1
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Wernlé K, Thiel CS, Ullrich O. Increased H3K9me3 and F-Actin Reorganization in the Rapid Adaptive Response to Hypergravity in Human T Lymphocytes. Int J Mol Sci 2023; 24:17232. [PMID: 38139061 PMCID: PMC10743231 DOI: 10.3390/ijms242417232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Our study explored the impact of hypergravity on human T cells, which experience additional acceleration forces beyond Earth's gravity due to various factors, such as pulsatile blood flow, and technology, such as high-performance aircraft flights or spaceflights. We investigated the histone modifications Histone 3 lysine 4 and 9 trimethylation (H3K4me3 and H3K9me3, respectively), as well as the structural and cytoskeletal organization of Jurkat T cells in response to hypergravity. Histone modifications play a crucial role in gene regulation, chromatin organization and DNA repair. In response to hypergravity, we found only minimal changes of H3K4me3 and a rapid increase in H3K9me3, which was sustained for up to 15 min and then returned to control levels after 1 h. Furthermore, rapid changes in F-actin fluorescence were observed within seconds of hypergravity exposure, indicating filament depolymerization and cytoskeletal restructuring, which subsequently recovered after 1 h of hypergravity. Our study demonstrated the rapid, dynamic and adaptive cellular response to hypergravity, particularly in terms of histone modifications and cytoskeletal changes. These responses are likely necessary for maintaining genome stability and structural integrity under hypergravity conditions as they are constantly occurring in the human body during blood cell circulation.
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Affiliation(s)
- Kendra Wernlé
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland;
- Faculty of Medical Sciences, Private University of the Principality of Liechtenstein (UFL), Dorfstrasse 24, 9495 Triesen, Liechtenstein
| | - Cora S. Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland;
- Institute of Machine Design, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center, 505 Odyssey Way, Exploration Park, Merritt Island, FL 32953, USA
- UZH Space Hub, Air Force Center, Air Base Dübendorf, Überlandstrasse 270, 8600 Dubendorf, Switzerland
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland;
- Institute of Machine Design, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center, 505 Odyssey Way, Exploration Park, Merritt Island, FL 32953, USA
- UZH Space Hub, Air Force Center, Air Base Dübendorf, Überlandstrasse 270, 8600 Dubendorf, Switzerland
- Department of Industrial Engineering, Ernst-Abbe-Hochschule (EAH) Jena, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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2
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González J, Bosch-Presegué L, Marazuela-Duque A, Guitart-Solanes A, Espinosa-Alcantud M, Fernandez AF, Brown JP, Ausió J, Vazquez BN, Singh PB, Fraga MF, Vaquero A. A complex interplay between H2A.Z and HP1 isoforms regulates pericentric heterochromatin. Front Cell Dev Biol 2023; 11:1293122. [PMID: 38020886 PMCID: PMC10665487 DOI: 10.3389/fcell.2023.1293122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Pericentric heterochromatin (PCH) plays an essential role in the maintenance of genome integrity and alterations in PCH have been linked to cancer and aging. HP1 α, β, and γ, are hallmarks of constitutive heterochromatin that are thought to promote PCH structure through binding to heterochromatin-specific histone modifications and interaction with a wide range of factors. Among the less understood components of PCH is the histone H2A variant H2A.Z, whose role in the organization and maintenance of PCH is poorly defined. Here we show that there is a complex interplay between H2A.Z and HP1 isoforms in PCH. While the loss of HP1α results in the accumulation of H2A.Z.1 in PCH, which is associated with a significant decrease in its mobile fraction, H2A.Z.1 binds preferentially to HP1β in these regions. Of note, H2A.Z.1 downregulation results in increased heterochromatinization and instability of PCH, reflected by accumulation of the major epigenetic hallmarks of heterochromatin in these regions and increased frequency of chromosome aberrations related to centromeric/pericentromeric defects. Our studies support a role for H2A.Z in genome stability and unveil a key role of H2A.Z in the regulation of heterochromatin-specific epigenetic modifications through a complex interplay with the HP1 isoforms.
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Affiliation(s)
- Jessica González
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Laia Bosch-Presegué
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
- Tissue Repair and Regeneration Laboratory (TR2Lab), Institut de Recerca I Innovació en Ciències de La Vida i de La Salut a La Catalunya Central (IrisCC), Barcelona, Spain
| | - Anna Marazuela-Duque
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Anna Guitart-Solanes
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - María Espinosa-Alcantud
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Agustín F. Fernandez
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), El Entrego, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), Madrid, Spain
| | - Jeremy P. Brown
- Department of Immunology and Inflammation, Imperial College London, Commonwealth Building, The Hammersmith Hospital, London, United Kingdom
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Berta N. Vazquez
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
- Cytology and Histology Unit. Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Prim B. Singh
- Nazarbayev University School of Medicine, Astana, Kazakhstan
| | - Mario F. Fraga
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), El Entrego, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain
- Spanish Biomedical Research Network in Rare Diseases (CIBERER), Madrid, Spain
| | - Alejandro Vaquero
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
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3
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Desaulniers D, Cummings-Lorbetskie C, Leingartner K, Meier MJ, Pickles JC, Yauk CL. DNA methylation changes from primary cultures through senescence-bypass in Syrian hamster fetal cells initially exposed to benzo[a]pyrene. Toxicology 2023; 487:153451. [PMID: 36754249 DOI: 10.1016/j.tox.2023.153451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Current chemical testing strategies are limited in their ability to detect non-genotoxic carcinogens (NGTxC). Epigenetic anomalies develop during carcinogenesis regardless of whether the molecular initiating event is associated with genotoxic (GTxC) or NGTxC events; therefore, epigenetic markers may be harnessed to develop new approach methodologies that improve the detection of both types of carcinogens. This study used Syrian hamster fetal cells to establish the chronology of carcinogen-induced DNA methylation changes from primary cells until senescence-bypass as an essential carcinogenic step. Cells exposed to solvent control for 7 days were compared to naïve primary cultures, to cells exposed for 7 days to benzo[a]pyrene, and to cells at the subsequent transformation stages: normal colonies, morphologically transformed colonies, senescence, senescence-bypass, and sustained proliferation in vitro. DNA methylation changes identified by reduced representation bisulphite sequencing were minimal at day-7. Profound DNA methylation changes arose during cellular senescence and some of these early differentially methylated regions (DMRs) were preserved through the final sustained proliferation stage. A set of these DMRs (e.g., Pou4f1, Aifm3, B3galnt2, Bhlhe22, Gja8, Klf17, and L1l) were validated by pyrosequencing and their reproducibility was confirmed across multiple clones obtained from a different laboratory. These DNA methylation changes could serve as biomarkers to enhance objectivity and mechanistic understanding of cell transformation and could be used to predict senescence-bypass and chemical carcinogenicity.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Karen Leingartner
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
| | | | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
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4
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Ballmer D, Tardat M, Ortiz R, Graff-Meyer A, Ozonov E, Genoud C, Peters A, Fanourgakis G. HP1 proteins regulate nucleolar structure and function by secluding pericentromeric constitutive heterochromatin. Nucleic Acids Res 2022; 51:117-143. [PMID: 36533441 PMCID: PMC9841413 DOI: 10.1093/nar/gkac1159] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Nucleoli are nuclear compartments regulating ribosome biogenesis and cell growth. In embryonic stem cells (ESCs), nucleoli containing transcriptionally active ribosomal genes are spatially separated from pericentromeric satellite repeat sequences packaged in largely repressed constitutive heterochromatin (PCH). To date, mechanisms underlying such nuclear partitioning and the physiological relevance thereof are unknown. Here we show that repressive chromatin at PCH ensures structural integrity and function of nucleoli during cell cycle progression. Loss of heterochromatin proteins HP1α and HP1β causes deformation of PCH, with reduced H3K9 trimethylation (H3K9me3) and HP1γ levels, absence of H4K20me3 and upregulated major satellites expression. Spatially, derepressed PCH aberrantly associates with nucleoli accumulating severe morphological defects during S/G2 cell cycle progression. Hp1α/β deficiency reduces cell proliferation, ribosomal RNA biosynthesis and mobility of Nucleophosmin, a major nucleolar component. Nucleolar integrity and function require HP1α/β proteins to be recruited to H3K9me3-marked PCH and their ability to dimerize. Correspondingly, ESCs deficient for both Suv39h1/2 H3K9 HMTs display similar nucleolar defects. In contrast, Suv4-20h1/2 mutant ESCs lacking H4K20me3 at PCH do not. Suv39h1/2 and Hp1α/β deficiency-induced nucleolar defects are reminiscent of those defining human ribosomopathy disorders. Our results reveal a novel role for SUV39H/HP1-marked repressive constitutive heterochromatin in regulating integrity, function and physiology of nucleoli.
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Affiliation(s)
- Daniel Ballmer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland,Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Mathieu Tardat
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Raphael Ortiz
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alexandra Graff-Meyer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Christel Genoud
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | | | - Grigorios Fanourgakis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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5
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Sommer JU, Merlitz H, Schiessel H. Polymer-Assisted Condensation: A Mechanism for Hetero-Chromatin Formation and Epigenetic Memory. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, 01069 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
| | - Holger Merlitz
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, 01069 Dresden, Germany
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, Zellescher Weg 17, 01062 Dresden, Germany
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6
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Maeda R, Tachibana M. HP1 maintains protein stability of H3K9 methyltransferases and demethylases. EMBO Rep 2022; 23:e53581. [PMID: 35166421 PMCID: PMC8982598 DOI: 10.15252/embr.202153581] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/09/2022] Open
Abstract
Di- or tri-methylated H3K9 (H3K9me2/3) is an epigenetic mark of heterochromatin. Heterochromatin protein 1 (HP1) specifically recognizes H3K9me2/3, contributing to transcriptional suppression and spread of H3K9me2/3. Here, we demonstrate another role of HP1 in heterochromatin organization: regulation of protein stability of H3K9 methyltransferases (H3K9 MTs) and demethylases (H3K9 DMs). We show that HP1 interaction-defective mutants of H3K9 MTs, Suv39h1 and Setdb1, undergo protein degradation. We further establish mouse embryonic stem cell lines lacking all three HP1 paralogs. In the HP1-deficient cells, Suv39h1, Suv39h2, Setdb1, and G9a/GLP complex decrease at the protein level, and the enzymes are released from chromatin. HP1 mutants that cannot recognize H3K9me2/3 or form dimers cannot stabilize these enzymes, indicating that the tethering of H3K9 MTs to chromatin is critical for their protein stability. We show that HP1 also stabilizes H3K9 DMs, Jmjd1a and Jmjd1b. Our study indicates that mammalian HP1 forms a heterochromatin hub that governs protein stability of H3K9 MTs and H3K9 DMs.
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Affiliation(s)
- Ryo Maeda
- Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan,Institute of Advanced Medical SciencesTokushima UniversityTokushimaJapan
| | - Makoto Tachibana
- Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan,Institute of Advanced Medical SciencesTokushima UniversityTokushimaJapan
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7
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:69-110. [DOI: 10.1007/978-3-031-11454-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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9
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Qin W, Stengl A, Ugur E, Leidescher S, Ryan J, Cardoso MC, Leonhardt H. HP1β carries an acidic linker domain and requires H3K9me3 for phase separation. Nucleus 2021; 12:44-57. [PMID: 33660589 PMCID: PMC7939559 DOI: 10.1080/19491034.2021.1889858] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) mediated formation of membraneless organelles has been proposed to coordinate biological processes in space and time. Previously, the formation of phase-separated droplets was described as a unique property of HP1α. Here, we demonstrate that the positive net charge of the intrinsically disordered hinge region (IDR-H) of HP1 proteins is critical for phase separation and that the exchange of four acidic amino acids is sufficient to confer LLPS properties to HP1β. Surprisingly, the addition of mono-nucleosomes promoted H3K9me3-dependent LLPS of HP1β which could be specifically disrupted with methylated but not acetylated H3K9 peptides. HP1β mutants defective in H3K9me3 binding were less efficient in phase separationin vitro and failed to accumulate at heterochromatin in vivo. We propose that multivalent interactions of HP1β with H3K9me3-modified nucleosomes via its chromodomain and dimerization via its chromoshadow domain enable phase separation and contribute to the formation of heterochromatin compartments in vivo.
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Affiliation(s)
- Weihua Qin
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Stengl
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Susanne Leidescher
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Joel Ryan
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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10
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Klutstein M. Cause and effect in epigenetics - where lies the truth, and how can experiments reveal it?: Epigenetic self-reinforcing loops obscure causation in cancer and aging. Bioessays 2020; 43:e2000262. [PMID: 33236359 DOI: 10.1002/bies.202000262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic changes are implicated in aging and cancer. Sometimes, it is clear whether the causing agent of the condition is a genetic factor or epigenetic. In other cases, the causative factor is unclear, and could be either genetic or epigenetic. Is there a general role for epigenetic changes in cancer and aging? Here, I present the paradigm of causative roles executed by epigenetic changes. I discuss cases with clear roles of the epigenome in cancer and aging, and other cases showing involvement of other factors. I also present the possibility that sometimes causality is difficult to assign because of the presence of self-reinforcing loops in epigenetic regulation. Such loops hinder the identification of the causative factor. I provide an experimental framework by which the role of the epigenome can be examined in a better setting and where the presence of such loops could be investigated in more detail.
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Affiliation(s)
- Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
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11
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Paluvai H, Di Giorgio E, Brancolini C. The Histone Code of Senescence. Cells 2020; 9:cells9020466. [PMID: 32085582 PMCID: PMC7072776 DOI: 10.3390/cells9020466] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Senescence is the end point of a complex cellular response that proceeds through a set of highly regulated steps. Initially, the permanent cell-cycle arrest that characterizes senescence is a pro-survival response to irreparable DNA damage. The maintenance of this prolonged condition requires the adaptation of the cells to an unfavorable, demanding and stressful microenvironment. This adaptation is orchestrated through a deep epigenetic resetting. A first wave of epigenetic changes builds a dam on irreparable DNA damage and sustains the pro-survival response and the cell-cycle arrest. Later on, a second wave of epigenetic modifications allows the genomic reorganization to sustain the transcription of pro-inflammatory genes. The balanced epigenetic dynamism of senescent cells influences physiological processes, such as differentiation, embryogenesis and aging, while its alteration leads to cancer, neurodegeneration and premature aging. Here we provide an overview of the most relevant histone modifications, which characterize senescence, aging and the activation of a prolonged DNA damage response.
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12
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Wang J, Yang Z, Wu NP, Yang J. Increased expression of BCL11B and its recruited chromatin remodeling factors during highly active antiretroviral therapy synergistically represses the transcription of human immunodeficiency virus type 1 and is associated with residual immune activation. Arch Virol 2019; 165:321-330. [PMID: 31828511 DOI: 10.1007/s00705-019-04475-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/19/2019] [Indexed: 12/13/2022]
Abstract
Persistence of human immunodeficiency virus 1 (HIV-1) latency and residual immune activation remain major barriers to treatment in patients receiving highly active antiretroviral therapy (HAART). In the present study, we investigated the molecular mechanisms of persistent HIV infection and residual immune activation in HAART-treated patients. We showed that the expression level of B-cell CLL/lymphoma 11B (BCL11B) was significantly increased in CD4+T cells from HIV-infected patients undergoing HAART, and this was accompanied by increased expression of BCL11B-associated chromatin modifiers and inflammatory factors in comparison to healthy controls and untreated patients with HIV. In vitro assays showed that BCL11B significantly inhibited HIV-1 long terminal repeat (LTR)-mediated transcription. Knockdown of BCL11B resulted in the activation of HIV latent cells, and dissociation of BCL11B and its related chromatin remodeling factors from the HIV LTR. Our findings suggested that increased expression of BCL11B and its related chromatin modifiers contribute to HIV-1 transcriptional silencing, and alteration of BCL11B levels might lead to abnormal transcription and inflammation.
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Affiliation(s)
- Juan Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Zongxing Yang
- The Second Department of Infectious Disease, Xixi Hospital of Hangzhou, Hangzhou, 310023, Zhejiang, People's Republic of China
| | - Nan-Ping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, People's Republic of China.
| | - Jin Yang
- Center for Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310015, Zhejiang, People's Republic of China.
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13
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Romero-Bueno R, de la Cruz Ruiz P, Artal-Sanz M, Askjaer P, Dobrzynska A. Nuclear Organization in Stress and Aging. Cells 2019; 8:cells8070664. [PMID: 31266244 PMCID: PMC6678840 DOI: 10.3390/cells8070664] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/23/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic nucleus controls most cellular processes. It is isolated from the cytoplasm by the nuclear envelope, which plays a prominent role in the structural organization of the cell, including nucleocytoplasmic communication, chromatin positioning, and gene expression. Alterations in nuclear composition and function are eminently pronounced upon stress and during premature and physiological aging. These alterations are often accompanied by epigenetic changes in histone modifications. We review, here, the role of nuclear envelope proteins and histone modifiers in the 3-dimensional organization of the genome and the implications for gene expression. In particular, we focus on the nuclear lamins and the chromatin-associated protein BAF, which are linked to Hutchinson–Gilford and Nestor–Guillermo progeria syndromes, respectively. We also discuss alterations in nuclear organization and the epigenetic landscapes during normal aging and various stress conditions, ranging from yeast to humans.
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Affiliation(s)
- Raquel Romero-Bueno
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
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14
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Gadecka A, Bielak-Zmijewska A. Slowing Down Ageing: The Role of Nutrients and Microbiota in Modulation of the Epigenome. Nutrients 2019; 11:nu11061251. [PMID: 31159371 PMCID: PMC6628342 DOI: 10.3390/nu11061251] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022] Open
Abstract
The human population is getting ageing. Both ageing and age-related diseases are correlated with an increased number of senescent cells in the organism. Senescent cells do not divide but are metabolically active and influence their environment by secreting many proteins due to a phenomenon known as senescence associated secretory phenotype (SASP). Senescent cells differ from young cells by several features. They possess more damaged DNA, more impaired mitochondria and an increased level of free radicals that cause the oxidation of macromolecules. However, not only biochemical and structural changes are related to senescence. Senescent cells have an altered chromatin structure, and in consequence, altered gene expression. With age, the level of heterochromatin decreases, and less condensed chromatin is more prone to DNA damage. On the one hand, some gene promoters are easily available for the transcriptional machinery; on the other hand, some genes are more protected (locally increased level of heterochromatin). The structure of chromatin is precisely regulated by the epigenetic modification of DNA and posttranslational modification of histones. The methylation of DNA inhibits transcription, histone methylation mostly leads to a more condensed chromatin structure (with some exceptions) and acetylation plays an opposing role. The modification of both DNA and histones is regulated by factors present in the diet. This means that compounds contained in daily food can alter gene expression and protect cells from senescence, and therefore protect the organism from ageing. An opinion prevailed for some time that compounds from the diet do not act through direct regulation of the processes in the organism but through modification of the physiology of the microbiome. In this review we try to explain the role of some food compounds, which by acting on the epigenetic level might protect the organism from age-related diseases and slow down ageing. We also try to shed some light on the role of microbiome in this process.
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Affiliation(s)
- Agnieszka Gadecka
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Anna Bielak-Zmijewska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
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15
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E3 ubiquitin ligase HECW2 mediates the proteasomal degradation of HP1 isoforms. Biochem Biophys Res Commun 2018; 503:2478-2484. [DOI: 10.1016/j.bbrc.2018.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/02/2018] [Indexed: 12/12/2022]
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16
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Mammalian HP1 Isoforms Have Specific Roles in Heterochromatin Structure and Organization. Cell Rep 2018; 21:2048-2057. [PMID: 29166597 DOI: 10.1016/j.celrep.2017.10.092] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 09/15/2017] [Accepted: 10/24/2017] [Indexed: 11/24/2022] Open
Abstract
HP1 is a structural component of heterochromatin. Mammalian HP1 isoforms HP1α, HP1β, and HP1γ play different roles in genome stability, but their precise role in heterochromatin structure is unclear. Analysis of Hp1α-/-, Hp1β-/-, and Hp1γ-/- MEFs show that HP1 proteins have both redundant and unique functions within pericentric heterochromatin (PCH) and also act globally throughout the genome. HP1α confines H4K20me3 and H3K27me3 to regions within PCH, while its absence results in a global hyper-compaction of chromatin associated with a specific pattern of mitotic defects. In contrast, HP1β is functionally associated with Suv4-20h2 and H4K20me3, and its loss induces global chromatin decompaction and an abnormal enrichment of CTCF in PCH and other genomic regions. Our work provides insight into the roles of HP1 proteins in heterochromatin structure and genome stability.
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17
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Oyama K, El-Nachef D, Fang C, Kajimoto H, Brown JP, Singh PB, MacLellan WR. Deletion of HP1γ in cardiac myocytes affects H4K20me3 levels but does not impact cardiac growth. Epigenetics Chromatin 2018; 11:18. [PMID: 29665845 PMCID: PMC5905015 DOI: 10.1186/s13072-018-0187-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/01/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Heterochromatin, which is formed when tri-methyl lysine 9 of histone H3 (H3K9me3) is bound by heterochromatin 1 proteins (HP1s), plays an important role in differentiation and senescence by silencing cell cycle genes. Cardiac myocytes (CMs) accumulate heterochromatin during differentiation and demethylation of H3K9me3 inhibits cell cycle gene silencing and cell cycle exit in CMs; however, it is unclear if this process is mediated by HP1s. In this study, we created a conditional CM-specific HP1 gamma (HP1γ) knockout (KO) mouse model and tested whether HP1γ is required for cell cycle gene silencing and cardiac growth. RESULTS HP1γ KO mice were generated by crossing HP1γ floxed mice (fl) with mice expressing Cre recombinase driven by the Nkx2.5 (cardiac progenitor gene) promoter (Cre). We confirmed that deletion of critical exons of HP1γ led to undetectable levels of HP1γ protein in HP1γ KO (Cre;fl/fl) CMs. Analysis of cardiac size and function by echo revealed no significant differences between HP1γ KO and control (WT, Cre, fl/fl) mice. No significant difference in expression of cell cycle genes or cardiac-specific genes was observed. Global transcriptome analysis demonstrated a very moderate effect of HP1γ deletion on global gene expression, with only 51 genes differentially expressed in HP1γ KO CMs. We found that HP1β protein, but not HP1α, was significantly upregulated and that subnuclear localization of HP1β to perinuclear heterochromatin was increased in HP1γ KO CMs. Although HP1γ KO had no effect on H3K9me3 levels, we found a significant reduction in another major heterochromatin mark, tri-methylated lysine 20 of histone H4 (H4K20me3). CONCLUSIONS These data indicate that HP1γ is dispensable for cell cycle exit and normal cardiac growth but has a significant role in maintaining H4K20me3 and regulating a limited number of genes in CMs.
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Affiliation(s)
- Kyohei Oyama
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, 1959 NE Pacific St, Box 356422, Seattle, WA, 98195-6422, USA
| | - Danny El-Nachef
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, 1959 NE Pacific St, Box 356422, Seattle, WA, 98195-6422, USA
| | - Chen Fang
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, 1959 NE Pacific St, Box 356422, Seattle, WA, 98195-6422, USA
| | - Hidemi Kajimoto
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, 1959 NE Pacific St, Box 356422, Seattle, WA, 98195-6422, USA
| | - Jeremy P Brown
- Fächerverbund Anatomie, Institut für Zell-und Neurobiologie, Charite-Universitätsmedizin, 10117, Berlin, Germany
| | - Prim B Singh
- Fächerverbund Anatomie, Institut für Zell-und Neurobiologie, Charite-Universitätsmedizin, 10117, Berlin, Germany.,Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, Kazakhstan, 010000.,Department of Natural Sciences, Laboratory of epigenetics, Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - W Robb MacLellan
- Division of Cardiology, Department of Medicine, Center for Cardiovascular Biology and Institute for Stem Cell and Regenerative Medicine, University of Washington, 1959 NE Pacific St, Box 356422, Seattle, WA, 98195-6422, USA.
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18
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Larson AG, Narlikar GJ. The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation. Biochemistry 2018; 57:2540-2548. [DOI: 10.1021/acs.biochem.8b00401] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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19
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Matsuura T, Miyazaki S, Miyazaki T, Tashiro F, Miyazaki JI. Zfp296 negatively regulates H3K9 methylation in embryonic development as a component of heterochromatin. Sci Rep 2017; 7:12462. [PMID: 28963472 PMCID: PMC5622089 DOI: 10.1038/s41598-017-12772-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022] Open
Abstract
The Cys2/His2-type zinc finger protein Zfp296 has been implicated in stem cell pluripotency and tumor pathogenesis. However, its mechanisms remain elusive. Here, we demonstrated that a Zfp296 deficiency in mice impairs germ-cell development and embryonic growth. Zfp296 was intracellularly localized to heterochromatin in embryos. A GST-Zfp296 pull-down experiment using ES cell nuclear extract followed by LC-MS/MS showed that Zfp296 interacts with component proteins of heterochromatin (such as HP1, Dnmt1, Dnmt3b, and ATRX) and the NuRD complex. We focused on H3K9 methylation as a hallmark of heterochromatin, and found that Zfp296 overexpression in cultured cells reduces the Suv39h1-mediated H3K9 methylation. Consistent with this finding, in Zfp296 -/- mouse embryos, we observed a global increase in H3K9 methylation in a developmental stage-dependent manner, and showed, by ChIP-qPCR, that the H3K9me3 levels at major satellite repeats were elevated in Zfp296 -/- embryos. Our results demonstrate that Zfp296 is a component of heterochromatin that affects embryonic development by negatively regulating H3K9 methylation.
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Affiliation(s)
- Takumi Matsuura
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Satsuki Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Tatsushi Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Fumi Tashiro
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Jun-Ichi Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan.
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