51
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Phosphorylated fraction of H2AX as a measurement for DNA damage in cancer cells and potential applications of a novel assay. PLoS One 2017; 12:e0171582. [PMID: 28158293 PMCID: PMC5291513 DOI: 10.1371/journal.pone.0171582] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/21/2017] [Indexed: 11/19/2022] Open
Abstract
Phosphorylated H2AX (γ-H2AX) is a sensitive marker for DNA double-strand breaks (DSBs), but the variability of H2AX expression in different cell and tissue types makes it difficult to interpret the meaning of the γ-H2AX level. Furthermore, the assays commonly used for γ-H2AX detection utilize laborious and low-throughput microscopy-based methods. We describe here an ELISA assay that measures both phosphorylated H2AX and total H2AX absolute amounts to determine the percentage of γ-H2AX, providing a normalized value representative of the amount of DNA damage. We demonstrate the utility of the assay to measure DSBs introduced by either ionizing radiation or DNA-damaging agents in cultured cells and in xenograft models. Furthermore, utilizing the NCI-60 cancer cell line panel, we show a correlation between the basal fraction of γ-H2AX and cellular mutation levels. This additional application highlights the ability of the assay to measure γ-H2AX levels in many extracts at once, making it possible to correlate findings with other cellular characteristics. Overall, the γ-H2AX ELISA represents a novel approach to quantifying DNA damage, which may lead to a better understanding of mutagenic pathways in cancer and provide a useful biomarker for monitoring the effectiveness of DNA-damaging anticancer agents.
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52
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Buschbeck M, Hake SB. Variants of core histones and their roles in cell fate decisions, development and cancer. Nat Rev Mol Cell Biol 2017; 18:299-314. [DOI: 10.1038/nrm.2016.166] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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53
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Kujirai T, Horikoshi N, Xie Y, Taguchi H, Kurumizaka H. Identification of the amino acid residues responsible for stable nucleosome formation by histone H3.Y. Nucleus 2017; 8:239-248. [PMID: 28118111 DOI: 10.1080/19491034.2016.1277303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Histone H3.Y is conserved among primates. We previously reported that exogenously produced H3.Y accumulates around transcription start sites, suggesting that it may play a role in transcription regulation. The H3.Y nucleosome forms a relaxed chromatin conformation with flexible DNA ends. The H3.Y-specific Lys42 residue is partly responsible for enhancing the flexibility of the nucleosomal DNA. To our surprise, we found that H3.Y stably associates with chromatin and nucleosomes in vivo and in vitro. However, the H3.Y residues responsible for its stable nucleosome incorporation have not been identified yet. In the present study, we performed comprehensive mutational analyses of H3.Y, and determined that the H3.Y C-terminal region including amino acid residues 124-135 is responsible for its stable association with DNA. Among the H3.Y C-terminal residues, the H3.Y Met124 residue significantly contributed to the stable DNA association with the H3.Y-H4 tetramer. The H3.Y M124I mutation substantially reduced the H3.Y-H4 association in the nucleosome. In contrast, the H3.Y K42R mutation affected the nucleosome stability less, although it contributes to the flexible DNA ends of the nucleosome. Therefore, these H3.Y-specific residues, Lys42 and Met124, play different and specific roles in nucleosomal DNA relaxation and stable nucleosome formation, respectively, in chromatin.
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Affiliation(s)
- Tomoya Kujirai
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Naoki Horikoshi
- b Research Institute for Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Yan Xie
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Hiroyuki Taguchi
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan
| | - Hitoshi Kurumizaka
- a Laboratory of Structural Biology , Graduate School of Advanced Science and Engineering , Shinjuku-ku, Tokyo , Japan.,b Research Institute for Science and Engineering , Shinjuku-ku, Tokyo , Japan.,c Institute for Medical-oriented Structural Biology , Waseda University , Shinjuku-ku, Tokyo , Japan
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54
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Talbert PB, Henikoff S. Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 2016; 18:115-126. [PMID: 27924075 DOI: 10.1038/nrm.2016.148] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most histones are assembled into nucleosomes behind the replication fork to package newly synthesized DNA. By contrast, histone variants, which are encoded by separate genes, are typically incorporated throughout the cell cycle. Histone variants can profoundly change chromatin properties, which in turn affect DNA replication and repair, transcription, and chromosome packaging and segregation. Recent advances in the study of histone replacement have elucidated the dynamic processes by which particular histone variants become substrates of histone chaperones, ATP-dependent chromatin remodellers and histone-modifying enzymes. Here, we review histone variant dynamics and the effects of replacing DNA synthesis-coupled histones with their replication-independent variants on the chromatin landscape.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
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55
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Hajdu M, Calle J, Puno A, Haruna A, Arenas-Mena C. Transcriptional and post-transcriptional regulation of histone variantH2A.Zduring sea urchin development. Dev Growth Differ 2016; 58:727-740. [DOI: 10.1111/dgd.12329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/06/2016] [Accepted: 10/27/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Mihai Hajdu
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - Jasmine Calle
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - Andrea Puno
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - Aminat Haruna
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
| | - César Arenas-Mena
- Department of Biology; College of Staten Island and Graduate Center; The City University of New York (CUNY); Staten Island New York 10314 USA
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56
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Canonical and Variant Forms of Histone H3 Are Deposited onto the Human Cytomegalovirus Genome during Lytic and Latent Infections. J Virol 2016; 90:10309-10320. [PMID: 27605676 DOI: 10.1128/jvi.01220-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/30/2016] [Indexed: 01/16/2023] Open
Abstract
Chromatin is the nucleoprotein complex that protects and compacts eukaryotic genomes. It is responsible for a large part of the epigenetic control of transcription. The genomes of DNA viruses such as human cytomegalovirus (HCMV) are devoid of histones within virions but are chromatinized and epigenetically regulated following delivery to the host cell nucleus. How chromatin is initially assembled on viral genomes and which variant forms of the core histone proteins are deposited are incompletely understood. We monitored the deposition of both ectopically expressed and endogenous histones H3.1 and H3.2 (collectively, H3.1/2) and H3.3 during lytic and latent HCMV infections. Here, we show that they are deposited on HCMV genomes during lytic and latent infections, suggesting similar mechanisms of viral chromatin assembly during the different infection types and indicating that both canonical and variant core histones may be important modulators of infecting viral genomes. We further show that association of both H3.1/2 and H3.3 occurs independent of viral DNA synthesis or de novo viral gene expression, implicating cellular factors and/or virion components in the formation of chromatin on virion-delivered genomes during both lytic and latent infections. IMPORTANCE It is well established that infecting herpesvirus genomes are chromatinized upon entry into the host cell nucleus. Why or how this occurs is a mystery. It is important to know why they are chromatinized in order to better understand cellular pathogen recognition (DNA sensing) pathways and viral fate determinations (lytic or latent) and to anticipate how artificially modulating chromatinization may impact viral infections. It is important to know how the genomes are chromatinized in order to potentially modulate the process for therapeutic effect. Our work showing that HCMV genomes are loaded with canonical and variant H3 histones during both lytic and latent infections strengthens the hypothesis that chromatinization pathways are similar between the two infection types, implicates virion or cellular factors in this process, and exposes the possibility that histone variants, in addition to posttranslational modification, may impact viral gene expression. These revelations are important to understanding and intelligently intervening in herpesvirus infections.
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57
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Pazienza V, Panebianco C, Rappa F, Memoli D, Borghesan M, Cannito S, Oji A, Mazza G, Tamburrino D, Fusai G, Barone R, Bolasco G, Villarroya F, Villarroya J, Hatsuzawa K, Cappello F, Tarallo R, Nakanishi T, Vinciguerra M. Histone macroH2A1.2 promotes metabolic health and leanness by inhibiting adipogenesis. Epigenetics Chromatin 2016; 9:45. [PMID: 27800025 PMCID: PMC5078890 DOI: 10.1186/s13072-016-0098-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
Background Obesity has tremendous impact on the health systems. Its epigenetic bases are unclear. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1.1 and macroH2A1.2, regulating cell plasticity and proliferation, during pluripotency and tumorigenesis. Their role in adipose tissue plasticity is unknown. Results Here, we show evidence that macroH2A1.1 protein levels in the visceral adipose tissue of obese humans positively correlate with BMI, while macroH2A1.2 is nearly absent. We thus introduced a constitutive GFP-tagged transgene for macroH2A1.2 in mice, and we characterized their metabolic health upon being fed a standard chow diet or a high fat diet. Despite unchanged food intake, these mice exhibit lower adipose mass and improved glucose metabolism both under a chow and an obesogenic diet. In the latter regimen, transgenic mice display smaller pancreatic islets and significantly less inflammation. MacroH2A1.2 overexpression in the mouse adipose tissue induced dramatic changes in the transcript levels of key adipogenic genes; genomic analyses comparing pre-adipocytes to mature adipocytes uncovered only minor changes in macroH2A1.2 genomic distribution upon adipogenic differentiation and suggested differential cooperation with transcription factors. MacroH2A1.2 overexpression markedly inhibited adipogenesis, while overexpression of macroH2A1.1 had opposite effects. Conclusions MacroH2A1.2 is an unprecedented chromatin component powerfully promoting metabolic health by modulating anti-adipogenic transcriptional networks in the differentiating adipose tissue. Strategies aiming at enhancing macroH2A1.2 expression might counteract excessive adiposity in humans. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0098-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valerio Pazienza
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy
| | - Concetta Panebianco
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy
| | - Francesca Rappa
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, 90127 Palermo, Italy ; Department of Legal, Society and Sport Sciences, University of Palermo, 90133 Palermo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, 84081 Baronissi, SA Italy
| | - Michela Borghesan
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy ; Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital, London, NW3 2PF UK
| | - Sara Cannito
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy
| | - Asami Oji
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 5650871 Japan
| | - Giuseppe Mazza
- Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital, London, NW3 2PF UK
| | - Domenico Tamburrino
- Centre for HPB Surgery and Liver Transplantation, Royal Free Hospital, London, NW3 2QG UK
| | - Giuseppe Fusai
- Centre for HPB Surgery and Liver Transplantation, Royal Free Hospital, London, NW3 2QG UK
| | - Rosario Barone
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, 90127 Palermo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy
| | - Giulia Bolasco
- Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), 00015 Monterotondo, Italy
| | - Francesc Villarroya
- Departament de Bioquimica i Biologia Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), and CIBER Fisiopatologia de la Obesidad y Nutricion, University of Barcelona, Barcelona, 08007 Spain ; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBEROBN) ISCIII, Madrid, Spain
| | - Joan Villarroya
- Departament de Bioquimica i Biologia Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), and CIBER Fisiopatologia de la Obesidad y Nutricion, University of Barcelona, Barcelona, 08007 Spain ; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBEROBN) ISCIII, Madrid, Spain
| | | | - Francesco Cappello
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, 90127 Palermo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, 84081 Baronissi, SA Italy
| | - Tomoko Nakanishi
- Faculty of Medicine, Tottori University, Yonago, 683-8503 Japan ; The Institute of Medical Sciences, University of Tokyo, Tokyo, 108-8639 Japan
| | - Manlio Vinciguerra
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, 71013 San Giovanni Rotondo, Italy ; Euro-Mediterranean Institute of Science and Technology (IEMEST), 90146 Palermo, Italy ; Institute for Liver and Digestive Health, University College London (UCL), Royal Free Hospital, London, NW3 2PF UK ; Center for Translational Medicine (CTM), International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, 656 91 Czech Republic
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58
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Abstract
Over the past decade, a growing number of studies have revealed that progressive changes to epigenetic information accompany aging in both dividing and nondividing cells. Functional studies in model organisms and humans indicate that epigenetic changes have a huge influence on the aging process. These epigenetic changes occur at various levels, including reduced bulk levels of the core histones, altered patterns of histone posttranslational modifications and DNA methylation, replacement of canonical histones with histone variants, and altered noncoding RNA expression, during both organismal aging and replicative senescence. The end result of epigenetic changes during aging is altered local accessibility to the genetic material, leading to aberrant gene expression, reactivation of transposable elements, and genomic instability. Strikingly, certain types of epigenetic information can function in a transgenerational manner to influence the life span of the offspring. Several important conclusions emerge from these studies: rather than being genetically predetermined, our life span is largely epigenetically determined; diet and other environmental influences can influence our life span by changing the epigenetic information; and inhibitors of epigenetic enzymes can influence life span of model organisms. These new findings provide better understanding of the mechanisms involved in aging. Given the reversible nature of epigenetic information, these studies highlight exciting avenues for therapeutic intervention in aging and age-associated diseases, including cancer.
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Affiliation(s)
- Sangita Pal
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Genes and Development Graduate Program, University of Texas Graduate School of the Biomedical Sciences at Houston, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jessica K. Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Corresponding author.
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59
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Rea M, Jiang T, Eleazer R, Eckstein M, Marshall AG, Fondufe-Mittendorf YN. Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation. Mol Cell Proteomics 2016; 15:2411-22. [PMID: 27169413 PMCID: PMC4937513 DOI: 10.1074/mcp.m116.058412] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/09/2016] [Indexed: 11/06/2022] Open
Abstract
Exposure to inorganic arsenic, a ubiquitous environmental toxic metalloid, leads to carcinogenesis. However, the mechanism is unknown. Several studies have shown that inorganic arsenic exposure alters specific gene expression patterns, possibly through alterations in chromatin structure. While most studies on understanding the mechanism of chromatin-mediated gene regulation have focused on histone post-translational modifications, the role of histone variants remains largely unknown. Incorporation of histone variants alters the functional properties of chromatin. To understand the global dynamics of chromatin structure and function in arsenic-mediated carcinogenesis, analysis of the histone variants incorporated into the nucleosome and their covalent modifications is required. Here we report the first global mass spectrometric analysis of histone H2B variants as cells undergo arsenic-mediated epithelial to mesenchymal transition. We used electron capture dissociation-based top-down tandem mass spectrometry analysis validated with quantitative reverse transcription real-time polymerase chain reaction to identify changes in the expression levels of H2B variants in inorganic arsenic-mediated epithelial-mesenchymal transition. We identified changes in the expression levels of specific histone H2B variants in two cell types, which are dependent on dose and length of exposure of inorganic arsenic. In particular, we found increases in H2B variants H2B1H/1K/1C/1J/1O and H2B2E/2F, and significant decreases in H2B1N/1D/1B as cells undergo inorganic arsenic-mediated epithelial-mesenchymal transition. The analysis of these histone variants provides a first step toward an understanding of the functional significance of the diversity of histone structures, especially in inorganic arsenic-mediated gene expression and carcinogenesis.
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Affiliation(s)
- Matthew Rea
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536
| | - Tingting Jiang
- §Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Rebekah Eleazer
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536
| | - Meredith Eckstein
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536
| | - Alan G Marshall
- §Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306; ¶Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Yvonne N Fondufe-Mittendorf
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536;
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60
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Deaton AM, Gómez-Rodríguez M, Mieczkowski J, Tolstorukov MY, Kundu S, Sadreyev RI, Jansen LE, Kingston RE. Enhancer regions show high histone H3.3 turnover that changes during differentiation. eLife 2016; 5. [PMID: 27304074 PMCID: PMC4965263 DOI: 10.7554/elife.15316] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/14/2016] [Indexed: 01/09/2023] Open
Abstract
The organization of DNA into chromatin is dynamic; nucleosomes are frequently displaced to facilitate the ability of regulatory proteins to access specific DNA elements. To gain insight into nucleosome dynamics, and to follow how dynamics change during differentiation, we used a technique called time-ChIP to quantitatively assess histone H3.3 turnover genome-wide during differentiation of mouse ESCs. We found that, without prior assumptions, high turnover could be used to identify regions involved in gene regulation. High turnover was seen at enhancers, as observed previously, with particularly high turnover at super-enhancers. In contrast, regions associated with the repressive Polycomb-Group showed low turnover in ESCs. Turnover correlated with DNA accessibility. Upon differentiation, numerous changes in H3.3 turnover rates were observed, the majority of which occurred at enhancers. Thus, time-ChIP measurement of histone turnover shows that active enhancers are unusually dynamic in ESCs and changes in highly dynamic nucleosomes predominate at enhancers during differentiation.
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Affiliation(s)
- Aimee M Deaton
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | | | - Jakub Mieczkowski
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Sharmistha Kundu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, United States
| | - Lars Et Jansen
- Laboratory for Epigenetic Mechanisms, Instituto Gulbenkian de Ciencia, Oeiras, Portugal
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
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61
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Abstract
Organism viability relies on the stable maintenance of specific chromatin landscapes, established during development, that shape cell functions and identities by driving distinct gene expression programs. Yet epigenome maintenance is challenged during transcription, replication, and repair of DNA damage, all of which elicit dynamic changes in chromatin organization. Here, we review recent advances that have shed light on the specialized mechanisms contributing to the restoration of epigenome structure and function after DNA damage in the mammalian cell nucleus. By drawing a parallel with epigenome maintenance during replication, we explore emerging concepts and highlight open issues in this rapidly growing field. In particular, we present our current knowledge of molecular players that support the coordinated maintenance of genome and epigenome integrity in response to DNA damage, and we highlight how nuclear organization impacts genome stability. Finally, we discuss possible functional implications of epigenome plasticity in response to genotoxic stress.
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Affiliation(s)
- Juliette Dabin
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Anna Fortuny
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Sophie E Polo
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France.
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62
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Konstantinov NK, Ulff-Møller CJ, Dimitrov S. Histone variants and melanoma: facts and hypotheses. Pigment Cell Melanoma Res 2016; 29:426-33. [DOI: 10.1111/pcmr.12467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/10/2016] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Stefan Dimitrov
- Institut Albert Bonniot; U823, INSERM/Université Joseph Fourier; Grenoble Cedex 9 France
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63
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Noberini R, Sigismondo G, Bonaldi T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics 2016; 8:429-45. [DOI: 10.2217/epi.15.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, via Adamello 16, Milano, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
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64
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Lulla RR, Saratsis AM, Hashizume R. Mutations in chromatin machinery and pediatric high-grade glioma. SCIENCE ADVANCES 2016; 2:e1501354. [PMID: 27034984 PMCID: PMC4803494 DOI: 10.1126/sciadv.1501354] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/04/2016] [Indexed: 05/24/2023]
Abstract
Pediatric central nervous system tumors are the most common solid tumor of childhood. Of these, approximately one-third are gliomas that exhibit diverse biological behaviors in the unique context of the developing nervous system. Although low-grade gliomas predominate and have favorable outcomes, up to 20% of pediatric gliomas are high-grade. These tumors are a major contributor to cancer-related morbidity and mortality in infants, children, and adolescents, with long-term survival rates of only 10 to 15%. The recent discovery of somatic oncogenic mutations affecting chromatin regulation in pediatric high-grade glioma has markedly improved our understanding of disease pathogenesis, and these findings have stimulated the development of novel therapeutic approaches targeting epigenetic regulators for disease treatment. We review the current perspective on pediatric high-grade glioma genetics and epigenetics, and discuss the emerging and experimental therapeutics targeting the unique molecular abnormalities present in these deadly childhood brain tumors.
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Affiliation(s)
- Rishi R. Lulla
- Department of Pediatrics—Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Amanda Muhs Saratsis
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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65
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Lahiri S, Sun N, Buck A, Imhof A, Walch A. MALDI imaging mass spectrometry as a novel tool for detecting histone modifications in clinical tissue samples. Expert Rev Proteomics 2016; 13:275-84. [DOI: 10.1586/14789450.2016.1146598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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66
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Dell'Orso S, Wang AH, Shih HY, Saso K, Berghella L, Gutierrez-Cruz G, Ladurner AG, O'Shea JJ, Sartorelli V, Zare H. The Histone Variant MacroH2A1.2 Is Necessary for the Activation of Muscle Enhancers and Recruitment of the Transcription Factor Pbx1. Cell Rep 2016; 14:1156-1168. [PMID: 26832413 DOI: 10.1016/j.celrep.2015.12.103] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/10/2015] [Accepted: 12/23/2015] [Indexed: 01/21/2023] Open
Abstract
Histone variants complement and integrate histone post-translational modifications in regulating transcription. The histone variant macroH2A1 (mH2A1) is almost three times the size of its canonical H2A counterpart, due to the presence of an ∼25 kDa evolutionarily conserved non-histone macro domain. Strikingly, mH2A1 can mediate both gene repression and activation. However, the molecular determinants conferring these alternative functions remain elusive. Here, we report that mH2A1.2 is required for the activation of the myogenic gene regulatory network and muscle cell differentiation. H3K27 acetylation at prospective enhancers is exquisitely sensitive to mH2A1.2, indicating a role of mH2A1.2 in imparting enhancer activation. Both H3K27 acetylation and recruitment of the transcription factor Pbx1 at prospective enhancers are regulated by mH2A1.2. Overall, our findings indicate a role of mH2A1.2 in marking regulatory regions for activation.
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Affiliation(s)
- Stefania Dell'Orso
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - A Hongjun Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Kayoko Saso
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Libera Berghella
- Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Gustavo Gutierrez-Cruz
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Andreas G Ladurner
- Butenandt Institute, LMU Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA.
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
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67
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GŁADYCH M, NIJAK A, LOTA P, OLEKSIEWICZ U. Epigenetics: the guardian of pluripotency and differentiation. Turk J Biol 2016. [DOI: 10.3906/biy-1509-30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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68
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Becher OJ, Holland EC. Glioma Stem-like Cells Keep Their H3.3 Variant Levels at Bay. Cancer Cell 2015; 28:679-680. [PMID: 26678332 DOI: 10.1016/j.ccell.2015.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pediatric glioblastomas (GBMs) commonly harbor mutations in histone variant H3.3, while adult GBMs do not. In this issue of Cancer Cell, Gallo and colleagues demonstrate that adult GBM stem-like cells repress H3.3 expression to maintain self-renewal properties.
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Affiliation(s)
- Oren J Becher
- Division of Pediatric Hematology-Oncology, Duke University Medical Center, Durham, NC 27710, USA; Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA.
| | - Eric C Holland
- Division of Human Biology, Solid Tumor and Translational Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Alvord Brain Tumor Center, University of Washington, Seattle, WA 98104, USA.
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69
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Alabert C, Barth TK, Reverón-Gómez N, Sidoli S, Schmidt A, Jensen ON, Imhof A, Groth A. Two distinct modes for propagation of histone PTMs across the cell cycle. Genes Dev 2015; 29:585-90. [PMID: 25792596 PMCID: PMC4378191 DOI: 10.1101/gad.256354.114] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Epigenetic states defined by chromatin can be maintained through mitotic cell division. However, it remains unknown how histone-based information is transmitted. Here we combine nascent chromatin capture (NCC) and triple-SILAC (stable isotope labeling with amino acids in cell culture) labeling to track histone modifications and histone variants during DNA replication and across the cell cycle. We show that post-translational modifications (PTMs) are transmitted with parental histones to newly replicated DNA. Di- and trimethylation marks are diluted twofold upon DNA replication, as a consequence of new histone deposition. Importantly, within one cell cycle, all PTMs are restored. In general, new histones are modified to mirror the parental histones. However, H3K9 trimethylation (H3K9me3) and H3K27me3 are propagated by continuous modification of parental and new histones because the establishment of these marks extends over several cell generations. Together, our results reveal how histone marks propagate and demonstrate that chromatin states oscillate within the cell cycle.
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Affiliation(s)
- Constance Alabert
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Teresa K Barth
- Munich Centre of Integrated Protein Science, Ludwig-Maximillians University of Munich, 80336 Munich, Germany; Adolf Butenandt Institute, Ludwig-Maximillians University of Munich, 80336 Munich, Germany
| | - Nazaret Reverón-Gómez
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simone Sidoli
- Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Andreas Schmidt
- Munich Centre of Integrated Protein Science, Ludwig-Maximillians University of Munich, 80336 Munich, Germany; Adolf Butenandt Institute, Ludwig-Maximillians University of Munich, 80336 Munich, Germany
| | - Ole N Jensen
- Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Axel Imhof
- Munich Centre of Integrated Protein Science, Ludwig-Maximillians University of Munich, 80336 Munich, Germany; Adolf Butenandt Institute, Ludwig-Maximillians University of Munich, 80336 Munich, Germany;
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark;
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70
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Gao R, Liu X, Gao S. Progress in understanding epigenetic remodeling during induced pluripotency. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0919-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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71
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Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells. Genome Biol 2015; 16:213. [PMID: 26415775 PMCID: PMC4587738 DOI: 10.1186/s13059-015-0760-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/25/2015] [Indexed: 11/22/2022] Open
Abstract
Background Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. Results Here we identify Heterochromatin Protein 1β (HP1β) as an essential protein for proper differentiation, and, unexpectedly, for the maintenance of pluripotency in ESCs. In pluripotent and differentiated cells HP1β is differentially localized and differentially associated with chromatin. Deletion of HP1β, but not HP1α, in ESCs provokes a loss of the morphological and proliferative characteristics of embryonic pluripotent cells, reduces expression of pluripotency factors and causes aberrant differentiation. However, in differentiated cells, loss of HP1β has the opposite effect, perturbing maintenance of the differentiation state and facilitating reprogramming to an induced pluripotent state. Microscopy, biochemical fractionation and chromatin immunoprecipitation reveal a diffuse nucleoplasmic distribution, weak association with chromatin and high expression levels for HP1β in ESCs. The minor fraction of HP1β that is chromatin-bound in ESCs is enriched within exons, unlike the situation in differentiated cells, where it binds heterochromatic satellite repeats and chromocenters. Conclusions We demonstrate an unexpected duality in the role of HP1β: it is essential in ESCs for maintaining pluripotency, while it is required for proper differentiation in differentiated cells. Thus, HP1β function both depends on, and regulates, the pluripotent state. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0760-8) contains supplementary material, which is available to authorized users.
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Abstract
Chromatin is a critical regulator of neural plasticity, but basic principles of chromatin function in neurons are unclear. In this issue of Neuron, Maze et al. (2015) establish histone H3.3 turnover as a novel mechanism contributing to CNS gene regulation, synaptic plasticity, and cognition.
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73
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Melters DP, Nye J, Zhao H, Dalal Y. Chromatin Dynamics in Vivo: A Game of Musical Chairs. Genes (Basel) 2015; 6:751-76. [PMID: 26262644 PMCID: PMC4584328 DOI: 10.3390/genes6030751] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/17/2015] [Accepted: 07/28/2015] [Indexed: 01/30/2023] Open
Abstract
Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.
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Affiliation(s)
- Daniël P Melters
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Jonathan Nye
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Haiqing Zhao
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
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74
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Snyers L, Zupkovitz G, Almeder M, Fliesser M, Stoisser A, Weipoltshammer K, Schöfer C. Distinct chromatin signature of histone H3 variant H3.3 in human cells. Nucleus 2015; 5:449-61. [PMID: 25482197 PMCID: PMC4164487 DOI: 10.4161/nucl.36229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Actively transcribed regions of the genome have been found enriched for the histone H3 variant H3.3. This variant is incorporated into nucleosomes throughout the cell cycle whereas the canonical isoforms are predominately deposited in association with replication. In order to obtain a global picture of the deposition pattern at the single cell level we expressed H3.3 in both normal and malignant human cells and analyzed nuclei using conventional and structured illumination imaging (SIM). We found that the distribution pattern of H3.3 in interphase differs from that of the canonical histone H3 variants and this difference is conveyed to mitotic chromosomes which display a distinct H3.3 banding pattern. Histone H3.3 localization positively correlated with markers for transcriptionally active chromatin and, notably, H3.3 was almost completely absent from the inactive X chromosome. Collectively, our data show that histone variant H3.3 occupies distinct intranuclear chromatin domains and that these genomic loci are associated with gene expression.
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Affiliation(s)
- Luc Snyers
- a Department for Cell and Developmental Biology; Medical Imaging Cluster; Medical University of Vienna; Vienna, Austria
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75
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Abstract
Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.
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Affiliation(s)
- Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
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76
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Saade E, Pirozhkova I, Aimbetov R, Lipinski M, Ogryzko V. Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis). Aging Cell 2015; 14:322-33. [PMID: 25720734 PMCID: PMC4406661 DOI: 10.1111/acel.12332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 12/22/2022] Open
Abstract
The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed.
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Affiliation(s)
- Evelyne Saade
- Faculty of Public Health Lebanese University LU Beirut Lebanon
| | - Iryna Pirozhkova
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Rakhan Aimbetov
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Marc Lipinski
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Vasily Ogryzko
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
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77
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Discovering centromere proteins: from cold white hands to the A, B, C of CENPs. Nat Rev Mol Cell Biol 2015; 16:443-9. [PMID: 25991376 DOI: 10.1038/nrm4001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The kinetochore is a complex molecular machine that directs chromosome segregation during mitosis. It is one of the most elaborate subcellular protein structures in eukaryotes, comprising more than 100 different proteins. Inner kinetochore proteins associate with specialized centromeric chromatin containing the histone H3 variant centromere protein A (CENP-A) in place of H3. Outer kinetochore proteins bind to microtubules and signal to delay anaphase onset when microtubules are absent. Since the first kinetochore proteins were discovered and cloned 30 years ago using autoimmune sera from patients with scleroderma-spectrum disease, much has been learnt about the composition, functions and regulation of this remarkable structure.
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78
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Ito M, Machida Y. Reprogramming of plant cells induced by 6b oncoproteins from the plant pathogen Agrobacterium. JOURNAL OF PLANT RESEARCH 2015; 128:423-435. [PMID: 25694001 DOI: 10.1007/s10265-014-0694-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
Reprogramming of plant cells is an event characterized by dedifferentiation, reacquisition of totipotency, and enhanced cell proliferation, and is typically observed during formation of the callus, which is dependent on plant hormones. The callus-like cell mass, called a crown gall tumor, is induced at the sites of infection by Agrobacterium species through the expression of hormone-synthesizing genes encoded in the T-DNA region, which probably involves a similar reprogramming process. One of the T-DNA genes, 6b, can also by itself induce reprogramming of differentiated cells to generate tumors and is therefore recognized as an oncogene acting in plant cells. The 6b genes belong to a group of Agrobacterium T-DNA genes, which include rolB, rolC, and orf13. These genes encode proteins with weakly conserved sequences and may be derived from a common evolutionary origin. Most of these members can modify plant growth and morphogenesis in various ways, in most cases without affecting the levels of plant hormones. Recent studies have suggested that the molecular function of 6b might be to modify the patterns of transcription in the host nuclei, particularly by directly targeting the host transcription factors or by changing the epigenetic status of the host chromatin through intrinsic histone chaperone activity. In light of the recent findings on zygotic resetting of nucleosomal histone variants in Arabidopsis thaliana, one attractive idea is that acquisition of totipotency might be facilitated by global changes of epigenetic status, which might be induced by replacement of histone variants in the zygote after fertilization and in differentiated cells upon stimulation by plant hormones as well as by expression of the 6b gene.
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Affiliation(s)
- Masaki Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan,
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79
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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80
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Schwanbeck R. The role of epigenetic mechanisms in Notch signaling during development. J Cell Physiol 2015; 230:969-81. [PMID: 25336183 DOI: 10.1002/jcp.24851] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 10/16/2014] [Indexed: 12/16/2022]
Abstract
The Notch pathway is a highly conserved cell-cell communication pathway in metazoan involved in numerous processes during embryogenesis, development, and adult organisms. Ligand-receptor interaction of Notch components on adjacent cells facilitates controlled sequential proteolytic cleavage resulting in the nuclear translocation of the intracellular domain of Notch (NICD). There it binds to the Notch effector protein RBP-J, displaces a corepressor complex and enables the induction of target genes by recruitment of coactivators in a cell-context dependent manner. Both, the gene-specific repression and the context dependent activation require an intense communication with the underlying chromatin of the regulatory regions. Since the epigenetic landscape determines the function of the genome, processes like cell fate decision, differentiation, and self-renewal depend on chromatin structure and its remodeling during development. In this review, structural features enabling the Notch pathway to read these epigenetic marks by proteins interacting with RBP-J/Notch will be discussed. Furthermore, mechanisms of the Notch pathway to write and erase chromatin marks like histone acetylation and methylation are depicted as well as ATP-dependent chromatin remodeling during the activation of target genes. An additional fine-tuning of transcriptional regulation upon Notch activation seems to be controlled by the commitment of miRNAs. Since cells within an organism have to react to environmental changes, and developmental and differentiation cues in a proper manner, different signaling pathways have to crosstalk to each other. The chromatin status may represent one major platform to integrate these different pathways including the canonical Notch signaling.
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Affiliation(s)
- Ralf Schwanbeck
- Institute of Biochemistry, Medical Faculty, University of Kiel, Kiel, Germany
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81
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Paranjpe SS, Veenstra GJC. Establishing pluripotency in early development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:626-36. [PMID: 25857441 DOI: 10.1016/j.bbagrm.2015.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 01/23/2023]
Abstract
The earliest steps of embryonic development involve important changes in chromatin and transcription factor networks, which are orchestrated to establish pluripotent cells that will form the embryo. DNA methylation, histone modifications, the pluripotency regulatory network of transcription factors, maternal factors and newly translated proteins all contribute to these transitions in dynamic ways. Moreover, these dynamics are linked to the onset of zygotic transcription. We will review recent progress in our understanding of chromatin state and regulation of gene expression in the context of embryonic development in vertebrates, in particular mouse, Xenopus and zebrafish. We include work on mouse embryonic stem cells and highlight work that illustrates how early embryonic dynamics establish gene regulatory networks and the state of pluripotency.
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Affiliation(s)
- Sarita S Paranjpe
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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82
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Subramanian* V, Fields* PA, Boyer LA. H2A.Z: a molecular rheostat for transcriptional control. F1000PRIME REPORTS 2015; 7:01. [PMID: 25705384 PMCID: PMC4311278 DOI: 10.12703/p7-01] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The replacement of nucleosomal H2A with the histone variant H2A.Z is critical for regulating DNA-mediated processes across eukaryotes and for early development of multicellular organisms. How this variant performs these seemingly diverse roles has remained largely enigmatic. Here, we discuss recent mechanistic insights that have begun to reveal how H2A.Z functions as a molecular rheostat for gene control. We focus on specific examples in metazoans as a model for understanding how H2A.Z integrates information from histone post-translational modifications, other histone variants, and transcription factors (TFs) to regulate proper induction of gene expression programs in response to cellular cues. Finally, we propose a general model of how H2A.Z incorporation regulates chromatin states in diverse processes.
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83
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Abstract
Epigenetic regulation of gene expression is an important event for normal cellular homeostasis. Gene expression may be "switched" on or "turned" off via epigenetic means through adjustments in the architecture of DNA. These structural alterations result from histone posttranslation modifications such as acetylation and methylation on key arginine and lysine residues, or by alterations to DNA methylation. Other known epigenetic mechanisms invoke histone variant exchange or utilize noncoding RNAs (lncRNA/miRNA). Drugs which can target the epigenetic regulatory machinery are currently undergoing clinical trials in a wide variety of autoimmune diseases and cancer. Here we describe RNA isolation and the subsequent Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) methods, post-epigenetic drug treatment, to identify genes, which may be responsive to such epigenetic targeting agents. In addition, we depict a chromatin immunoprecipitation (ChIP) assay to determine the association between chromatin transcription markers and DNA following pretreatment of cell cultures with a histone deacetylase inhibitor (HDi). This assay allows us to determine whether treatment with an HDi dynamically remodels the promoter region of genes, as judged by the differences in the PCR product between our treated and untreated samples. Finally we describe two commonly used methodologies for analyzing DNA methylation. The first, methylation-sensitive high resolution melt analysis (MS-HRM) is used for methylation screening of regions of interest, to identify potential epigenetic "hotspots." The second, quantitative methylation specific PCR (qMSP) is best applied when these hotspots are known, and offers a high-throughput, highly sensitive means of quantifying methylation at specific CpG dinucleotides.
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Affiliation(s)
- Antoinette S Perry
- Prostate Molecular Oncology, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland
| | - Anne-Marie Baird
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
- Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Science, St. James's Hospital, Dublin 8, Ireland
- Cancer & Ageing Research Program, Queensland University of Technology, Brisbane, QLD, Australia
| | - Steven G Gray
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.
- Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Science, St. James's Hospital, Dublin 8, Ireland.
- HOPE Directorate, St. James's Hospital, Dublin, Ireland.
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84
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Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG. Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics 2014; 15:1104. [PMID: 25494698 PMCID: PMC4378318 DOI: 10.1186/1471-2164-15-1104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, differences in nucleosome composition or dynamics may also regulate accessibility. Methods for mapping nucleosome positions and occupancies genome-wide (MNase-seq) have uncovered the nucleosome landscapes of many different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays. RESULTS Here we probe the genome-wide accessibility of multiple cell types in an unbiased manner using restriction endonuclease digestion of chromatin coupled to deep sequencing (RED-seq). Using this method, we identified differences in chromatin accessibility between populations of cells, not only in nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the majority of the genome that is packaged into nucleosome arrays. Furthermore, we identified both large differences in chromatin accessibility in distinct cell lineages and subtle but significant changes during differentiation of mouse embryonic stem cells (ESCs). Most significantly, using RED-seq, we identified differences in accessibility among nucleosomes harboring well-studied histone variants, and show that these differences depend on factors required for their deposition. CONCLUSIONS Using an unbiased method to probe chromatin accessibility genome-wide, we uncover unique features of chromatin structure that are not observed using more widely-utilized methods. We demonstrate that different types of nucleosomes within mammalian cells exhibit different degrees of accessibility. These findings provide significant insight into the regulation of DNA accessibility.
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Affiliation(s)
| | | | | | | | - Thomas G Fazzio
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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85
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Rai TS, Cole JJ, Nelson DM, Dikovskaya D, Faller WJ, Vizioli MG, Hewitt RN, Anannya O, McBryan T, Manoharan I, van Tuyn J, Morrice N, Pchelintsev NA, Ivanov A, Brock C, Drotar ME, Nixon C, Clark W, Sansom OJ, Anderson KI, King A, Blyth K, Adams PD. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes Dev 2014; 28:2712-25. [PMID: 25512559 PMCID: PMC4265675 DOI: 10.1101/gad.247528.114] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 11/04/2014] [Indexed: 01/06/2023]
Abstract
Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in nonproliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene-induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression.
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Affiliation(s)
- Taranjit Singh Rai
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom; Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, United Kingdom
| | - John J Cole
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - David M Nelson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Dina Dikovskaya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - William J Faller
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Maria Grazia Vizioli
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Rachael N Hewitt
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Orchi Anannya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Tony McBryan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Indrani Manoharan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - John van Tuyn
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Nicholas Morrice
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Nikolay A Pchelintsev
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Andre Ivanov
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Claire Brock
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Mark E Drotar
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Colin Nixon
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - William Clark
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Owen J Sansom
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Kurt I Anderson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Ayala King
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Karen Blyth
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Peter D Adams
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom;
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86
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Shah MA, Denton EL, Arrowsmith CH, Lupien M, Schapira M. A global assessment of cancer genomic alterations in epigenetic mechanisms. Epigenetics Chromatin 2014; 7:29. [PMID: 25484917 PMCID: PMC4258301 DOI: 10.1186/1756-8935-7-29] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/14/2014] [Indexed: 12/22/2022] Open
Abstract
Background The notion that epigenetic mechanisms may be central to cancer initiation and progression is supported by recent next-generation sequencing efforts revealing that genes involved in chromatin-mediated signaling are recurrently mutated in cancer patients. Results Here, we analyze mutational and transcriptional profiles from TCGA and the ICGC across a collection 441 chromatin factors and histones. Chromatin factors essential for rapid replication are frequently overexpressed, and those that maintain genome stability frequently mutated. We identify novel mutation hotspots such as K36M in histone H3.1, and uncover a general trend in which transcriptional profiles and somatic mutations in tumor samples favor increased transcriptionally repressive histone methylation, and defective chromatin remodeling. Conclusions This unbiased approach confirms previously published data, uncovers novel cancer-associated aberrations targeting epigenetic mechanisms, and justifies continued monitoring of chromatin-related alterations as a class, as more cancer types and distinct cancer stages are represented in cancer genomics data repositories. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-7-29) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad A Shah
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada
| | - Emily L Denton
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Courant Institute, New York University, 12th floor, 715 Broadway, New York, 10003 USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, M5G 2M9 ON Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, M5G 2M9 ON Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON Canada
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87
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Taguchi H, Horikoshi N, Arimura Y, Kurumizaka H. A method for evaluating nucleosome stability with a protein-binding fluorescent dye. Methods 2014; 70:119-26. [DOI: 10.1016/j.ymeth.2014.08.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 11/29/2022] Open
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88
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Ishibashi N, Kitakura S, Terakura S, Machida C, Machida Y. Protein encoded by oncogene 6b from Agrobacterium tumefaciens has a reprogramming potential and histone chaperone-like activity. FRONTIERS IN PLANT SCIENCE 2014; 5:572. [PMID: 25389429 PMCID: PMC4211554 DOI: 10.3389/fpls.2014.00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/05/2014] [Indexed: 05/31/2023]
Abstract
Crown gall tumors are formed mainly by actions of a group of genes in the T-DNA that is transferred from Agrobacterium tumefaciens and integrated into the nuclear DNA of host plants. These genes encode enzymes for biosynthesis of auxin and cytokinin in plant cells. Gene 6b in the T-DNA affects tumor morphology and this gene alone is able to induce small tumors on certain plant species. In addition, unorganized calli are induced from leaf disks of tobacco that are incubated on phytohormone-free media; shooty teratomas, and morphologically abnormal plants, which might be due to enhanced competence of cell division and meristematic states, are regenerated from the calli. Thus, the 6b gene appears to stimulate a reprogramming process in plants. To uncover mechanisms behind this process, various approaches including the yeast-two-hybrid system have been exploited and histone H3 was identified as one of the proteins that interact with 6b. It has been also demonstrated that 6b acts as a histone H3 chaperon in vitro and affects the expression of various genes related to cell division competence and the maintenance of meristematic states. We discuss current views on a role of 6b protein in tumorigenesis and reprogramming in plants.
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Affiliation(s)
- Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
| | - Saeko Kitakura
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
- Graduate School of Bioscience and Biotechnology, Chubu UniversityKasugai, Japan
| | - Shinji Terakura
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu UniversityKasugai, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoya, Japan
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89
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Filipescu D, Müller S, Almouzni G. Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control. Annu Rev Cell Dev Biol 2014; 30:615-46. [DOI: 10.1146/annurev-cellbio-100913-013311] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, F-75248 France; , ,
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90
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Abstract
Diffuse high-grade gliomas (HGGs) of childhood are a devastating spectrum of disease with no effective cures. The two-year survival for paediatric HGG ranges from 30%, for tumours arising in the cerebral cortex, to less than 10% for diffuse intrinsic pontine gliomas (DIPGs), which arise in the brainstem. Recent genome-wide studies provided abundant evidence that unique selective pressures drive HGG in children compared to adults, identifying novel oncogenic mutations connecting tumorigenesis and chromatin regulation, as well as developmental signalling pathways. These new genetic findings give insights into disease pathogenesis and the challenges and opportunities for improving patient survival in these mostly incurable childhood brain tumours.
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91
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Jullien J, Miyamoto K, Pasque V, Allen GE, Bradshaw CR, Garrett NJ, Halley-Stott RP, Kimura H, Ohsumi K, Gurdon JB. Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming. Mol Cell 2014; 55:524-36. [PMID: 25066233 PMCID: PMC4156308 DOI: 10.1016/j.molcel.2014.06.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/15/2014] [Accepted: 06/12/2014] [Indexed: 12/31/2022]
Abstract
Nuclear transfer to oocytes is an efficient way to transcriptionally reprogram somatic nuclei, but its mechanisms remain unclear. Here, we identify a sequence of molecular events that leads to rapid transcriptional reprogramming of somatic nuclei after transplantation to Xenopus oocytes. RNA-seq analyses reveal that reprogramming by oocytes results in a selective switch in transcription toward an oocyte rather than pluripotent type, without requiring new protein synthesis. Time-course analyses at the single-nucleus level show that transcriptional reprogramming is induced in most transplanted nuclei in a highly hierarchical manner. We demonstrate that an extensive exchange of somatic- for oocyte-specific factors mediates reprogramming and leads to robust oocyte RNA polymerase II binding and phosphorylation on transplanted chromatin. Moreover, genome-wide binding of oocyte-specific linker histone B4 supports its role in transcriptional reprogramming. Thus, our study reveals the rapid, abundant, and stepwise loading of oocyte-specific factors onto somatic chromatin as important determinants for successful reprogramming. Xenopus oocytes induce an oocyte transcription pattern in mouse nuclei in 2 days Reprogramming requires a switch from somatic to oocyte transcriptional components Unusually high amounts of oocyte-derived RNA polymerase II drive reprogramming The pattern of oocyte linker histone binding to somatic chromatin is revealed
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Affiliation(s)
- Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Kei Miyamoto
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Vincent Pasque
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - George E Allen
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Charles R Bradshaw
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Nigel J Garrett
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Richard P Halley-Stott
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Keita Ohsumi
- Laboratory of Molecular Genetics, Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - John B Gurdon
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Cambridge CB2 1QN, UK.
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92
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Sequeira-Mendes J, Aragüez I, Peiró R, Mendez-Giraldez R, Zhang X, Jacobsen SE, Bastolla U, Gutierrez C. The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States. THE PLANT CELL 2014; 26:2351-2366. [PMID: 24934173 PMCID: PMC4114938 DOI: 10.1105/tpc.114.124578] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/16/2014] [Accepted: 05/27/2014] [Indexed: 05/18/2023]
Abstract
Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.
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Affiliation(s)
- Joana Sequeira-Mendes
- Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Irene Aragüez
- Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Ramón Peiró
- Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Raul Mendez-Giraldez
- Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Xiaoyu Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Steven E Jacobsen
- Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Ugo Bastolla
- Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Crisanto Gutierrez
- Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
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93
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Han SK, Wagner D. Role of chromatin in water stress responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2785-99. [PMID: 24302754 PMCID: PMC4110454 DOI: 10.1093/jxb/ert403] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
As sessile organisms, plants are exposed to environmental stresses throughout their life. They have developed survival strategies such as developmental and morphological adaptations, as well as physiological responses, to protect themselves from adverse environments. In addition, stress sensing triggers large-scale transcriptional reprogramming directed at minimizing the deleterious effect of water stress on plant cells. Here, we review recent findings that reveal a role of chromatin in water stress responses. In addition, we discuss data in support of the idea that chromatin remodelling and modifying enzymes may be direct targets of stress signalling pathways. Modulation of chromatin regulator activity by these signaling pathways may be critical in minimizing potential trade-offs between growth and stress responses. Alterations in the chromatin organization and/or in the activity of chromatin remodelling and modifying enzymes may furthermore contribute to stress memory. Mechanistic insight into these phenomena derived from studies in model plant systems should allow future engineering of broadly drought-tolerant crop plants that do not incur unnecessary losses in yield or growth.
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Affiliation(s)
- Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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94
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Kupershmit I, Khoury-Haddad H, Awwad SW, Guttmann-Raviv N, Ayoub N. KDM4C (GASC1) lysine demethylase is associated with mitotic chromatin and regulates chromosome segregation during mitosis. Nucleic Acids Res 2014; 42:6168-82. [PMID: 24728997 PMCID: PMC4041427 DOI: 10.1093/nar/gku253] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 03/11/2014] [Accepted: 03/15/2014] [Indexed: 12/11/2022] Open
Abstract
Various types of human cancers exhibit amplification or deletion of KDM4A-D members, which selectively demethylate H3K9 and H3K36, thus implicating their activity in promoting carcinogenesis. On this basis, it was hypothesized that dysregulated expression of KDM4A-D family promotes chromosomal instabilities by largely unknown mechanisms. Here, we show that unlike KDM4A-B, KDM4C is associated with chromatin during mitosis. This association is accompanied by a decrease in the mitotic levels of H3K9me3. We also show that the C-terminal region, containing the Tudor domains of KDM4C, is essential for its association with mitotic chromatin. More specifically, we show that R919 residue on the proximal Tudor domain of KDM4C is critical for its association with chromatin during mitosis. Interestingly, we demonstrate that depletion or overexpression of KDM4C, but not KDM4B, leads to over 3-fold increase in the frequency of abnormal mitotic cells showing either misaligned chromosomes at metaphase, anaphase-telophase lagging chromosomes or anaphase-telophase bridges. Furthermore, overexpression of KDM4C demethylase-dead mutant has no detectable effect on mitotic chromosome segregation. Altogether, our findings implicate KDM4C demethylase activity in regulating the fidelity of mitotic chromosome segregation by a yet unknown mechanism.
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Affiliation(s)
- Ilana Kupershmit
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Hanan Khoury-Haddad
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Samah W Awwad
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Noga Guttmann-Raviv
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
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95
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Vossaert L, Meert P, Scheerlinck E, Glibert P, Van Roy N, Heindryckx B, De Sutter P, Dhaenens M, Deforce D. Identification of histone H3 clipping activity in human embryonic stem cells. Stem Cell Res 2014; 13:123-34. [PMID: 24874291 DOI: 10.1016/j.scr.2014.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 01/17/2023] Open
Abstract
Posttranslational histone modifications are essential features in epigenetic regulatory networks. One of these modifications has remained largely understudied: regulated histone proteolysis. In analogy to the histone H3 clipping during early mouse embryonic stem cell differentiation, we report for the first time that also in human embryonic stem cells this phenomenon takes place in the two different analyzed cell lines. Employing complementary techniques, different cleavage sites could be identified, namely A21, R26 and residue 31. The enzyme responsible for this cleavage is found to be a serine protease. The formation of cleaved H3 follows a considerably variable pattern, depending on the timeframe, culture conditions and culture media applied. Contrary to earlier findings on H3 clipping, our results disconnect the link between declining Oct4 expression and H3 cleavage.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Paulien Meert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Ellen Scheerlinck
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Glibert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Department of Medical Genetics, Ghent University, Ghent, Belgium
| | - Björn Heindryckx
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Petra De Sutter
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Maarten Dhaenens
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium.
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96
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Mandemaker IK, Vermeulen W, Marteijn JA. Gearing up chromatin: A role for chromatin remodeling during the transcriptional restart upon DNA damage. Nucleus 2014; 5:203-10. [PMID: 24809693 PMCID: PMC4133215 DOI: 10.4161/nucl.29085] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
During transcription, RNA polymerase may encounter DNA lesions, which causes stalling of transcription. To overcome the RNA polymerase blocking lesions, the transcribed strand is repaired by a dedicated repair mechanism, called transcription coupled nucleotide excision repair (TC-NER). After repair is completed, it is essential that transcription restarts. So far, the regulation and exact molecular mechanism of this transcriptional restart upon genotoxic damage has remained elusive. Recently, three different chromatin remodeling factors, HIRA, FACT, and Dot1L, were identified to stimulate transcription restart after DNA damage. These factors either incorporate new histones or establish specific chromatin marks that will gear up the chromatin to subsequently promote transcription recovery. This adds a new layer to the current model of chromatin remodeling necessary for repair and indicates that this specific form of transcription, i.e., the transcriptional restart upon DNA damage, needs specific chromatin remodeling events.
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Affiliation(s)
- Imke K Mandemaker
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
| | - Wim Vermeulen
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
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97
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Histone variant H3.3 is an essential maternal factor for oocyte reprogramming. Proc Natl Acad Sci U S A 2014; 111:7325-30. [PMID: 24799717 DOI: 10.1073/pnas.1406389111] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mature oocyte cytoplasm can reprogram somatic cell nuclei to the pluripotent state through a series of sequential events including protein exchange between the donor nucleus and ooplasm, chromatin remodeling, and pluripotency gene reactivation. Maternal factors that are responsible for this reprogramming process remain largely unidentified. Here, we demonstrate that knockdown of histone variant H3.3 in mouse oocytes results in compromised reprogramming and down-regulation of key pluripotency genes; and this compromised reprogramming for developmental potentials and transcription of pluripotency genes can be rescued by injecting exogenous H3.3 mRNA, but not H3.2 mRNA, into oocytes in somatic cell nuclear transfer embryos. We show that maternal H3.3, and not H3.3 in the donor nucleus, is essential for successful reprogramming of somatic cell nucleus into the pluripotent state. Furthermore, H3.3 is involved in this reprogramming process by remodeling the donor nuclear chromatin through replacement of donor nucleus-derived H3 with de novo synthesized maternal H3.3 protein. Our study shows that H3.3 is a crucial maternal factor for oocyte reprogramming and provides a practical model to directly dissect the oocyte for its reprogramming capacity.
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98
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Biterge B, Schneider R. Histone variants: key players of chromatin. Cell Tissue Res 2014; 356:457-66. [PMID: 24781148 DOI: 10.1007/s00441-014-1862-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/27/2014] [Indexed: 01/01/2023]
Abstract
Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.
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Affiliation(s)
- Burcu Biterge
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404, Illkirch, France
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99
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Van der Meulen J, Van Roy N, Van Vlierberghe P, Speleman F. The epigenetic landscape of T-cell acute lymphoblastic leukemia. Int J Biochem Cell Biol 2014; 53:547-57. [PMID: 24786297 DOI: 10.1016/j.biocel.2014.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 12/29/2022]
Abstract
The genetic landscape of T-ALL has been very actively explored during the past decades. This leads to an overwhelming body of exciting novel findings providing insight into (1) the genetic heterogeneity of the disease with marked genetic subsets, (2) the mechanisms by which aberrant T-cell development drive leukemogenesis and (3) emerging opportunities for novel therapeutic interventions. Of further interest, recent genome wide sequencing studies identified proteins that actively participate in the regulation of the T-cell epigenome as novel oncogenes and tumor suppressor genes in T-ALL. The identification of these perturbed molecular epigenetic events in the pathogenesis of T-ALL will contribute to the further exploration of novel therapies in this cancer type. As some epigenetic therapies have recently been approved for a number of hematological neoplasms, one could speculate that targeted therapies against epigenetic regulators might offer good prospects for T-ALL treatment in the near future. In this review, we summarize the epigenetic discoveries made in T-ALL hitherto and discuss possible new venues for epigenetic therapeutic intervention in this aggressive subtype of human leukemia. This article is part of a Directed Issue entitled: Rare Cancers.
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Affiliation(s)
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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100
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Abstract
Rheumatic disease is a large spectrum of heterogeneous conditions affecting the loco-motor system including joints, muscles, connective tissues, and soft tissues around the joints and bones. Many rheumatic diseases have an element of autoimmunity including systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Aberrant epigenetic regulation of gene expression is emerging as a major factor within rheumatic disease, and indicates potential new therapeutic avenues of approach to these debilitating conditions. Understanding the precise role of epigenetics in the development and treatment of rheumatic diseases particularly those which have an associated autoimmune element may be important for the long-term management of such conditions.
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