Topoisomerase I (Top1) is a Type IB enzyme that nicks and rejoins only one strand of duplex DNA, and it is especially important during transcription. By resolving transcription-associated torsional stress, Top1 reduces the accumulation of genome-destabilizing R-loops and non-B DNA structures. The DNA nicking activity of Top1, however, can also initiate genome instability in the form of illegitimate recombination, homologous recombination and mutagenesis. In this review, we focus on the diverse, and often opposing, roles of Top1 in regulating eukaryotic genome stability.
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161
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Physiological functions of programmed DNA breaks in signal-induced transcription. Nat Rev Mol Cell Biol 2017; 18:471-476. [PMID: 28537575 DOI: 10.1038/nrm.2017.43] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The idea that signal-dependent transcription might involve the generation of transient DNA nicks or even breaks in the regulatory regions of genes, accompanied by activation of DNA damage repair pathways, would seem to be counterintuitive, as DNA damage is usually considered harmful to cellular integrity. However, recent studies have generated a substantial body of evidence that now argues that programmed DNA single- or double-strand breaks can, at least in specific cases, have a role in transcription regulation. Here, we discuss the emerging functions of DNA breaks in the relief of DNA torsional stress and in promoter and enhancer activation.
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162
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Guha M, Saare M, Maslovskaja J, Kisand K, Liiv I, Haljasorg U, Tasa T, Metspalu A, Milani L, Peterson P. DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes. J Biol Chem 2017; 292:6542-6554. [PMID: 28242760 PMCID: PMC5399106 DOI: 10.1074/jbc.m116.764704] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/30/2017] [Indexed: 12/22/2022] Open
Abstract
The autoimmune regulator (AIRE) protein is the key factor in thymic negative selection of autoreactive T cells by promoting the ectopic expression of tissue-specific genes in the thymic medullary epithelium. Mutations in AIRE cause a monogenic autoimmune disease called autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. AIRE has been shown to promote DNA breaks via its interaction with topoisomerase 2 (TOP2). In this study, we investigated topoisomerase-induced DNA breaks and chromatin structural alterations in conjunction with AIRE-dependent gene expression. Using RNA sequencing, we found that inhibition of TOP2 religation activity by etoposide in AIRE-expressing cells had a synergistic effect on genes with low expression levels. AIRE-mediated transcription was not only enhanced by TOP2 inhibition but also by the TOP1 inhibitor camptothecin. The transcriptional activation was associated with structural rearrangements in chromatin, notably the accumulation of γH2AX and the exchange of histone H1 with HMGB1 at AIRE target gene promoters. In addition, we found the transcriptional up-regulation to co-occur with the chromatin structural changes within the genomic cluster of carcinoembryonic antigen-like cellular adhesion molecule genes. Overall, our results suggest that the presence of AIRE can trigger molecular events leading to an altered chromatin landscape and the enhanced transcription of low-expressed genes.
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Affiliation(s)
- Mithu Guha
- From the Molecular Pathology, Institute of Biomedical and Translational Medicine
| | - Mario Saare
- From the Molecular Pathology, Institute of Biomedical and Translational Medicine
| | - Julia Maslovskaja
- From the Molecular Pathology, Institute of Biomedical and Translational Medicine
| | - Kai Kisand
- From the Molecular Pathology, Institute of Biomedical and Translational Medicine
| | - Ingrid Liiv
- From the Molecular Pathology, Institute of Biomedical and Translational Medicine
| | - Uku Haljasorg
- From the Molecular Pathology, Institute of Biomedical and Translational Medicine
| | | | - Andres Metspalu
- Estonian Genome Center, and
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 50411, Estonia
| | | | - Pärt Peterson
- From the Molecular Pathology, Institute of Biomedical and Translational Medicine,
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163
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Bansal K, Yoshida H, Benoist C, Mathis D. The transcriptional regulator Aire binds to and activates super-enhancers. Nat Immunol 2017; 18:263-273. [PMID: 28135252 PMCID: PMC5310976 DOI: 10.1038/ni.3675] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/21/2016] [Indexed: 12/15/2022]
Abstract
Aire is a transcription factor that controls T cell tolerance by inducing the expression of a large repertoire of genes specifically in thymic stromal cells. It interacts with scores of protein partners of diverse functional classes. We found that Aire and some of its partners, notably those implicated in the DNA-damage response, preferentially localized to and activated long chromatin stretches that were overloaded with transcriptional regulators, known as super-enhancers. We also identified topoisomerase 1 as a cardinal Aire partner that colocalized on super-enhancers and was required for the interaction of Aire with all of its other associates. We propose a model that entails looping of super-enhancers to efficiently deliver Aire-containing complexes to local and distal transcriptional start sites.
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Affiliation(s)
- Kushagra Bansal
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - Hideyuki Yoshida
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
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164
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The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol 2017; 18:263-273. [PMID: 28248323 DOI: 10.1038/nrm.2017.10] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The carboxy-terminal domain (CTD) extends from the largest subunit of RNA polymerase II (Pol II) as a long, repetitive and largely unstructured polypeptide chain. Throughout the transcription process, the CTD is dynamically modified by post-translational modifications, many of which facilitate or hinder the recruitment of key regulatory factors of Pol II that collectively constitute the 'CTD code'. Recent studies have revealed how the physicochemical properties of the CTD promote phase separation in the presence of other low-complexity domains. Here, we discuss the intricacies of the CTD code and how the newly characterized physicochemical properties of the CTD expand the function of the CTD beyond the code.
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165
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Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. Cell Syst 2017; 4:344-356.e7. [PMID: 28237796 DOI: 10.1016/j.cels.2017.01.013] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 09/06/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022]
Abstract
DNA in cells is predominantly B-form double helix. Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and prevalence of these structures in vivo are not known. Here, using computational analysis of sequence motifs, RNA polymerase II binding data, and genome-wide potassium permanganate-dependent nuclease footprinting data, we map thousands of putative non-B DNA sites at high resolution in mouse B cells. Computational analysis associates these non-B DNAs with particular structures and indicates that they form at locations compatible with an involvement in gene regulation. Further analyses support the notion that non-B DNA structure formation influences the occupancy and positioning of nucleosomes in chromatin. These results suggest that non-B DNAs contribute to the control of a variety of critical cellular and organismal processes.
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166
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Abstract
Drosophila genetic studies demonstrate that cell and tissue growth regulation is a primary developmental function of P-element somatic inhibitor (Psi), the sole ortholog of FUBP family RNA/DNA-binding proteins. Psi achieves growth control through interaction with Mediator, observations that should put to rest controversy surrounding Pol II transcriptional functions for these KH domain proteins.
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Affiliation(s)
- Leonie M Quinn
- a Department of Cancer Biology and Therapeutics , The John Curtin School of Medical Research, The Australian National University , Canberra , ACT , Australia
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167
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Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
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168
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Abstract
DNA topological transitions occur when replication forks encounter other DNA transactions such as transcription. Failure in resolving such conflicts leads to generation of aberrant replication and transcription intermediates that might have adverse effects on genome stability. Cells have evolved numerous surveillance mechanisms to avoid, tolerate, and resolve such replication-transcription conflicts. Defects or non-coordination in such cellular mechanisms might have catastrophic effect on cell viability. In this chapter, we review consequences of replication encounters with transcription and its associated events, topological challenges, and how these inevitable conflicts alter the genome structure and functions.
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169
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Nicholas DA, Andrieu G, Strissel KJ, Nikolajczyk BS, Denis GV. BET bromodomain proteins and epigenetic regulation of inflammation: implications for type 2 diabetes and breast cancer. Cell Mol Life Sci 2017; 74:231-243. [PMID: 27491296 PMCID: PMC5222701 DOI: 10.1007/s00018-016-2320-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/16/2016] [Accepted: 07/29/2016] [Indexed: 12/18/2022]
Abstract
Chronic inflammation drives pathologies associated with type 2 diabetes (T2D) and breast cancer. Obesity-driven inflammation may explain increased risk and mortality of breast cancer with T2D reported in the epidemiology literature. Therapeutic approaches to target inflammation in both T2D and cancer have so far fallen short of the expected improvements in disease pathogenesis or outcomes. The targeting of epigenetic regulators of cytokine transcription and cytokine signaling offers one promising, untapped approach to treating diseases driven by inflammation. Recent work has deeply implicated the Bromodomain and Extra-Terminal domain (BET) proteins, which are acetylated histone "readers", in epigenetic regulation of inflammation. This review focuses on inflammation associated with T2D and breast cancer, and the possibility of targeting BET proteins as an approach to regulating inflammation in the clinic. Understanding inflammation in the context of BET protein regulation may provide a basis for designing promising therapeutics for T2D and breast cancer.
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Affiliation(s)
- Dequina A Nicholas
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
- Department of Microbiology, Training Program in Inflammatory Disorders, 72 East Concord Street, K520, Boston, MA, 02118, USA
| | - Guillaume Andrieu
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
| | - Katherine J Strissel
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA
| | - Barbara S Nikolajczyk
- Department of Microbiology, Training Program in Inflammatory Disorders, 72 East Concord Street, K520, Boston, MA, 02118, USA
| | - Gerald V Denis
- Cancer Center, Boston University School of Medicine, 72 East Concord Street, Room K520, Boston, MA, 02118, USA.
- Section of Hematology/Oncology, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, K520, Boston, MA, 02118, USA.
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170
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Yao J. Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook. J Mol Biol 2017; 429:14-31. [DOI: 10.1016/j.jmb.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 01/07/2023]
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171
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Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev 2016; 8:23-32. [PMID: 28510218 DOI: 10.1007/s12551-016-0243-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022] Open
Abstract
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
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172
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:145-155. [PMID: 28035245 PMCID: PMC5153831 DOI: 10.1007/s12551-016-0241-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 01/09/2023] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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173
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Abstract
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo.
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174
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Pommier Y, Sun Y, Huang SYN, Nitiss JL. Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 2016; 17:703-721. [DOI: 10.1038/nrm.2016.111] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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175
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Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA. O-GlcNAcase Is an RNA Polymerase II Elongation Factor Coupled to Pausing Factors SPT5 and TIF1β. J Biol Chem 2016; 291:22703-22713. [PMID: 27601472 DOI: 10.1074/jbc.m116.751420] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/29/2016] [Indexed: 12/24/2022] Open
Abstract
We describe here the identification and functional characterization of the enzyme O-GlcNAcase (OGA) as an RNA polymerase II elongation factor. Using in vitro transcription elongation assays, we show that OGA activity is required for elongation in a crude nuclear extract system, whereas in a purified system devoid of OGA the addition of rOGA inhibited elongation. Furthermore, OGA is physically associated with the known RNA polymerase II (pol II) pausing/elongation factors SPT5 and TRIM28-KAP1-TIF1β, and a purified OGA-SPT5-TIF1β complex has elongation properties. Lastly, ChIP-seq experiments show that OGA maps to the transcriptional start site/5' ends of genes, showing considerable overlap with RNA pol II, SPT5, TRIM28-KAP1-TIF1β, and O-GlcNAc itself. These data all point to OGA as a component of the RNA pol II elongation machinery regulating elongation genome-wide. Our results add a novel and unexpected dimension to the regulation of elongation by the insertion of O-GlcNAc cycling into the pol II elongation regulatory dynamics.
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Affiliation(s)
- Melissa Resto
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Bong-Hyun Kim
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Alfonso G Fernandez
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893
| | - Brian J Abraham
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, and.,Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Keji Zhao
- Laboratory of Epigenome Biology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Brian A Lewis
- From the Transcriptional Regulation and Biochemistry Unit, Metabolism Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 30893,
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176
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Peter S, Yu H, Ivanyi-Nagy R, Dröge P. Cell-based high-throughput compound screening reveals functional interaction between oncofetal HMGA2 and topoisomerase I. Nucleic Acids Res 2016; 44:e162. [PMID: 27587582 PMCID: PMC5159536 DOI: 10.1093/nar/gkw759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 12/21/2022] Open
Abstract
HMGA2 is an important chromatin factor that interacts with DNA via three AT-hook domains, thereby regulating chromatin architecture and transcription during embryonic and fetal development. The protein is absent from differentiated somatic cells, but aberrantly re-expressed in most aggressive human neoplasias where it is causally linked to cell transformation and metastasis. DNA-binding also enables HMGA2 to protect cancer cells from DNA-damaging agents. HMGA2 therefore is considered to be a prime drug target for many aggressive malignancies. Here, we have developed a broadly applicable cell-based reporter system which can identify HMGA2 antagonists targeting functionally important protein domains, as validated with the known AT-hook competitor netropsin. In addition, high-throughput screening can uncover functional links between HMGA2 and cellular factors important for cell transformation. This is demonstrated with the discovery that HMGA2 potentiates the clinically important topoisomerase I inhibitor irinotecan/SN-38 in trapping the enzyme in covalent DNA-complexes, thereby attenuating transcription.
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Affiliation(s)
- Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Haojie Yu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Roland Ivanyi-Nagy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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177
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Canela A, Sridharan S, Sciascia N, Tubbs A, Meltzer P, Sleckman BP, Nussenzweig A. DNA Breaks and End Resection Measured Genome-wide by End Sequencing. Mol Cell 2016; 63:898-911. [PMID: 27477910 PMCID: PMC6299834 DOI: 10.1016/j.molcel.2016.06.034] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/14/2016] [Accepted: 06/21/2016] [Indexed: 12/18/2022]
Abstract
DNA double-strand breaks (DSBs) arise during physiological transcription, DNA replication, and antigen receptor diversification. Mistargeting or misprocessing of DSBs can result in pathological structural variation and mutation. Here we describe a sensitive method (END-seq) to monitor DNA end resection and DSBs genome-wide at base-pair resolution in vivo. We utilized END-seq to determine the frequency and spectrum of restriction-enzyme-, zinc-finger-nuclease-, and RAG-induced DSBs. Beyond sequence preference, chromatin features dictate the repertoire of these genome-modifying enzymes. END-seq can detect at least one DSB per cell among 10,000 cells not harboring DSBs, and we estimate that up to one out of 60 cells contains off-target RAG cleavage. In addition to site-specific cleavage, we detect DSBs distributed over extended regions during immunoglobulin class-switch recombination. Thus, END-seq provides a snapshot of DNA ends genome-wide, which can be utilized for understanding genome-editing specificities and the influence of chromatin on DSB pathway choice.
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MESH Headings
- Animals
- Ataxia Telangiectasia Mutated Proteins/genetics
- Ataxia Telangiectasia Mutated Proteins/immunology
- B-Lymphocytes/cytology
- B-Lymphocytes/immunology
- Chromatin/chemistry
- Chromatin/immunology
- DNA/genetics
- DNA/immunology
- DNA Breaks, Double-Stranded
- DNA Replication
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/immunology
- Gene Expression Regulation
- Genome
- High-Throughput Nucleotide Sequencing/methods
- Histones/genetics
- Histones/immunology
- Immunoglobulin Class Switching/genetics
- Mice
- Precursor Cells, B-Lymphoid/cytology
- Precursor Cells, B-Lymphoid/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombination, Genetic
- Thymocytes/cytology
- Thymocytes/immunology
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Affiliation(s)
- Andres Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sriram Sridharan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nicholas Sciascia
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anthony Tubbs
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Paul Meltzer
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weil Cornell Medical College, New York, NY 10065, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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178
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Levens D, Baranello L, Kouzine F. Controlling gene expression by DNA mechanics: emerging insights and challenges. Biophys Rev 2016; 8:259-268. [PMID: 28510225 DOI: 10.1007/s12551-016-0216-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
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Affiliation(s)
- David Levens
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Laura Baranello
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fedor Kouzine
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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179
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:233-243. [PMID: 27738452 PMCID: PMC5039213 DOI: 10.1007/s12551-016-0208-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 12/31/2022] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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180
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Cho JE, Jinks-Robertson S. Ribonucleotides and Transcription-Associated Mutagenesis in Yeast. J Mol Biol 2016; 429:3156-3167. [PMID: 27511624 DOI: 10.1016/j.jmb.2016.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 12/26/2022]
Abstract
High levels of transcription stimulate mutation rates in microorganisms, and this occurs primarily through an enhanced accumulation of DNA damage. The major source of transcription-associated damage in yeast is Topoisomerase I (Top1), an enzyme that removes torsional stress that accumulates when DNA strands are separated. Top1 relieves torsional stress by nicking and resealing one DNA strand, and some Top1-dependent mutations are due to trapping and processing of the covalent cleavage intermediate. Most, however, reflect enzyme incision at ribonucleotides, which are the most abundant noncanonical component of DNA. In either case, Top1 generates a distinctive mutation signature composed of short deletions in tandem repeats; in the specific case of ribonucleotide-initiated events, mutations reflect sequential cleavage by the enzyme. Top1-dependent mutations do not require highly activated transcription, but their levels are greatly increased by transcription, which partially reflects an interaction of Top1 with RNA polymerase. Recent studies have demonstrated that Top1-dependent mutations exhibit a strand bias, with the nature of the bias differing depending on the transcriptional status of the underlying DNA. Under low-transcription conditions, most Top1-dependent mutations arise in the context of replication and reflect incision at ribonucleotides incorporated during leading-strand synthesis. Under high-transcription conditions, most Top1-dependent events arise when the enzyme cleaves the non-transcribed strand of DNA. In addition to increasing genetic instability in growing cells, Top1 activity in transcriptionally active regions may be a source of mutations in quiescent cells.
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Affiliation(s)
- Jang-Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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181
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Devaiah BN, Gegonne A, Singer DS. Bromodomain 4: a cellular Swiss army knife. J Leukoc Biol 2016; 100:679-686. [PMID: 27450555 DOI: 10.1189/jlb.2ri0616-250r] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/11/2016] [Indexed: 12/19/2022] Open
Abstract
Bromodomain protein 4 (BRD4) is a transcriptional and epigenetic regulator that plays a pivotal role in cancer and inflammatory diseases. BRD4 binds and stays associated with chromatin during mitosis, bookmarking early G1 genes and reactivating transcription after mitotic silencing. BRD4 plays an important role in transcription, both as a passive scaffold via its recruitment of vital transcription factors and as an active kinase that phosphorylates RNA polymerase II, directly and indirectly regulating transcription. Through its HAT activity, BRD4 contributes to the maintenance of chromatin structure and nucleosome clearance. This review summarizes the known functions of BRD4 and proposes a model in which BRD4 actively coordinates chromatin structure and transcription.
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Affiliation(s)
- Ballachanda N Devaiah
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anne Gegonne
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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182
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Corless S, Gilbert N. Effects of DNA supercoiling on chromatin architecture. Biophys Rev 2016; 8:245-258. [PMID: 27738453 PMCID: PMC5039215 DOI: 10.1007/s12551-016-0210-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022] Open
Abstract
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo.
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Affiliation(s)
- Samuel Corless
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH42XU UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH42XU UK
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183
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Compensatory RNA polymerase 2 loading determines the efficacy and transcriptional selectivity of JQ1 in Myc-driven tumors. Leukemia 2016; 31:479-490. [PMID: 27443262 PMCID: PMC5310924 DOI: 10.1038/leu.2016.182] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/18/2016] [Accepted: 06/10/2016] [Indexed: 12/15/2022]
Abstract
Inhibition of bromodomain and extraterminal motif (BET) proteins such as BRD4 bears great promise for cancer treatment and its efficacy has been frequently attributed to Myc downregulation. Here, we use B-cell tumors as a model to address the mechanism of action of JQ1, a widely used BET inhibitor. Although JQ1 led to widespread eviction of BRD4 from chromatin, its effect on gene transcription was limited to a restricted set of genes. This was unlinked to Myc downregulation or its chromatin association. Yet, JQ1-sensitive genes were enriched for Myc and E2F targets, were expressed at high levels, and showed high promoter occupancy by RNAPol2, BRD4, Myc and E2F. Their marked decrease in transcriptional elongation upon JQ1 treatment, indicated that BRD4-dependent promoter clearance was rate limiting for transcription. At JQ1-insensitive genes the drop in transcriptional elongation still occurred, but was compensated by enhanced RNAPol2 recruitment. Similar results were obtained with other inhibitors of transcriptional elongation. Thus, the selective transcriptional effects following JQ1 treatment are linked to the inability of JQ1-sensitive genes to sustain compensatory RNAPol2 recruitment to promoters. These observations highlight the role of BET proteins in supporting transcriptional elongation and rationalize how a general suppression of elongation may selectively affects transcription.
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184
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BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin. Nat Struct Mol Biol 2016; 23:540-8. [PMID: 27159561 PMCID: PMC4899182 DOI: 10.1038/nsmb.3228] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 04/14/2016] [Indexed: 12/31/2022]
Abstract
Bromodomain protein 4 (BRD4) is a chromatin-binding protein implicated in cancer and autoimmune diseases that functions as a scaffold for transcription factors at promoters and super-enhancers. Whereas chromatin de-compaction and transcriptional activation of target genes are associated with BRD4 binding, the mechanism(s) involved are unknown. We report that BRD4 is a novel histone acetyltransferase (HAT) that acetylates histones H3 and H4 with a pattern distinct from other HAT’s. Both mouse and human BRD4 demonstrate intrinsic HAT activity. Importantly, BRD4 acetylates H3K122, a residue critical for nucleosome stability, resulting in nucleosome eviction and chromatin de-compaction. Nucleosome clearance by BRD4 occurs genome-wide, including at its targets MYC, FOS and AURKB (Aurora B kinase), resulting in increased transcription. Since BRD4 regulates transcription, these findings lead to a model where BRD4 actively links chromatin structure and transcription: It mediates chromatin de-compaction by acetylating and evicting nucleosomes of target genes, thereby activating their transcription.
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185
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