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Cristini A, Géraud M, Sordet O. Transcription-associated DNA breaks and cancer: A matter of DNA topology. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:195-240. [PMID: 34507784 DOI: 10.1016/bs.ircmb.2021.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transcription is an essential cellular process but also a major threat to genome integrity. Transcription-associated DNA breaks are particularly detrimental as their defective repair can induce gene mutations and oncogenic chromosomal translocations, which are hallmarks of cancer. The past few years have revealed that transcriptional breaks mainly originate from DNA topological problems generated by the transcribing RNA polymerases. Defective removal of transcription-induced DNA torsional stress impacts on transcription itself and promotes secondary DNA structures, such as R-loops, which can induce DNA breaks and genome instability. Paradoxically, as they relax DNA during transcription, topoisomerase enzymes introduce DNA breaks that can also endanger genome integrity. Stabilization of topoisomerases on chromatin by various anticancer drugs or by DNA alterations, can interfere with transcription machinery and cause permanent DNA breaks and R-loops. Here, we review the role of transcription in mediating DNA breaks, and discuss how deregulation of topoisomerase activity can impact on transcription and DNA break formation, and its connection with cancer.
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Affiliation(s)
- Agnese Cristini
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.
| | - Mathéa Géraud
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France
| | - Olivier Sordet
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.
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2
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Irinotecan-Still an Important Player in Cancer Chemotherapy: A Comprehensive Overview. Int J Mol Sci 2020; 21:ijms21144919. [PMID: 32664667 PMCID: PMC7404108 DOI: 10.3390/ijms21144919] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 02/06/2023] Open
Abstract
Irinotecan has been used in the treatment of various malignancies for many years. Still, the knowledge regarding this drug is expanding. The pharmacogenetics of the drug is the crucial component of response to irinotecan. Furthermore, new formulations of the drug are introduced in order to better deliver the drug and avoid potentially life-threatening side effects. Here, we give a comprehensive overview on irinotecan’s molecular mode of action, metabolism, pharmacogenetics, and toxicity. Moreover, this article features clinically used combinations of the drug with other anticancer agents and introduces novel formulations of drugs (e.g., liposomal formulations, dendrimers, and nanoparticles). It also outlines crucial mechanisms of tumor cells’ resistance to the active metabolite, ethyl-10-hydroxy-camptothecin (SN-38). We are sure that the article will constitute an important source of information for both new researchers in the field of irinotecan chemotherapy and professionals or clinicians who are interested in the topic.
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3
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Khan FA, Ali SO. Physiological Roles of DNA Double-Strand Breaks. J Nucleic Acids 2017; 2017:6439169. [PMID: 29181194 PMCID: PMC5664317 DOI: 10.1155/2017/6439169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/24/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic integrity is constantly threatened by sources of DNA damage, internal and external alike. Among the most cytotoxic lesions is the DNA double-strand break (DSB) which arises from the cleavage of both strands of the double helix. Cells boast a considerable set of defences to both prevent and repair these breaks and drugs which derail these processes represent an important category of anticancer therapeutics. And yet, bizarrely, cells deploy this very machinery for the intentional and calculated disruption of genomic integrity, harnessing potentially destructive DSBs in delicate genetic transactions. Under tight spatiotemporal regulation, DSBs serve as a tool for genetic modification, widely used across cellular biology to generate diverse functionalities, ranging from the fundamental upkeep of DNA replication, transcription, and the chromatin landscape to the diversification of immunity and the germline. Growing evidence points to a role of aberrant DSB physiology in human disease and an understanding of these processes may both inform the design of new therapeutic strategies and reduce off-target effects of existing drugs. Here, we review the wide-ranging roles of physiological DSBs and the emerging network of their multilateral regulation to consider how the cell is able to harness DNA breaks as a critical biochemical tool.
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Affiliation(s)
- Farhaan A. Khan
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
| | - Syed O. Ali
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
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4
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Imre L, Simándi Z, Horváth A, Fenyőfalvi G, Nánási P, Niaki EF, Hegedüs É, Bacsó Z, Weyemi U, Mauser R, Ausio J, Jeltsch A, Bonner W, Nagy L, Kimura H, Szabó G. Nucleosome stability measured in situ by automated quantitative imaging. Sci Rep 2017; 7:12734. [PMID: 28986581 PMCID: PMC5630628 DOI: 10.1038/s41598-017-12608-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023] Open
Abstract
Current approaches have limitations in providing insight into the functional properties of particular nucleosomes in their native molecular environment. Here we describe a simple and powerful method involving elution of histones using intercalators or salt, to assess stability features dependent on DNA superhelicity and relying mainly on electrostatic interactions, respectively, and measurement of the fraction of histones remaining chromatin-bound in the individual nuclei using histone type- or posttranslational modification- (PTM-) specific antibodies and automated, quantitative imaging. The method has been validated in H3K4me3 ChIP-seq experiments, by the quantitative assessment of chromatin loop relaxation required for nucleosomal destabilization, and by comparative analyses of the intercalator and salt induced release from the nucleosomes of different histones. The accuracy of the assay allowed us to observe examples of strict association between nucleosome stability and PTMs across cell types, differentiation state and throughout the cell-cycle in close to native chromatin context, and resolve ambiguities regarding the destabilizing effect of H2A.X phosphorylation. The advantages of the in situ measuring scenario are demonstrated via the marked effect of DNA nicking on histone eviction that underscores the powerful potential of topological relaxation in the epigenetic regulation of DNA accessibility.
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Affiliation(s)
- László Imre
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Zoltán Simándi
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4032, Hungary.,Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA
| | - Attila Horváth
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - György Fenyőfalvi
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Péter Nánási
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Erfaneh Firouzi Niaki
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Éva Hegedüs
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Zsolt Bacsó
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary
| | - Urbain Weyemi
- Center for Cancer Research National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Rebekka Mauser
- Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
| | - Juan Ausio
- University of Victoria, Department of Biochemistry, Victoria, BC, V8W 3P6, Canada
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
| | - William Bonner
- Center for Cancer Research National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - László Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4032, Hungary.,Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, USA.,MTA-DE "Lendulet" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4032, Hungary.
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5
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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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6
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Jain CK, Majumder HK, Roychoudhury S. Natural Compounds as Anticancer Agents Targeting DNA Topoisomerases. Curr Genomics 2017; 18:75-92. [PMID: 28503091 PMCID: PMC5321768 DOI: 10.2174/1389202917666160808125213] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/23/2015] [Accepted: 11/26/2015] [Indexed: 12/14/2022] Open
Abstract
DNA topoisomerases are important cellular enzymes found in almost all types of living cells (eukaryotic and prokaryotic). These enzymes are essential for various DNA metabolic processes e.g. replication, transcription, recombination, chromosomal decatenation etc. These enzymes are important molecular drug targets and inhibitors of these enzymes are widely used as effective anticancer and antibacterial drugs. However, topoisomerase inhibitors have some therapeutic limitations and they exert serious side effects during cancer chemotherapy. Thus, development of novel anticancer topoisomerase inhibitors is necessary for improving cancer chemotherapy. Nature serves as a repertoire of structurally and chemically diverse molecules and in the recent years many DNA topoisomerase inhibitors have been identified from natural sources. The present review discusses anticancer properties and therapeutic importance of eighteen recently identified natural topoisomerase inhibitors (from the year 2009 to 2015). Structural characteristics of these novel inhibitors provide backbones for designing and developing new anticancer drugs.
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Affiliation(s)
- Chetan Kumar Jain
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Hemanta Kumar Majumder
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Susanta Roychoudhury
- Division of Research, Saroj Gupta Cancer Centre & Research Institute, M G Road, Thakurpukur, Kolkata-700 063, India
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7
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Allam WR, Ashour ME, Waly AA, El-Khamisy S. Role of Protein Linked DNA Breaks in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:41-58. [PMID: 28840551 DOI: 10.1007/978-3-319-60733-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Topoisomerases are a group of specialized enzymes that function to maintain DNA topology by introducing transient DNA breaks during transcription and replication. As a result of abortive topoisomerases activity, topoisomerases catalytic intermediates may be trapped on the DNA forming topoisomerase cleavage complexes (Topcc). Topoisomerases trapping on the DNA is the mode of action of several anticancer drugs, it lead to formation of protein linked DAN breaks (PDBs). PDBs are now considered as one of the most dangerous forms of endogenous DNA damage and a major threat to genomic stability. The repair of PDBs involves both the sensing and repair pathways. Unsuccessful repair of PDBs leads to different signs of genomic instabilities such as chromosomal rearrangements and cancer predisposition. In this chapter we will summarize the role of topoisomerases induced PDBs, identification and signaling, repair, role in transcription. We will also discuss the role of PDBs in cancer with a special focus on prostate cancer.
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Affiliation(s)
- Walaa R Allam
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.
| | - Mohamed E Ashour
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Amr A Waly
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Sherif El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt. .,Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, Sheffield, S10 2TN, UK.
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8
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Glorieux C, Sandoval JM, Fattaccioli A, Dejeans N, Garbe JC, Dieu M, Verrax J, Renard P, Huang P, Calderon PB. Chromatin remodeling regulates catalase expression during cancer cells adaptation to chronic oxidative stress. Free Radic Biol Med 2016; 99:436-450. [PMID: 27591797 DOI: 10.1016/j.freeradbiomed.2016.08.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/27/2016] [Accepted: 08/28/2016] [Indexed: 12/31/2022]
Abstract
Regulation of ROS metabolism plays a major role in cellular adaptation to oxidative stress in cancer cells, but the molecular mechanism that regulates catalase, a key antioxidant enzyme responsible for conversion of hydrogen peroxide to water and oxygen, remains to be elucidated. Therefore, we investigated the transcriptional regulatory mechanism controlling catalase expression in three human mammary cell lines: the normal mammary epithelial 250MK primary cells, the breast adenocarcinoma MCF-7 cells and an experimental model of MCF-7 cells resistant against oxidative stress resulting from chronic exposure to H2O2 (Resox), in which catalase was overexpressed. Here we identify a novel promoter region responsible for the regulation of catalase expression at -1518/-1226 locus and the key molecules that interact with this promoter and affect catalase transcription. We show that the AP-1 family member JunB and retinoic acid receptor alpha (RARα) mediate catalase transcriptional activation and repression, respectively, by controlling chromatin remodeling through a histone deacetylases-dependent mechanism. This regulatory mechanism plays an important role in redox adaptation to chronic exposure to H2O2 in breast cancer cells. Our study suggests that cancer adaptation to oxidative stress may be regulated by transcriptional factors through chromatin remodeling, and reveals a potential new mechanism to target cancer cells.
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Affiliation(s)
- Christophe Glorieux
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510275 Guangzhou, China.
| | - Juan Marcelo Sandoval
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Facultad de Ciencias de la Salud, Universidad Arturo Prat, 1100000 Iquique, Chile
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Nicolas Dejeans
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium
| | - James C Garbe
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marc Dieu
- Mass Spectrometry University of Namur (MaSUN), University of Namur, 5000 Namur, Belgium
| | - Julien Verrax
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Peng Huang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510275 Guangzhou, China; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pedro Buc Calderon
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Facultad de Ciencias de la Salud, Universidad Arturo Prat, 1100000 Iquique, Chile.
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9
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Calderwood SK. A critical role for topoisomerase IIb and DNA double strand breaks in transcription. Transcription 2016; 7:75-83. [PMID: 27100743 DOI: 10.1080/21541264.2016.1181142] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent studies have indicated a novel role for topoisomerase IIb in transcription. Transcription of heat shock genes, serum-induced immediate early genes and nuclear receptor-activated genes, each required DNA double strands generated by topoisomerase IIb. Such strand breaks seemed both necessary and sufficient for transcriptional activation. In addition, such transcription was associated with initiation of the DNA damage response pathways, including the activation of the enzymes: ataxia-telangiectasia mutated (ATM), DNA-dependent protein kinase and poly (ADP ribose) polymerase 1. DNA damage response signaling was involved both in transcription and in repair of DNA breaks generated by topoisomerase IIb.
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Affiliation(s)
- Stuart K Calderwood
- a Department of Radiation Oncology , Harvard Medical School at Beth Israel Deaconess Medical Center , Boston , MA , USA
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10
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Solhaug A, Wisbech C, Christoffersen T, Hult L, Lea T, Eriksen G, Holme J. The mycotoxin alternariol induces DNA damage and modify macrophage phenotype and inflammatory responses. Toxicol Lett 2015; 239:9-21. [DOI: 10.1016/j.toxlet.2015.08.1107] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/24/2015] [Accepted: 08/28/2015] [Indexed: 02/07/2023]
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11
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Allshire RC, Ekwall K. Epigenetic Regulation of Chromatin States in Schizosaccharomyces pombe. Cold Spring Harb Perspect Biol 2015; 7:a018770. [PMID: 26134317 DOI: 10.1101/cshperspect.a018770] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article discusses the advances made in epigenetic research using the model organism fission yeast Schizosaccharomyces pombe. S. pombe has been used for epigenetic research since the discovery of position effect variegation (PEV). This is a phenomenon in which a transgene inserted within heterochromatin is variably expressed, but can be stably inherited in subsequent cell generations. PEV occurs at centromeres, telomeres, ribosomal DNA (rDNA) loci, and mating-type regions of S. pombe chromosomes. Heterochromatin assembly in these regions requires enzymes that modify histones and the RNA interference (RNAi) machinery. One of the key histone-modifying enzymes is the lysine methyltransferase Clr4, which methylates histone H3 on lysine 9 (H3K9), a classic hallmark of heterochromatin. The kinetochore is assembled on specialized chromatin in which histone H3 is replaced by the variant CENP-A. Studies in fission yeast have contributed to our understanding of the establishment and maintenance of CENP-A chromatin and the epigenetic activation and inactivation of centromeres.
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Affiliation(s)
- Robin C Allshire
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Center for Biosciences, NOVUM, S-141 83, Huddinge, Sweden
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12
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Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 2014; 10:e1004446. [PMID: 24992598 PMCID: PMC4080997 DOI: 10.1371/journal.pgen.1004446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology. DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. Here, we uncovered an unexpected role of DNA topoisomerase 1α (TOP1α) in the maintenance of genome stability. Eukaryotic genomes are usually littered with transposable elements (TEs) and repeats, which pose threats to genome stability due to their tendency to move or recombine. Mechanisms are in place to silence these elements, such as RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) in plants. Two plant-specific RNA polymerases, Pol IV and Pol V, generate small and long noncoding RNAs, respectively, from TEs and repeats. These RNAs then recruit protein factors to deposit DNA methylation or H3K9me2 to silence the loci. In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. The role of TOP1α in RdDM could be attributed to its promotion of Pol V, but not Pol IV, transcription to generate long noncoding RNAs.
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Affiliation(s)
- Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- ChemGen IGERT program, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Lei Gao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Xigang Liu
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Dongming Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shengben Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Michael O'Leary
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Brandon Le
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert J. Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Pablo Manavella
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shaofang Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Olga Pontes
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California Riverside, Riverside, California, United States of America
- * E-mail:
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13
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Liu X, Gao L, Dinh TT, Shi T, Li D, Wang R, Guo L, Xiao L, Chen X. DNA topoisomerase I affects polycomb group protein-mediated epigenetic regulation and plant development by altering nucleosome distribution in Arabidopsis. THE PLANT CELL 2014; 26:2803-17. [PMID: 25070639 PMCID: PMC4145115 DOI: 10.1105/tpc.114.124941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
It has been perplexing that DNA topoisomerases, enzymes that release DNA supercoils, play specific roles in development. In this study, using a floral stem cell model in Arabidopsis thaliana, we uncovered a role for TOPOISOMERASE1α (TOP1α) in Polycomb Group (PcG) protein-mediated histone 3 lysine 27 trimethylation (H3K27me3) at, and transcriptional repression of, the stem cell maintenance gene WUSCHEL (WUS). We demonstrated that H3K27me3 deposition at other PcG targets also requires TOP1α. Intriguingly, the repression of some, as well as the expression of many, PcG target genes requires TOP1α. The mechanism that unifies the opposing effects of TOP1α appears to lie in its role in decreasing nucleosome density, which probably allows the binding of factors that either recruit PcG, as we demonstrated for AGAMOUS at the WUS locus, or counteract PcG-mediated regulation. Although TOP1α reduces nucleosome density at all genes, the lack of a 5' nucleosome-free region is a feature that distinguishes PcG targets from nontargets and may condition the requirement for TOP1α for their expression. This study uncovers a connection between TOP1α and PcG, which explains the specific developmental functions of TOP1α.
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Affiliation(s)
- Xigang Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Ting Shi
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongming Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Ruozhong Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lin Guo
- Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Langtao Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Howard Hughes Medical Institute, University of California, Riverside, California 92521
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14
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Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol 2013; 21:88-94. [PMID: 24317489 PMCID: PMC3947361 DOI: 10.1038/nsmb.2723] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/30/2013] [Indexed: 01/03/2023]
Abstract
As RNA polymerase II (Pol II) transcribes a gene, it encounters an array of well-ordered nucleosomes. How it traverses through this array in vivo remains unresolved. One model proposes that torsional stress generated during transcription destabilizes nucleosomes ahead of Pol II. Here, we describe a method for high-resolution mapping of underwound DNA, using next-generation sequencing, and show that torsion is correlated with gene expression in Drosophila melanogaster cells. Accumulation of torsional stress, through topoisomerase inhibition, results in increased Pol II at transcription start sites. Whereas topoisomerase I inhibition results in increased nascent RNA transcripts, topoisomerase II inhibition causes little change. Despite the different effects on Pol II elongation, topoisomerase inhibition results in increased nucleosome turnover and salt solubility within gene bodies, thus suggesting that the elongation-independent effects of torsional stress on nucleosome dynamics contributes to the destabilization of nucleosomes.
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15
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Rosenberg M, Fan AX, Lin IJ, Liang SY, Bungert J. Cell-cycle specific association of transcription factors and RNA polymerase ii with the human β-globin gene locus. J Cell Biochem 2013; 114:1997-2006. [PMID: 23519692 DOI: 10.1002/jcb.24542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 03/05/2013] [Indexed: 12/28/2022]
Abstract
The human β-globin genes are regulated by a locus control region (LCR) and are expressed at extremely high levels in erythroid cells. How transcriptional fidelity of highly expressed genes is regulated and maintained during the cell cycle is not completely understood. Here, we analyzed the association of transcription factor USF, the co-activator CBP, topoisomerase I (Topo I), basal transcription factor TFIIB, and RNA polymerase II (Pol II) with the β-globin gene locus at specific cell-cycle stages. The data demonstrate that while association of Pol II with globin locus associated chromatin decreased in mitotically arrested cells, it remained bound at lower levels at the γ-globin gene promoter. During early S-phase, association of CBP, USF, and Pol II with the globin gene locus decreased. The re-association of CBP and USF2 with the LCR preceded re-association of Pol II, suggesting that these proteins together mediate recruitment of Pol II to the β-globin gene locus during S-phase. Finally, we analyzed the association of Topo I with the globin gene locus during late S-phase. In general, Topo I association correlated with the binding of Pol II. Inhibition of Topo I activity reduced Pol II binding at the LCR and intergenic regions but not at the γ-globin gene promoter. The data demonstrate dynamic associations of transcription factors with the globin gene locus during the cell cycle and support previous results showing that specific components of transcription complexes remain associated with highly transcribed genes during mitosis.
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Affiliation(s)
- Michael Rosenberg
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Alex Xiucheng Fan
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - I-Ju Lin
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Shermi Y Liang
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
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16
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Veloso A, Biewen B, Paulsen MT, Berg N, Carmo de Andrade Lima L, Prasad J, Bedi K, Magnuson B, Wilson TE, Ljungman M. Genome-wide transcriptional effects of the anti-cancer agent camptothecin. PLoS One 2013; 8:e78190. [PMID: 24194914 PMCID: PMC3806802 DOI: 10.1371/journal.pone.0078190] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/02/2013] [Indexed: 11/19/2022] Open
Abstract
The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a "cleavable complex". To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment primarily affected transcription elongation. We also observed that camptothecin increased RNA reads past transcription termination sites as well as at enhancer elements. Following removal of camptothecin, transcription spread as a wave from the 5'-end of genes with no recovery of transcription apparent from RNA polymerases stalled in the body of genes. As a result, camptothecin preferentially inhibited the expression of large genes such as proto-oncogenes, and anti-apoptotic genes while smaller ribosomal protein genes, pro-apoptotic genes and p53 target genes showed relative higher expression. Cockayne syndrome group B fibroblasts (CS-B), which are defective in transcription-coupled repair (TCR), showed an RNA synthesis recovery profile similar to normal fibroblasts suggesting that TCR is not involved in the repair of or RNA synthesis recovery from transcription-blocking Top1 lesions. These findings of the effects of camptothecin on transcription have important implications for its anti-cancer activities and may aid in the design of improved combinatorial treatments involving Top1 poisons.
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Affiliation(s)
- Artur Veloso
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Bioinformatics Program and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Benjamin Biewen
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Gustavus Adolphus College, St. Peter, Minnesota, United States of America
| | - Michelle T. Paulsen
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nathan Berg
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leonardo Carmo de Andrade Lima
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- University of Sao Paulo, Sao Paulo, Brazil
| | - Jayendra Prasad
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Brian Magnuson
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas E. Wilson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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17
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Norman-Axelsson U, Durand-Dubief M, Prasad P, Ekwall K. DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast. PLoS Genet 2013; 9:e1003371. [PMID: 23516381 PMCID: PMC3597498 DOI: 10.1371/journal.pgen.1003371] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 01/25/2013] [Indexed: 11/21/2022] Open
Abstract
Centromeres are specialized chromatin regions marked by the presence of nucleosomes containing the centromere-specific histone H3 variant CENP-A, which is essential for chromosome segregation. Assembly and disassembly of nucleosomes is intimately linked to DNA topology, and DNA topoisomerases have previously been implicated in the dynamics of canonical H3 nucleosomes. Here we show that Schizosaccharomyces pombe Top3 and its partner Rqh1 are involved in controlling the levels of CENP-ACnp1 at centromeres. Both top3 and rqh1 mutants display defects in chromosome segregation. Using chromatin immunoprecipitation and tiling microarrays, we show that Top3, unlike Top1 and Top2, is highly enriched at centromeric central domains, demonstrating that Top3 is the major topoisomerase in this region. Moreover, centromeric Top3 occupancy positively correlates with CENP-ACnp1 occupancy. Intriguingly, both top3 and rqh1 mutants display increased relative enrichment of CENP-ACnp1 at centromeric central domains. Thus, Top3 and Rqh1 normally limit the levels of CENP-ACnp1 in this region. This new role is independent of the established function of Top3 and Rqh1 in homologous recombination downstream of Rad51. Therefore, we hypothesize that the Top3-Rqh1 complex has an important role in controlling centromere DNA topology, which in turn affects the dynamics of CENP-ACnp1 nucleosomes. Centromeres are unique regions on eukaryotic chromosomes that are essential for chromosome segregation at mitosis and meiosis. Centromere identity and function depends on the presence of specialized chromatin with nucleosomes containing the centromere-specific histone H3 variant CENP-A. Assembly and disassembly of nucleosomes have previously been shown to involve a family of enzymes known as DNA topoisomerases. We show that centromeres are unique in that they are associated with high levels of Top3, but low levels of Top1 and Top2, suggesting that Top3 is particularly important for centromeric DNA topology. Impaired function of Top3 or its partner Rqh1 results in chromosome segregation defects and increased levels of CENP-ACnp1 at centromeres. This role in limiting the levels of CENP-ACnp1 at centromeres is independent of the established role for the Top3-Rqh1 complex in homologous recombination. Therefore, we hypothesize that the Top3-Rqh1 complex exerts this effect by regulating centromere DNA topology, which in turn affects CENP-ACnp1 nucleosome dynamics. Specific removal of negative supercoiling by Top3 could directly have a negative effect on assembly of CENP-ACnp1 nucleosomes with left-handed negative wrapping of DNA and/or act indirectly by inhibiting transcription-coupled CENP-ACnp1 assembly. Alternatively, Top3 may be a factor that promotes formation of CENP-ACnp1 hemisomes with right-handed wrapping of DNA over conventional octamers. This suggests a new role for the Top3-Rqh1 complex at centromeres and may contribute to the understanding of the structural and functional specification of centromeres.
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Affiliation(s)
- Ulrika Norman-Axelsson
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Mickaël Durand-Dubief
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Punit Prasad
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karl Ekwall
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- * E-mail:
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18
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Elucidating the temporal dynamics of chromatin-associated protein release upon DNA digestion by quantitative proteomic approach. J Proteomics 2012; 75:5493-506. [DOI: 10.1016/j.jprot.2012.06.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 06/13/2012] [Accepted: 06/29/2012] [Indexed: 02/03/2023]
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19
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Sadeghi L, Bonilla C, Strålfors A, Ekwall K, Svensson JP. Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis. PLoS Comput Biol 2011; 7:e1002163. [PMID: 21901086 PMCID: PMC3161910 DOI: 10.1371/journal.pcbi.1002163] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 05/26/2011] [Indexed: 11/19/2022] Open
Abstract
Epigenetic regulation consists of a multitude of different modifications that determine active and inactive states of chromatin. Conditions such as cell differentiation or exposure to environmental stress require concerted changes in gene expression. To interpret epigenomics data, a spectrum of different interconnected datasets is needed, ranging from the genome sequence and positions of histones, together with their modifications and variants, to the transcriptional output of genomic regions. Here we present a tool, Podbat (Positioning database and analysis tool), that incorporates data from various sources and allows detailed dissection of the entire range of chromatin modifications simultaneously. Podbat can be used to analyze, visualize, store and share epigenomics data. Among other functions, Podbat allows data-driven determination of genome regions of differential protein occupancy or RNA expression using Hidden Markov Models. Comparisons between datasets are facilitated to enable the study of the comprehensive chromatin modification system simultaneously, irrespective of data-generating technique. Any organism with a sequenced genome can be accommodated. We exemplify the power of Podbat by reanalyzing all to-date published genome-wide data for the histone variant H2A.Z in fission yeast together with other histone marks and also phenotypic response data from several sources. This meta-analysis led to the unexpected finding of H2A.Z incorporation in the coding regions of genes encoding proteins involved in the regulation of meiosis and genotoxic stress responses. This incorporation was partly independent of the H2A.Z-incorporating remodeller Swr1. We verified an Swr1-independent role for H2A.Z following genotoxic stress in vivo. Podbat is open source software freely downloadable from www.podbat.org, distributed under the GNU LGPL license. User manuals, test data and instructions are available at the website, as well as a repository for third party-developed plug-in modules. Podbat requires Java version 1.6 or higher.
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Affiliation(s)
- Laia Sadeghi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Carolina Bonilla
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Annelie Strålfors
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - J. Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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