1
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Ding Z, Peng L, Zeng J, Yuan K, Tang Y, Yi Q. Functions of HP1 in preventing chromosomal instability. Cell Biochem Funct 2024; 42:e4017. [PMID: 38603595 DOI: 10.1002/cbf.4017] [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: 12/14/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Chromosomal instability (CIN), caused by errors in the segregation of chromosomes during mitosis, is a hallmark of many types of cancer. The fidelity of chromosome segregation is governed by a sophisticated cellular signaling network, one crucial orchestrator of which is Heterochromatin protein 1 (HP1). HP1 dynamically localizes to distinct sites at various stages of mitosis, where it regulates key mitotic events ranging from chromosome-microtubule attachment to sister chromatid cohesion to cytokinesis. Our evolving comprehension of HP1's multifaceted role has positioned it as a central protein in the orchestration of mitotic processes.
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Affiliation(s)
- Zexian Ding
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Lei Peng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Jinghua Zeng
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Kejia Yuan
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Yan Tang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Qi Yi
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, Hunan, China
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2
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Dong L, Liao H, Zhao L, Wang J, Wang C, Wang B, Sun Y, Xu L, Xia Y, Ling S, Lou X, Qin J. A functional crosstalk between the H3K9 methylation writers and their reader HP1 in safeguarding embryonic stem cell identity. Stem Cell Reports 2023; 18:1775-1792. [PMID: 37703822 PMCID: PMC10545489 DOI: 10.1016/j.stemcr.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Histone H3 lysine 9 (H3K9) methylation, as a hallmark of heterochromatin, has a central role in cell lineage and fate determination. Although evidence of a cooperation between H3K9 methylation writers and their readers has started to emerge, their actual interplay remains elusive. Here, we show that loss of H3K9 methylation readers, the Hp1 family, causes reduced expression of H3K9 methyltransferases, and that this subsequently leads to the exit of embryonic stem cells (ESCs) from pluripotency and a reciprocal gain of lineage-specific characteristics. Importantly, the phenotypes of Hp1-null ESCs can be rescued by ectopic expression of Setdb1, Nanog, and Oct4. Furthermore, Setdb1 ablation results in loss of ESC identity, which is accompanied by a reduction in the expression of Hp1 genes. Together, our data support a model in which the safeguarding of ESC identity involves the cooperation between the H3K9 methylation writers and their readers.
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Affiliation(s)
- Lixia Dong
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Huaqi Liao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Linchun Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Jingnan Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Congcong Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Bowen Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Yanqi Sun
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Lijun Xu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Yin Xia
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shizhang Ling
- The Translational Research Institute for Neurological Disorders, Department of Neurosurgery, The First Affiliated Hospital (Yijishan Hospital) of Wannan Medical College, Wannan Medical College, Wuhu, China.
| | - Xin Lou
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou 311100, China.
| | - Jinzhong Qin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China.
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3
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Kuroda Y, Iwata-Otsubo A, Dias KR, Temple SEL, Nagao K, De Hayr L, Zhu Y, Isobe SY, Nishibuchi G, Fiordaliso SK, Fujita Y, Rippert AL, Baker SW, Leung ML, Koboldt DC, Harman A, Keena BA, Kazama I, Subramanian GM, Manickam K, Schmalz B, Latsko M, Zackai EH, Edwards M, Evans CA, Dulik MC, Buckley MF, Yamashita T, O'Brien WT, Harvey RJ, Obuse C, Roscioli T, Izumi K. Dominant-negative variants in CBX1 cause a neurodevelopmental disorder. Genet Med 2023; 25:100861. [PMID: 37087635 DOI: 10.1016/j.gim.2023.100861] [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: 01/17/2023] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023] Open
Abstract
PURPOSE This study aimed to establish variants in CBX1, encoding heterochromatin protein 1β (HP1β), as a cause of a novel syndromic neurodevelopmental disorder. METHODS Patients with CBX1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. To investigate the pathogenicity of identified variants, we performed in vitro cellular assays and neurobehavioral and cytological analyses of neuronal cells obtained from newly generated Cbx1 mutant mouse lines. RESULTS In 3 unrelated individuals with developmental delay, hypotonia, and autistic features, we identified heterozygous de novo variants in CBX1. The identified variants were in the chromodomain, the functional domain of HP1β, which mediates interactions with chromatin. Cbx1 chromodomain mutant mice displayed increased latency-to-peak response, suggesting the possibility of synaptic delay or myelination deficits. Cytological and chromatin immunoprecipitation experiments confirmed the reduction of mutant HP1β binding to heterochromatin, whereas HP1β interactome analysis demonstrated that the majority of HP1β-interacting proteins remained unchanged between the wild-type and mutant HP1β. CONCLUSION These collective findings confirm the role of CBX1 in developmental disabilities through the disruption of HP1β chromatin binding during neurocognitive development. Because HP1β forms homodimers and heterodimers, mutant HP1β likely sequesters wild-type HP1β and other HP1 proteins, exerting dominant-negative effects.
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Affiliation(s)
- Yukiko Kuroda
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Aiko Iwata-Otsubo
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kerith-Rae Dias
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Suzanna E L Temple
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Lachlan De Hayr
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, Australia; Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Ying Zhu
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Shin-Ya Isobe
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Gohei Nishibuchi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Sarah K Fiordaliso
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Samuel W Baker
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Department of Pathology, The Ohio State University College of Medicine, Columbus, OH
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Adele Harman
- Transgenic core, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Beth A Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Izumi Kazama
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Kandamurugu Manickam
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Betsy Schmalz
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Maeson Latsko
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Matt Edwards
- Hunter Genetics, Newcastle, NSW, Australia; University of Western Sydney School of Medicine, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Matthew C Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Michael F Buckley
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - W Timothy O'Brien
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Robert J Harvey
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, Australia; Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Tony Roscioli
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, PA; Laboratory of Rare Disease Research, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan; Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX.
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4
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Cermakova K, Hodges HC. Interaction modules that impart specificity to disordered protein. Trends Biochem Sci 2023; 48:477-490. [PMID: 36754681 PMCID: PMC10106370 DOI: 10.1016/j.tibs.2023.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/09/2023]
Abstract
Intrinsically disordered regions (IDRs) are especially enriched among proteins that regulate chromatin and transcription. As a result, mechanisms that influence specificity of IDR-driven interactions have emerged as exciting unresolved issues for understanding gene regulation. We review the molecular elements frequently found within IDRs that confer regulatory specificity. In particular, we summarize the differing roles of disordered low-complexity regions (LCRs) and short linear motifs (SLiMs) towards selective nuclear regulation. Examination of IDR-driven interactions highlights SLiMs as organizers of selectivity, with widespread roles in gene regulation and integration of cellular signals. Analysis of recurrent interactions between SLiMs and folded domains suggests diverse avenues for SLiMs to influence phase-separated condensates and highlights opportunities to manipulate these interactions for control of biological activity.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - H Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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5
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Singh PB, Newman AG. HP1-Driven Micro-Phase Separation of Heterochromatin-Like Domains/Complexes. Epigenet Insights 2022; 15:25168657221109766. [PMID: 35813402 PMCID: PMC9260563 DOI: 10.1177/25168657221109766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Prim B Singh
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan
| | - Andrew G Newman
- Institute of Cell and Neurobiology, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, 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: 17] [Impact Index Per Article: 8.5] [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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Abstract
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription, RNA processing, DNA replication, and repair accumulate in self-organizing membraneless chromatin subcompartments. These structures contribute to efficiently conduct chromatin-mediated reactions and to establish specific cellular programs. However, the underlying mechanisms for their formation are only partly understood. Recent studies invoke liquid-liquid phase separation (LLPS) of proteins and RNAs in the establishment of chromatin activity patterns. At the same time, the folding of chromatin in the nucleus can drive genome partitioning into spatially distinct domains. Here, the interplay between chromatin organization, chromatin binding, and LLPS is discussed by comparing and contrasting three prototypical chromatin subcompartments: the nucleolus, clusters of active RNA polymerase II, and pericentric heterochromatin domains. It is discussed how the different ways of chromatin compartmentalization are linked to transcription regulation, the targeting of soluble factors to certain parts of the genome, and to disease-causing genetic aberrations.
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Affiliation(s)
- Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany
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8
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Kleene R, Loers G, Castillo G, Schachner M. Cell adhesion molecule L1 interacts with the chromo shadow domain of heterochromatin protein 1 isoforms α, β, and ɣ via its intracellular domain. FASEB J 2021; 36:e22074. [PMID: 34859928 DOI: 10.1096/fj.202100816r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/01/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022]
Abstract
Cell adhesion molecule L1 regulates multiple cell functions and L1 deficiency is linked to several neural diseases. Proteolytic processing generates functionally decisive L1 fragments, which are imported into the nucleus. By computational analysis, we found at L1's C-terminal end the chromo shadow domain-binding motif PxVxL, which directs the binding of nuclear proteins to the heterochromatin protein 1 (HP1) isoforms α, β, and ɣ. By enzyme-linked immunosorbent assay, we show that the intracellular L1 domain binds to all HP1 isoforms. These interactions involve the HP1 chromo shadow domain and are mediated via the sequence 1158 KDET1161 in the intracellular domain of murine L1, but not by L1's C-terminal PxVxL motif. Immunoprecipitation using nuclear extracts from the brain and from cultured cerebellar and cortical neurons indicates that HP1 isoforms interact with a yet unknown nuclear L1 fragment of approximately 55 kDa (L1-55), which carries ubiquitin residues. Proximity ligation indicates a close association between L1-55 and the HP1 isoforms in neuronal nuclei. This association is reduced after the treatment of neurons with inhibitors of metalloproteases, β-site of amyloid precursor protein cleaving enzyme (BACE1), or ɣ-secretase, suggesting that cleavage of full-length L1 by these proteases generates L1-55. Reduction of HP1α, -β, or -ɣ expression by siRNA decreases L1-dependent neurite outgrowth from cultured cortical neurons and decreases the L1-dependent migration of L1-transfected HEK293 cells in a scratch assay. These findings indicate that the interaction of the novel fragment L1-55 with HP1 isoforms in nuclei affects L1-dependent functions, such as neurite outgrowth and neuronal migration.
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Affiliation(s)
- Ralf Kleene
- Research Group Biosynthesis of Neural Structures, Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Loers
- Research Group Biosynthesis of Neural Structures, Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gaston Castillo
- Research Group Biosynthesis of Neural Structures, Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Department of Cell Biology and Neuroscience, Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, New Jersey, USA
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9
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Li M, Larsen PA. Primate-specific retrotransposons and the evolution of circadian networks in the human brain. Neurosci Biobehav Rev 2021; 131:988-1004. [PMID: 34592258 DOI: 10.1016/j.neubiorev.2021.09.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/03/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
The circadian rhythm of the human brain is attuned to sleep-wake cycles that entail global alterations in neuronal excitability. This periodicity involves a highly coordinated regulation of gene expression. A growing number of studies are documenting a fascinating connection between primate-specific retrotransposons (Alu elements) and key epigenetic regulatory processes in the primate brain. Collectively, these studies indicate that Alu elements embedded in the human neuronal genome mediate post-transcriptional processes that unite human-specific neuroepigenetic landscapes and circadian rhythm. Here, we review evidence linking Alu retrotransposon-mediated posttranscriptional pathways to circadian gene expression. We hypothesize that Alu retrotransposons participate in the organization of circadian brain function through multidimensional neuroepigenetic pathways. We anticipate that these pathways are closely tied to the evolution of human cognition and their perturbation contributes to the manifestation of human-specific neurological diseases. Finally, we address current challenges and accompanying opportunities in studying primate- and human-specific transposable elements.
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Affiliation(s)
- Manci Li
- University of Minnesota, St. Paul, MN, 55108, United States
| | - Peter A Larsen
- University of Minnesota, St. Paul, MN, 55108, United States.
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10
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Qin W, Ugur E, Mulholland CB, Bultmann S, Solovei I, Modic M, Smets M, Wierer M, Forné I, Imhof A, Cardoso MC, Leonhardt H. Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency. Nucleic Acids Res 2021; 49:7406-7423. [PMID: 34214177 PMCID: PMC8287961 DOI: 10.1093/nar/gkab548] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β−/− embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1β−/− and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1−/− cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.
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Affiliation(s)
- Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Enes Ugur
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Sebastian Bultmann
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Irina Solovei
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London NW1 1AT, United Kingdom
| | - Martha Smets
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
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11
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Zenk F, Zhan Y, Kos P, Löser E, Atinbayeva N, Schächtle M, Tiana G, Giorgetti L, Iovino N. HP1 drives de novo 3D genome reorganization in early Drosophila embryos. Nature 2021; 593:289-293. [PMID: 33854237 PMCID: PMC8116211 DOI: 10.1038/s41586-021-03460-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/16/2021] [Indexed: 12/03/2022]
Abstract
Fundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo. The heterochromatin protein HP1 has an essential role in establishing several features of the 3D nuclear organization of the genome during early embryonic development in Drosophila.
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Affiliation(s)
- Fides Zenk
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.,Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Pavel Kos
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Eva Löser
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Nazerke Atinbayeva
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.,Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany.,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Melanie Schächtle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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12
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Tien CL, Mohammadparast S, Chang C. Heterochromatin protein 1 beta regulates neural and neural crest development by repressing pluripotency-associated gene pou5f3.2/oct25 in Xenopus. Dev Dyn 2021; 250:1113-1124. [PMID: 33595886 DOI: 10.1002/dvdy.319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Heterochromatin protein 1 (HP1) is associated with and plays a role in compact chromatin conformation, but the function of HP1 in vertebrate embryogenesis is not understood completely. RESULTS Here, we explore the activity of HP1 in early neural development in the frog Xenopus laevis. We show that the three isoforms of HP1, HP1α, β, and γ, are expressed in similar patterns in the neural and neural crest derivatives in early embryos. Despite this, knockdown of HP1β and HP1γ, but not HP1α, in presumptive neural tissues leads to head defects. Late pan-neural markers and neural crest specifier genes are reduced, but early neural and neural plate border genes are less affected in the morphant embryos. Further investigation reveals that neuronal differentiation is impaired and a pluripotency-associated gene, pou5f3.2/oct25, is expanded in HP1β morphants. Ectopic expression of pou5f3.2/oct25 mimics the effect of HP1β knockdown on marker expression, whereas simultaneous knockdown of HP1β and pou5f3.2/oct25 partially rescues expression of these genes. CONCLUSION Taken together, the data suggest that HP1β regulates transition from precursor to more differentiated cell types during neural and neural crest development in Xenopus, and it does so at least partially via repression of the pluripotency-associated transcription regulator pou5f3.2/oct25.
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Affiliation(s)
- Chih-Liang Tien
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Saeid Mohammadparast
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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13
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Xie J, Lin L, Sánchez OF, Bryan C, Freeman JL, Yuan C. Pre-differentiation exposure to low-dose of atrazine results in persistent phenotypic changes in human neuronal cell lines. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116379. [PMID: 33388679 DOI: 10.1016/j.envpol.2020.116379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/04/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Exposures to organic pesticides, particularly during a developmental window, have been associated with various neurodegenerative diseases later in life. Atrazine (ATZ), one of the most used pesticides in the U.S., is suspected to be associated with increased neurodegeneration later in life but few studies assessed the neurotoxicity of developmental ATZ exposure using human neuronal cells. Here, we exposed human SH-SY5Y cells to 0.3, 3, and 30 ppb of ATZ prior to differentiating them into dopaminergic-like neurons in ATZ-free medium to mimic developmental exposure. The differentiated neurons exhibit altered neurite outgrowth and SNCA pathology depending on the ATZ treatment doses. Epigenome changes, such as decreases in 5mC (for 0.3 ppb only), H3K9me3, and H3K27me3 were observed immediately after exposure. These alterations persist in a compensatory manner in differentiated neurons. Specifically, we observed significant reductions in 5mC and H3K9me3, as well as, an increase in H3K27me3 in ATZ-exposed cells after differentiation, suggesting substantial chromatin rearrangements after developmental ATZ exposure. Transcriptional changes of relevant epigenetic enzymes were also quantified but found to only partially explain the observed epigenome alteration. Our results thus collectively suggest that exposure to low-dose of ATZ prior to differentiation can result in long-lasting changes in epigenome and increase risks of SNCA-related Parkinson's Disease.
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Affiliation(s)
- Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Oscar F Sánchez
- Department of Nutrition and Biochemistry, Pontificia Universidad Javeriana, Bogotá, 110231, Colombia
| | - Chris Bryan
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA.
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14
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van Wijnen AJ, Bagheri L, Badreldin AA, Larson AN, Dudakovic A, Thaler R, Paradise CR, Wu Z. Biological functions of chromobox (CBX) proteins in stem cell self-renewal, lineage-commitment, cancer and development. Bone 2021; 143:115659. [PMID: 32979540 DOI: 10.1016/j.bone.2020.115659] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/02/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic regulatory proteins support mammalian development, cancer, aging and tissue repair by controlling many cellular processes including stem cell self-renewal, lineage-commitment and senescence in both skeletal and non-skeletal tissues. We review here our knowledge of epigenetic regulatory protein complexes that support the formation of inaccessible heterochromatin and suppress expression of cell and tissue-type specific biomarkers during development. Maintenance and formation of heterochromatin critically depends on epigenetic regulators that recognize histone 3 lysine trimethylation at residues K9 and K27 (respectively, H3K9me3 and H3K27me3), which represent transcriptionally suppressive epigenetic marks. Three chromobox proteins (i.e., CBX1, CBX3 or CBX5) associated with the heterochromatin protein 1 (HP1) complex are methyl readers that interpret H3K9me3 marks which are mediated by H3K9 methyltransferases (i.e., SUV39H1 or SUV39H2). Other chromobox proteins (i.e., CBX2, CBX4, CBX6, CBX7 and CBX8) recognize H3K27me3, which is deposited by Polycomb Repressive Complex 2 (PRC2; a complex containing SUZ12, EED, RBAP46/48 and the methyl transferases EZH1 or EZH2). This second set of CBX proteins resides in PRC1, which has many subunits including other polycomb group factors (PCGF1, PCGF2, PCGF3, PCGF4, PCGF5, PCGF6), human polyhomeotic homologs (HPH1, HPH2, HPH3) and E3-ubiquitin ligases (RING1 or RING2). The latter enzymes catalyze the subsequent mono-ubiquitination of lysine 119 in H2A (H2AK119ub). We discuss biological, cellular and molecular functions of CBX proteins and their physiological and pathological activities in non-skeletal cells and tissues in anticipation of new discoveries on novel roles for CBX proteins in bone formation and skeletal development.
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Affiliation(s)
- Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America; Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America; Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Leila Bagheri
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Amr A Badreldin
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - A Noelle Larson
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America; Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
| | - Christopher R Paradise
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States of America; Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States of America
| | - Zhong Wu
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States of America
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15
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Zaidan NZ, Sridharan R. HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells. Nucleic Acids Res 2020; 48:12660-12674. [PMID: 33237287 PMCID: PMC7736818 DOI: 10.1093/nar/gkaa1091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.
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Affiliation(s)
- Nur Zafirah Zaidan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA
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16
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Aparicio Pelaz D, Yerkesh Z, Kirchgäßner S, Mahler H, Kharchenko V, Azhibek D, Jaremko M, Mootz HD, Jaremko Ł, Schwarzer D, Fischle W. Examining histone modification crosstalk using immobilized libraries established from ligation-ready nucleosomes. Chem Sci 2020; 11:9218-9225. [PMID: 34123170 PMCID: PMC8163371 DOI: 10.1039/d0sc03407j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chromatin signaling relies on a plethora of posttranslational modifications (PTM) of the histone proteins which package the long DNA molecules of our cells in reoccurring units of nucleosomes. Determining the biological function and molecular working mechanisms of different patterns of histone PTMs requires access to various chromatin substrates of defined modification status. Traditionally, these are achieved by individual reconstitution of single nucleosomes or arrays of nucleosomes in conjunction with modified histones produced by means of chemical biology. Here, we report an alternative strategy for establishing a library of differentially modified nucleosomes that bypasses the need for many individual syntheses, purification and assembly reactions by installing modified histone tails on ligation-ready, immobilized nucleosomes reconstituted in a single batch. Using the ligation-ready nucleosome strategy with sortase-mediated ligation for histone H3 and intein splicing for histone H2A, we generated libraries of up to 280 individually modified nucleosomes in 96-well plate format. Screening these libraries for the effects of patterns of PTMs onto the recruitment of a well-known chromatin factor, HP1 revealed a previously unknown long-range cross-talk between two modifications. H3S28 phosphorylation enhances recruitment of the HP1 protein to the H3K9 methylated H3-tail only in nucleosomal context. Detailed structural analysis by NMR measurements implies negative charges at position 28 to increase nucleosomal H3-tail dynamics and flexibility. Our work shows that ligation-ready nucleosomes enable unprecedented access to the ample space and complexity of histone modification patterns for the discovery and dissection of chromatin regulatory principles. 280 different patterns of histone modifications were installed in preassembled nucleosomes using PTS and SML enabling screening of readout crosstalk.![]()
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Affiliation(s)
- Diego Aparicio Pelaz
- Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Germany
| | - Zhadyra Yerkesh
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Sören Kirchgäßner
- Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Germany
| | - Henriette Mahler
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry 37077 Göttingen Germany
| | - Vladlena Kharchenko
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Dulat Azhibek
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster Corrensstr. 36 48149 Münster Germany
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Germany
| | - Wolfgang Fischle
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia .,Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry 37077 Göttingen Germany
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17
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Singh PB, Belyakin SN, Laktionov PP. Biology and Physics of Heterochromatin- Like Domains/Complexes. Cells 2020; 9:E1881. [PMID: 32796726 PMCID: PMC7465696 DOI: 10.3390/cells9081881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 11/17/2022] Open
Abstract
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Stepan N. Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
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18
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Charaka V, Tiwari A, Pandita RK, Hunt CR, Pandita TK. Role of HP1β during spermatogenesis and DNA replication. Chromosoma 2020; 129:215-226. [PMID: 32651609 DOI: 10.1007/s00412-020-00739-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 11/25/2022]
Abstract
Heterochromatin protein 1β (HP1β), encoded by the Cbx1 gene, has been functionally linked to chromatin condensation, transcriptional regulation, and DNA damage repair. Here we report that testis-specific Cbx1 conditional knockout (Cbx1 cKO) impairs male germ cell development in mice. Depletion of HP1β negatively affected sperm maturation and increased seminiferous tubule degeneration in Cbx1 cKO mice. In addition, the spermatogonia have elevated γ-H2AX foci levels as do Cbx1 deficient mouse embryonic fibroblasts (MEFs) as compared to wild-type (WT) control MEFs. The increase in γ-H2AX foci in proliferating Cbx1 cKO cells indicates defective replication-dependent DNA damage repair. Depletion or loss of HP1β from human cells and MEFs increased DNA replication fork stalling and firing of new origins of replication, indicating defective DNA synthesis. Taken together, these results suggest that loss of HP1β in proliferating cells leads to DNA replication defects with associated DNA damage that impact spermatogenesis.
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Affiliation(s)
- Vijay Charaka
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Anjana Tiwari
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Raj K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, 77030, USA.
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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19
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How HP1 Post-Translational Modifications Regulate Heterochromatin Formation and Maintenance. Cells 2020; 9:cells9061460. [PMID: 32545538 PMCID: PMC7349378 DOI: 10.3390/cells9061460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Heterochromatin Protein 1 (HP1) is a highly conserved protein that has been used as a classic marker for heterochromatin. HP1 binds to di- and tri-methylated histone H3K9 and regulates heterochromatin formation, functions and structure. Besides the well-established phosphorylation of histone H3 Ser10 that has been shown to modulate HP1 binding to chromatin, several studies have recently highlighted the importance of HP1 post-translational modifications and additional epigenetic features for the modulation of HP1-chromatin binding ability and heterochromatin formation. In this review, we summarize the recent literature of HP1 post-translational modifications that have contributed to understand how heterochromatin is formed, regulated and maintained.
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20
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Epigenetic Factors That Control Pericentric Heterochromatin Organization in Mammals. Genes (Basel) 2020; 11:genes11060595. [PMID: 32481609 PMCID: PMC7349813 DOI: 10.3390/genes11060595] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Pericentric heterochromatin (PCH) is a particular form of constitutive heterochromatin that is localized to both sides of centromeres and that forms silent compartments enriched in repressive marks. These genomic regions contain species-specific repetitive satellite DNA that differs in terms of nucleotide sequences and repeat lengths. In spite of this sequence diversity, PCH is involved in many biological phenomena that are conserved among species, including centromere function, the preservation of genome integrity, the suppression of spurious recombination during meiosis, and the organization of genomic silent compartments in the nucleus. PCH organization and maintenance of its repressive state is tightly regulated by a plethora of factors, including enzymes (e.g., DNA methyltransferases, histone deacetylases, and histone methyltransferases), DNA and histone methylation binding factors (e.g., MECP2 and HP1), chromatin remodeling proteins (e.g., ATRX and DAXX), and non-coding RNAs. This evidence helps us to understand how PCH organization is crucial for genome integrity. It then follows that alterations to the molecular signature of PCH might contribute to the onset of many genetic pathologies and to cancer progression. Here, we describe the most recent updates on the molecular mechanisms known to underlie PCH organization and function.
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21
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Kumar A, Kono H. Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. Biophys Rev 2020; 12:387-400. [PMID: 32144738 PMCID: PMC7242596 DOI: 10.1007/s12551-020-00663-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/23/2020] [Indexed: 12/12/2022] Open
Abstract
Isoforms of heterochromatin protein 1 (HP1) have been known to perform a multitude of functions ranging from gene silencing, gene activation to cell cycle regulation, and cell differentiation. This functional diversity arises from the dissimilarities coded in protein sequence which confers different biophysical and biochemical properties to individual structural elements of HP1 and thereby different behavior and interaction patterns. Hence, an understanding of various interactions of the structural elements of HP1 will be of utmost importance to better elucidate chromatin dynamics in its presence. In this review, we have gathered available information about interactions of HP1 both within and with itself as well as with chromatin elements. Also, the possible implications of these interactions are discussed.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan.
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22
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Singh PB, Newman AG. On the relations of phase separation and Hi-C maps to epigenetics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191976. [PMID: 32257349 PMCID: PMC7062049 DOI: 10.1098/rsos.191976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
The relationship between compartmentalization of the genome and epigenetics is long and hoary. In 1928, Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller's discovery of position-effect variegation in 1930 went on to show that heterochromatin is a cytologically visible state of heritable (epigenetic) gene repression. Current insights into compartmentalization have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalization seen in Hi-C maps is owing to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5 Mb) heterochromatin-like domains and smaller (less than 100 kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes contributes to polymer-polymer phase separation that packages epigenetically heritable chromatin states during interphase. Contacts mediated by HP1 'bridging' are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic subcompartment that emerges from contacts between large KRAB-ZNF heterochromatin-like domains. Further, mutational analyses have revealed a finer, innate, compartmentalization in Hi-C experiments that probably reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres-where the HP1-H3K9me2/3 interaction represents the most evolutionarily conserved paradigm-could drive and generate the fundamental compartmentalization of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally differentiated fibroblast or a pluripotent embryonic stem cell.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Nur-Sultan Z05K4F4, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Street 2, Novosibirsk 630090, Russian Federation
| | - Andrew G. Newman
- Institute of Cell and Neurobiology, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
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23
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Naruse C, Abe K, Yoshihara T, Kato T, Nishiuchi T, Asano M. Heterochromatin protein 1γ deficiency decreases histone H3K27 methylation in mouse neurosphere neuronal genes. FASEB J 2020; 34:3956-3968. [PMID: 31961023 DOI: 10.1096/fj.201900139r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 09/12/2019] [Accepted: 12/30/2019] [Indexed: 11/11/2022]
Abstract
Heterochromatin protein (HP) 1γ, a component of heterochromatin in eukaryotes, is involved in H3K9 methylation. Although HP1γ is expressed strongly in neural tissues and neural stem cells, its functions are unclear. To elucidate the roles of HP1γ, we analyzed HP1γ -deficient (HP1γ KO) mouse embryonic neurospheres and determined that HP1γ KO neurospheres tended to differentiate after quaternary culture. Several genes normally expressed in neuronal cells were upregulated in HP1γ KO undifferentiated neurospheres, but not in the wild type (WT). Compared to that in the control neurospheres, the occupancy of H3K27me3 was lower around the transcription start sites (TSSs) of these genes in HP1γ KO neurospheres, while H3K9me2/3, H3K4me3, and H3K27ac amounts remained unchanged. Moreover, amounts of the H3K27me2/3 demethylases, UTX, and JMJD3, were increased around the TSSs of these genes. Treatment with GSK-J4, an inhibitor of H3K27 demethylases, decreased the expression of genes upregulated in HP1γ KO neurospheres, along with an increase of H3K27me3 amounts. Therefore, in murine neurospheres, HP1γ protected the promoter sites of differentiated cell-specific genes against H3K27 demethylases to repress the expression of these genes. A better understanding of central cellular processes such as histone methylation will help elucidate critical events such as cell-specific gene expression, epigenetics, and differentiation.
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Affiliation(s)
- Chie Naruse
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kanae Abe
- Division of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Toru Yoshihara
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoaki Kato
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Belman JP, Meng W, Wang HY, Li J, Strauser HT, Rosenfeld AM, Zhang Q, Prak ETL, Wasik M. Dramatic increase in gene mutational burden after transformation of follicular lymphoma into TdT + B-lymphoblastic leukemia/lymphoma. Cold Spring Harb Mol Case Stud 2019; 6:mcs.a004614. [PMID: 31776129 PMCID: PMC6996523 DOI: 10.1101/mcs.a004614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
Transformation of follicular lymphoma (FL) into B-lymphoblastic leukemia/lymphoma (B-ALL/LBL) is rare and results in greatly increased aggressiveness of clinical course. Here we present extensive molecular analysis of this unusual transformation, including immunoglobulin (Ig) gene rearrangement studies, cytogenetic analysis, and whole-exome sequencing (WES) of the patient's FL, B-ALL/LBL, and normal cells. Although FL showed marked somatic hypermutation (SHM) of the Ig genes, SHM appeared to be even more extensive in B-ALL/LBL. Cytogenetically, at least three translocations were identified in the B-ALL/LBL involving the BCL2, BCL6, and MYC genes; two of these, the BCL6 and BCL2 gene rearrangements, were already seen at the FL stage. WES identified 751 single-nucleotide variants with high allelic burden in the patient's cells, with the vast majority (575) present exclusively at the B-ALL/LBL stage. Of note, a TAF3 gene mutation was shared by normal, FL, and B-ALL/LBL tissue. A KMT2D nonsense mutation was identified in both FL and B-ALL/LBL and therefore may have contributed directly to lymphomagenesis. Mutations in KDM6A, SMARCA4, CBX1, and JMY were specific to the B-ALL/LBL stage, possibly contributing to the B-ALL/LBL transformation. Functionally, these identified mutations may lead to dysregulation of DNA repair, transcription, and cell differentiation. Thus, these genetic changes, together with the identified chromosomal translocations, may have contributed to lymphoma development and progression. Our findings may improve the mechanistic understanding of the FL-B-ALL/LBL transformation and may have therapeutic implications for this aggressive disease.
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Affiliation(s)
- Jonathan P Belman
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Wenzhao Meng
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hong Yi Wang
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jie Li
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Honore T Strauser
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Aaron M Rosenfeld
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Qian Zhang
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eline T Luning Prak
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mariusz Wasik
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Ninova M, Fejes Tóth K, Aravin AA. The control of gene expression and cell identity by H3K9 trimethylation. Development 2019; 146:dev181180. [PMID: 31540910 PMCID: PMC6803365 DOI: 10.1242/dev.181180] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histone 3 lysine 9 trimethylation (H3K9me3) is a conserved histone modification that is best known for its role in constitutive heterochromatin formation and the repression of repetitive DNA elements. More recently, it has become evident that H3K9me3 is also deposited at certain loci in a tissue-specific manner and plays important roles in regulating cell identity. Notably, H3K9me3 can repress genes encoding silencing factors, pointing to a fundamental principle of repressive chromatin auto-regulation. Interestingly, recent studies have shown that H3K9me3 deposition requires protein SUMOylation in different contexts, suggesting that the SUMO pathway functions as an important module in gene silencing and heterochromatin formation. In this Review, we discuss the role of H3K9me3 in gene regulation in various systems and the molecular mechanisms that guide the silencing machinery to target loci.
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Affiliation(s)
- Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
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26
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Nicetto D, Zaret KS. Role of H3K9me3 heterochromatin in cell identity establishment and maintenance. Curr Opin Genet Dev 2019; 55:1-10. [PMID: 31103921 DOI: 10.1016/j.gde.2019.04.013] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/18/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023]
Abstract
Compacted, transcriptionally repressed chromatin, referred to as heterochromatin, represents a major fraction of the higher eukaryotic genome and exerts pivotal functions of silencing repetitive elements, maintenance of genome stability, and control of gene expression. Among the different histone post-translational modifications (PTMs) associated with heterochromatin, tri-methylation of lysine 9 on histone H3 (H3K9me3) is gaining increased attention. Besides its known role in repressing repetitive elements and non-coding portions of the genome, recent observations indicate H3K9me3 as an important player in silencing lineage-inappropriate genes. The ability of H3K9me3 to influence cell identity challenges the original concept of H3K9me3-marked heterochromatin as mainly a constitutive type of chromatin and provides a further level of understanding of how to modulate cell fate control. Here, we summarize the role of H3K9me3 marked heterochromatin and its dynamics in establishing and maintaining cellular identity.
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Affiliation(s)
- Dario Nicetto
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports 2019; 10:627-641. [PMID: 29358085 PMCID: PMC5830946 DOI: 10.1016/j.stemcr.2017.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022] Open
Abstract
The heterochromatin protein 1 (HP1) family is involved in various functions with maintenance of chromatin structure. During murine somatic cell reprogramming, we find that early depletion of HP1γ reduces the generation of induced pluripotent stem cells, while late depletion enhances the process, with a concomitant change from a centromeric to nucleoplasmic localization and elongation-associated histone H3.3 enrichment. Depletion of heterochromatin anchoring protein SENP7 increased reprogramming efficiency to a similar extent as HP1γ, indicating the importance of HP1γ release from chromatin for pluripotency acquisition. HP1γ interacted with OCT4 and DPPA4 in HP1α and HP1β knockouts and in H3K9 methylation depleted H3K9M embryonic stem cell (ESC) lines. HP1α and HP1γ complexes in ESCs differed in association with histones, the histone chaperone CAF1 complex, and specific components of chromatin-modifying complexes such as DPY30, implying distinct functional contributions. Taken together, our results reveal the complex contribution of the HP1 proteins to pluripotency. Release of HP1γ from anchoring by Senp7 increases reprogramming efficiency HP1γ switches enrichment from histone H1 to histone H3.3 in pluripotent cells HP1γ interacts with OCT4 and DPPA4 independent of HP1α, HP1β, and H3K9 methylation Proteomic characterization of HP1 protein family in pluripotent cells
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Affiliation(s)
- Nur Zafirah Zaidan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Kolin J Walker
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Jaime E Brown
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA.
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Seo S, Mathison A, Grzenda A, Podratz J, Calvo E, Brimijoin S, Windebank A, Iovanna J, Lomberk G, Urrutia R. Mechanisms Underlying the Regulation of HP1γ by the NGF-PKA Signaling Pathway. Sci Rep 2018; 8:15077. [PMID: 30305677 PMCID: PMC6180112 DOI: 10.1038/s41598-018-33475-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/19/2018] [Indexed: 02/08/2023] Open
Abstract
Heterochromatin protein 1 γ (HP1γ) is a well-known chromatin protein, which regulates gene silencing during the execution of processes associated with embryogenesis, organ maturation, and cell differentiation. We find that, in vivo, the levels of HP1γ are downregulated during nervous system development. Similar results are recapitulated in vitro during nerve growth factor (NGF)-induced neuronal cell differentiation in PC12 cells. Mechanistically, our experiments demonstrate that in differentiating PC12 cells, NGF treatment decreases the association of HP1γ to silent heterochromatin, leads to phosphorylation of this protein at S83 via protein kinase A (PKA), and ultimately results in its degradation. Genome-wide experiments, using gain-of-function (overexpression) and loss-of-function (RNAi) paradigms, demonstrate that changing the level of HP1γ impacts on PC12 differentiation, at least in part, through gene networks involved in this process. Hence, inactivation of HP1γ by different post-translational mechanisms, including reduced heterochromatin association, phosphorylation, and degradation, is necessary for neuronal cell differentiation to occur. Indeed, we show that the increase of HP1γ levels has the reverse effect, namely antagonizing neuronal cell differentiation, supporting that this protein acts as a barrier for this process. Thus, these results describe the regulation and participation of HP1γ in a novel membrane-to-nucleus pathway, through NGF-PKA signaling, which is involved in NGF-induced neuronal cell differentiation.
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Affiliation(s)
- Seungmae Seo
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Angela Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Adrienne Grzenda
- University of California, Los Angeles, Psychiatry Residency Program, Los Angeles, CA, USA
| | - Jewel Podratz
- Department of Neuroscience, Mayo Clinic, Rochester, MN, USA
| | - Ezequiel Calvo
- Centre Génomique du Centre de Recherche du CHUL Research Center, Ville de Québec, Quebec, Canada
| | - Stephen Brimijoin
- Department of Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Gwen Lomberk
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA. .,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.
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29
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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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30
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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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31
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Watanabe S, Mishima Y, Shimizu M, Suetake I, Takada S. Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays. Biophys J 2018; 114:2336-2351. [PMID: 29685391 PMCID: PMC6129468 DOI: 10.1016/j.bpj.2018.03.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/27/2018] [Accepted: 03/26/2018] [Indexed: 01/01/2023] Open
Abstract
Heterochromatin protein 1 (HP1), associated with heterochromatin formation, recognizes an epigenetically repressive marker, trimethylated lysine 9 in histone H3 (H3K9me3), and generally contributes to long-term silencing. How HP1 induces heterochromatin is not fully understood. Recent experiments suggested that not one, but two nucleosomes provide a platform for this recognition. Integrating previous and new biochemical assays with computational modeling, we provide near-atomic structural models for HP1 binding to the dinucleosomes. We found that the dimeric HP1α tends to bind two H3K9me3s that are in adjacent nucleosomes, thus bridging two nucleosomes. We identified, to our knowledge, a novel DNA binding motif in the hinge region that is specific to HP1α and is essential for recognizing the H3K9me3 sites of two nucleosomes. An HP1 isoform, HP1γ, does not easily bridge two nucleosomes in extended conformations because of the absence of the above binding motif and its shorter hinge region. We propose a molecular mechanism for chromatin structural changes caused by HP1.
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Affiliation(s)
- Shuhei Watanabe
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Japan
| | - Yuichi Mishima
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masahiro Shimizu
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Japan
| | - Isao Suetake
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan; College of Nutrition, Koshien University, Takarazuka, Japan.
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto, Japan.
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32
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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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A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons. Nat Commun 2018; 9:1226. [PMID: 29581424 PMCID: PMC5964330 DOI: 10.1038/s41467-018-03538-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 02/21/2018] [Indexed: 12/22/2022] Open
Abstract
The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in small neuronal populations in vivo, we present a comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons, and embryonic neural progenitors. Furthermore, we utilize the map generated by our analysis to show that the transcriptional response of midbrain dopaminergic neurons following 6-OHDA or methamphetamine injection is characterized by increased expression of genes with promoters dually marked by H3K4me3/H3K27me3. Our study provides an in vivo genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare neuronal subtypes. The limited size of some neuronal types and their entangled environment renders it difficult to study their transcription regulation. Here the authors present a comparative analysis of histone modifications and transcription in dopaminergic and serotonergic neurons and embryonic neural progenitors.
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34
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Charó NL, Galigniana NM, Piwien-Pilipuk G. Heterochromatin protein (HP)1γ is not only in the nucleus but also in the cytoplasm interacting with actin in both cell compartments. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1865:432-443. [PMID: 29208528 DOI: 10.1016/j.bbamcr.2017.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/07/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022]
Abstract
Confocal and electron microscopy images, and WB analysis of cellular fractions revealed that HP1γ is in the nucleus but also in the cytoplasm of C2C12 myoblasts, myotubes, skeletal and cardiac muscles, N2a, HeLa and HEK293T cells. Signal specificity was tested with different antibodies and by HP1γ knockdown. Leptomycin B treatment of myoblasts increased nuclear HP1γ, suggesting that its nuclear export is Crm-1-dependent. HP1γ exhibited a filamentous pattern of staining partially co-localizing with actin in the cytoplasm of myotubes and myofibrils. Immunoelectron microscopic analysis showed high-density immunogold particles that correspond to HP1γ localized to the Z-disk and A-band of the sarcomere of skeletal muscle. HP1γ partially co-localized with actin in C2C12 myotubes and murine myofibrils. Importantly, actin co-immunoprecipitated with HP1γ in the nuclear and cytosolic fractions of myoblasts. Actin co-immunoprecipitated with HP1γ in myoblasts incubated in the absence or presence of the actin depolymerizing agent cytochalasin D, suggesting that HP1γ may interact with G-and F-actin. In the cytoplasm, HP1γ was associated to the perinuclear actin cap that controls nuclear shape and position. In the nucleus, re-ChIP assays showed that HP1γ-actin associates to the promoter and transcribed regions of the house keeping gene GAPDH, suggesting that HP1γ may function as a scaffold protein for the recruitment of actin to control gene expression. When HP1γ was knocked-down, myoblasts were unable to differentiate or originated thin myotubes. In summary, HP1γ is present in the nucleus and the cytoplasm interacting with actin, a protein complex that may exert different functions depending on its subcellular localization.
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Affiliation(s)
- Nancy L Charó
- Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Natalia M Galigniana
- Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Graciela Piwien-Pilipuk
- Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET, Ciudad Autónoma de Buenos Aires, Argentina.
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35
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Fisher CL, Marks H, Cho LTY, Andrews R, Wormald S, Carroll T, Iyer V, Tate P, Rosen B, Stunnenberg HG, Fisher AG, Skarnes WC. An efficient method for generation of bi-allelic null mutant mouse embryonic stem cells and its application for investigating epigenetic modifiers. Nucleic Acids Res 2017; 45:e174. [PMID: 28981838 PMCID: PMC5716182 DOI: 10.1093/nar/gkx811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/25/2017] [Accepted: 09/04/2017] [Indexed: 11/18/2022] Open
Abstract
Mouse embryonic stem (ES) cells are a popular model system to study biological processes, though uncovering recessive phenotypes requires inactivating both alleles. Building upon resources from the International Knockout Mouse Consortium (IKMC), we developed a targeting vector for second allele inactivation in conditional-ready IKMC 'knockout-first' ES cell lines. We applied our technology to several epigenetic regulators, recovering bi-allelic targeted clones with a high efficiency of 60% and used Flp recombinase to restore expression in two null cell lines to demonstrate how our system confirms causality through mutant phenotype reversion. We designed our strategy to select against re-targeting the 'knockout-first' allele and identify essential genes in ES cells, including the histone methyltransferase Setdb1. For confirmation, we exploited the flexibility of our system, enabling tamoxifen inducible conditional gene ablation while controlling for genetic background and tamoxifen effects. Setdb1 ablated ES cells exhibit severe growth inhibition, which is not rescued by exogenous Nanog expression or culturing in naive pluripotency '2i' media, suggesting that the self-renewal defect is mediated through pluripotency network independent pathways. Our strategy to generate null mutant mouse ES cells is applicable to thousands of genes and repurposes existing IKMC Intermediate Vectors.
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Affiliation(s)
- Cynthia L. Fisher
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- MRC London Institute of Medical Sciences and Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Lily Ting-yin Cho
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Robert Andrews
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Sam Wormald
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas Carroll
- MRC London Institute of Medical Sciences and Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Vivek Iyer
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Peri Tate
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Barry Rosen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Amanda G. Fisher
- MRC London Institute of Medical Sciences and Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - William C. Skarnes
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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36
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Bártová E, Malyšková B, Komůrková D, Legartová S, Suchánková J, Krejčí J, Kozubek S. Function of heterochromatin protein 1 during DNA repair. PROTOPLASMA 2017; 254:1233-1240. [PMID: 28236007 DOI: 10.1007/s00709-017-1090-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/14/2017] [Indexed: 05/04/2023]
Abstract
This review focuses on the function of heterochromatin protein HP1 in response to DNA damage. We specifically outline the regulatory mechanisms in which HP1 and its interacting partners are involved. HP1 protein subtypes (HP1α, HP1β, and HP1γ) are the main components of constitutive heterochromatin, and HP1α and HP1β in particular are responsible for heterochromatin maintenance. The recruitment of these proteins to DNA lesions is also important from the perspective of proper DNA repair mechanisms. For example, HP1α is necessary for the binding of the main DNA damage-related protein 53BP1 at DNA repair foci, which are positive not only for the HP1α protein but also for the RAD51 protein, a component of DNA repair machinery. The HP1β protein also appears in monomeric form in DNA lesions together with the evolutionarily well-conserved protein called proliferating cell nuclear antigen (PCNA). The role of HP1 in DNA lesions is also mediated via the Kap1 transcription repressor. Taken together, these results indicate that the function of HP1 after DNA injury depends strongly on the kinetics of other DNA repair-related factors and their post-translational modifications, such as the phosphorylation of Kap-1.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic.
| | - Barbora Malyšková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Denisa Komůrková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Suchánková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Krejčí
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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37
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Liu Y, Qin S, Lei M, Tempel W, Zhang Y, Loppnau P, Li Y, Min J. Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1. J Biol Chem 2017; 292:5655-5664. [PMID: 28223359 DOI: 10.1074/jbc.m116.768374] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/16/2017] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSDγ) in complex with an H3 peptide suggests that recognition of H3 by CSDγ to some extent resembles CSD-PXVXL interaction. Nevertheless, the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1β CSD-PXVXL complexes. We consequently generalize the historical CSD-PXVXL interaction model and expand the search scope for additional CSD binding partners.
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Affiliation(s)
- Yanli Liu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Su Qin
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Ming Lei
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Wolfram Tempel
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yuzhe Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yanjun Li
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Jinrong Min
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and .,the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Raurell-Vila H, Bosch-Presegue L, Gonzalez J, Kane-Goldsmith N, Casal C, Brown JP, Marazuela-Duque A, Singh PB, Serrano L, Vaquero A. An HP1 isoform-specific feedback mechanism regulates Suv39h1 activity under stress conditions. Epigenetics 2017; 12:166-175. [PMID: 28059589 DOI: 10.1080/15592294.2016.1278096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The presence of H3K9me3 and heterochromatin protein 1 (HP1) are hallmarks of heterochromatin conserved in eukaryotes. The spreading and maintenance of H3K9me3 is effected by the functional interplay between the H3K9me3-specific histone methyltransferase Suv39h1 and HP1. This interplay is complex in mammals because the three HP1 isoforms, HP1α, β, and γ, are thought to play a redundant role in Suv39h1-dependent deposition of H3K9me3 in pericentric heterochromatin (PCH). Here, we demonstrate that despite this redundancy, HP1α and, to a lesser extent, HP1γ have a closer functional link to Suv39h1, compared to HP1β. HP1α and γ preferentially interact in vivo with Suv39h1, regulate its dynamics in heterochromatin, and increase Suv39h1 protein stability through an inhibition of MDM2-dependent Suv39h1-K87 polyubiquitination. The reverse is also observed, where Suv39h1 increases HP1α stability compared HP1β and γ. The interplay between Suv39h1 and HP1 isoforms appears to be relevant under genotoxic stress. Specifically, loss of HP1α and γ isoforms inhibits the upregulation of Suv39h1 and H3K9me3 that is observed under stress conditions. Reciprocally, Suv39h1 deficiency abrogates stress-dependent upregulation of HP1α and γ, and enhances HP1β levels. Our work defines a specific role for HP1 isoforms in regulating Suv39h1 function under stress via a feedback mechanism that likely regulates heterochromatin formation.
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Affiliation(s)
- Helena Raurell-Vila
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Laia Bosch-Presegue
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain.,b Tissue Repair and Regeneration Group , Department of Systems Biology , Universitat de Vic, Universitat Central de Catalunya , Vic , Spain
| | - Jessica Gonzalez
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Noriko Kane-Goldsmith
- c Department of Genetics , Human Genetics Institute, Rutgers University , Piscataway , NJ , USA
| | - Carmen Casal
- d Microcopy Unit, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Jeremy P Brown
- e Fächerverbund Anatomie, Institut für Zell- und Neurobiologie, Charite - Universitätsmedizin , Berlin , Germany
| | - Anna Marazuela-Duque
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Prim B Singh
- e Fächerverbund Anatomie, Institut für Zell- und Neurobiologie, Charite - Universitätsmedizin , Berlin , Germany.,f Natural Sciences and Psychology, John Moores University , Liverpool , UK
| | - Lourdes Serrano
- c Department of Genetics , Human Genetics Institute, Rutgers University , Piscataway , NJ , USA
| | - Alejandro Vaquero
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
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39
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Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J Biosci 2016; 41:759-786. [DOI: 10.1007/s12038-016-9650-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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40
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Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH. The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 2016; 5. [PMID: 27514026 PMCID: PMC4981497 DOI: 10.7554/elife.16096] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.
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Affiliation(s)
- Joel M Swenson
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Amy R Strom
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Sylvain V Costes
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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41
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Mendelsohn AR, Larrick JW. Stem Cell Depletion by Global Disorganization of the H3K9me3 Epigenetic Marker in Aging. Rejuvenation Res 2016; 18:371-5. [PMID: 26160351 DOI: 10.1089/rej.2015.1742] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Epigenomic change and stem cell exhaustion are two of the hallmarks of aging. Accumulation of molecular damage is thought to underlie aging, but the precise molecular composition of the damage remains controversial. That some aging phenotypes, especially those that result from impaired stem cell function, are reversible suggest that such "damage" is repairable. Evidence is accumulating that dysfunction in aging stem cells results from increasing, albeit, subtle disorganization of the epigenome over time. Zhang et al. (2015) report that decreasing levels of WRN, Werner's syndrome (WS) helicase, with increasing age results in loss of heterochromatin marks in mesenchymal stem cells (MSCs) and correlates with an increased rate of cellular senescence. Although WRN plays a role in DNA repair, WRN exerted its effects on aging via maintaining heterochromatin, evidenced by reduced levels of interacting chromatin regulators heterochromatin protein 1α (HP1α), suppressor of variegation 3-9 homolog 1 (SUV39H1), and lamina-associated polypeptide 2β (LAP2β) as well as modified histone H3K9me3. Reducing expression of chromatin modeling co-factors SUV39H1 or HP1α in wild-type MSCs recapitulates the phenotype of WRN deficiency, resulting in reduced H3K9me3 levels and increased senescence without induction of markers of DNA damage, suggesting that chromatin disorganization and not DNA damage is responsible for the pathology of WS during aging in animals. Ectopic expression of HP1α restored H3K9me3 levels and repressed senescence in WRN-deficient MSCs. That HP1α can also suppress senescence in Hutchinson-Gilford progeria syndrome (HGPS) and extend life span in flies when over-expressed suggests that HP1α and H3K9me3 play conserved roles in maintenance of cell state. H3K9me3 levels are dynamic and expected to be potentially responsive to manipulation by extrinsic factors. Recent reports that migration inhibitory factor (MIF) or periodic fasting rejuvenate old MSCs provide the opportunity to link intrinsic and extrinsic mechanisms of aging in novel and potentially medically important ways and may lead to anti-aging treatments that reorganize the epigenome to rejuvenate cells and tissues.
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Affiliation(s)
- Andrew R Mendelsohn
- Panorama Research Institute and Regenerative Sciences Institute , Sunnyvale, California
| | - James W Larrick
- Panorama Research Institute and Regenerative Sciences Institute , Sunnyvale, California
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42
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Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, De La Rosa-Velázquez IA, Zenn HM, Kost N, Pohl W, Chernev A, Schwarzer D, Jenuwein T, Lorincz M, Zimmermann B, Walla PJ, Neumann H, Baubec T, Urlaub H, Fischle W. Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin. Nat Commun 2016; 7:11310. [PMID: 27090491 PMCID: PMC4838890 DOI: 10.1038/ncomms11310] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/13/2016] [Indexed: 12/12/2022] Open
Abstract
Histone H3 trimethylation of lysine 9 (H3K9me3) and proteins of the heterochromatin protein 1 (HP1) family are hallmarks of heterochromatin, a state of compacted DNA essential for genome stability and long-term transcriptional silencing. The mechanisms by which H3K9me3 and HP1 contribute to chromatin condensation have been speculative and controversial. Here we demonstrate that human HP1β is a prototypic HP1 protein exemplifying most basal chromatin binding and effects. These are caused by dimeric and dynamic interaction with highly enriched H3K9me3 and are modulated by various electrostatic interfaces. HP1β bridges condensed chromatin, which we postulate stabilizes the compacted state. In agreement, HP1β genome-wide localization follows H3K9me3-enrichment and artificial bridging of chromatin fibres is sufficient for maintaining cellular heterochromatic conformation. Overall, our findings define a fundamental mechanism for chromatin higher order structural changes caused by HP1 proteins, which might contribute to the plastic nature of condensed chromatin. Heterochromatin protein 1 (HP1), including HP1 α, β and γ, is a family of non-histone chromatin factors thought to be involved in chromatin organization. Here, the authors show that dimeric HP1β interacts dynamically with H3K9me3, a hallmark of heterochromatin, and bridges condensed chromatin.
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Affiliation(s)
- Kyoko Hiragami-Hamada
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Szabolcs Soeroes
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Miroslav Nikolov
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Bryan Wilkins
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Sarah Kreuz
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Carol Chen
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Inti A De La Rosa-Velázquez
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Hans Michael Zenn
- Biaffin GmbH &Co KG, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
| | - Nils Kost
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Wiebke Pohl
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Thomas Jenuwein
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Matthew Lorincz
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | | | - Peter Jomo Walla
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Department of Biophysical Chemistry, Technische Universität Braunschweig, Hans-Sommerstr. 10, 38106 Braunschweig, Germany
| | - Heinz Neumann
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
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43
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Isidor B, Küry S, Rosenfeld JA, Besnard T, Schmitt S, Joss S, Davies SJ, Lebel RR, Henderson A, Schaaf CP, Streff HE, Yang Y, Jain V, Chida N, Latypova X, Le Caignec C, Cogné B, Mercier S, Vincent M, Colin E, Bonneau D, Denommé AS, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Piton A, Dina C, Donnart A, Lindenbaum P, Charpentier E, Redon R, Iemura K, Ikeda M, Tanaka K, Bézieau S. De Novo Truncating Mutations in the Kinetochore-Microtubules Attachment Gene CHAMP1 Cause Syndromic Intellectual Disability. Hum Mutat 2016; 37:354-8. [PMID: 26751395 DOI: 10.1002/humu.22952] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/18/2015] [Indexed: 12/26/2022]
Abstract
A rare syndromic form of intellectual disability with impaired speech was recently found associated with mutations in CHAMP1 (chromosome alignment-maintaining phosphoprotein 1), the protein product of which is directly involved in microtubule-kinetochore attachment. Through whole-exome sequencing in six unrelated nonconsanguineous families having a sporadic case of intellectual disability, we identified six novel de novo truncating mutations in CHAMP1: c.1880C>G p.(Ser627*), c.1489C>T; p.(Arg497*), c.1876_1877delAG; p.(Ser626Leufs*4), c.1043G>A; p.(Trp348*), c.1002G>A; p.(Trp334*), and c.958_959delCC; p.(Pro320*). Our clinical observations confirm the phenotypic homogeneity of the syndrome, which represents therefore a distinct clinical entity. Besides, our functional studies show that CHAMP1 protein variants are delocalized from chromatin and are unable to bind to two of its direct partners, POGZ and HP1. These data suggest a pathogenic mechanism of the CHAMP1-associated intellectual disability syndrome mediated by direct interacting partners of CHAMP1, several of which are involved in chromo/kinetochore-related disorders.
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Affiliation(s)
- Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France.,INSERM, UMR-S 957, Nantes, 44035, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
| | - Sébastien Schmitt
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
| | - Shelagh Joss
- Department of Clinical Genetics, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Sally J Davies
- All Wales Medical Genetic Service, University Hospital of Wales, Cardiff, United Kingdom
| | - Robert Roger Lebel
- Genetics Section, Department of Pediatrics, SUNY Upstate Medical University, Syracuse, New York
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Haley E Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Vani Jain
- All Wales Medical Genetic Service, University Hospital of Wales, Cardiff, United Kingdom
| | - Nodoka Chida
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Xenia Latypova
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
| | - Cédric Le Caignec
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France.,INSERM, UMR-S 957, Nantes, 44035, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
| | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
| | - Estelle Colin
- Département de Biochimie et Génétique, CHU Angers, Angers, 49100, France et UMR INSERM 1083 - CNRS 6214
| | - Dominique Bonneau
- Département de Biochimie et Génétique, CHU Angers, Angers, 49100, France et UMR INSERM 1083 - CNRS 6214
| | - Anne-Sophie Denommé
- Département de Biochimie et Génétique, CHU Angers, Angers, 49100, France et UMR INSERM 1083 - CNRS 6214
| | | | | | - Sylvie Odent
- Service de Génétique Clinique, CHU Rennes, CNRS UMR6290, Université Rennes1, Rennes, France
| | | | - Amélie Piton
- Département Médecine Translationelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 7104/Université de Strasbourg, Illkirch, 67404, France.,Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg 67000, France
| | - Christian Dina
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - Audrey Donnart
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - Pierre Lindenbaum
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - Eric Charpentier
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - Richard Redon
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - Kenji Iemura
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masanori Ikeda
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, Nantes CEDEX 1, 44093, France
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Bártová E, Večeřa J, Krejčí J, Legartová S, Pacherník J, Kozubek S. The level and distribution pattern of HP1β in the embryonic brain correspond to those of H3K9me1/me2 but not of H3K9me3. Histochem Cell Biol 2016; 145:447-61. [PMID: 26794325 DOI: 10.1007/s00418-015-1402-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 01/13/2023]
Abstract
We studied the histone signature of embryonic and adult brains to strengthen existing evidence of the importance of the histone code in mouse brain development. We analyzed the levels and distribution patterns of H3K9me1, H3K9me2, H3K9me3, and HP1β in both embryonic and adult brains. Western blotting showed that during mouse brain development, the levels of H3K9me1, H3K9me2, and HP1β exhibited almost identical trends, with the highest protein levels occurring at E15 stage. These trends differed from the relatively stable level of H3K9me3 at developmental stages E8, E13, E15, and E18. Compared with embryonic brains, adult brains were characterized by very low levels of H3K9me1/me2/me3 and HP1β. Manipulation of the embryonic epigenome through histone deacetylase inhibitor treatment did not affect the distribution patterns of the studied histone markers in embryonic ventricular ependyma. Similarly, Hdac3 depletion in adult animals had no effect on histone methylation in the adult hippocampus. Our results indicate that the distribution of HP1β in the embryonic mouse brain is related to that of H3K9me1/me2 but not to that of H3K9me3. The unique status of H3K9me3 in the brain was confirmed by its pronounced accumulation in the granular layer of the adult olfactory bulb. Moreover, among the studied proteins, H3K9me3 was the only posttranslational histone modification that was highly abundant at clusters of centromeric heterochromatin, called chromocenters. When we focused on the hippocampus, we found this region to be rich in H3K9me1 and H3K9me3, whereas H3K9me2 and HP1β were present at a very low level or even absent in the hippocampal blade. Taken together, these results revealed differences in the epigenome of the embryonic and adult mouse brain and showed that the adult hippocampus, the granular layer of the adult olfactory bulb, and the ventricular ependyma of the embryonic brain are colonized by specific epigenetic marks.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic.
| | - Josef Večeřa
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Jana Krejčí
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jiří Pacherník
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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Becker JS, Nicetto D, Zaret KS. H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes. Trends Genet 2015; 32:29-41. [PMID: 26675384 DOI: 10.1016/j.tig.2015.11.001] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 01/26/2023]
Abstract
Establishing and maintaining cell identity depends on the proper regulation of gene expression, as specified by transcription factors and reinforced by epigenetic mechanisms. Among the epigenetic mechanisms, heterochromatin formation is crucial for the preservation of genome stability and the cell type-specific silencing of genes. The heterochromatin-associated histone mark H3K9me3, although traditionally associated with the noncoding portions of the genome, has emerged as a key player in repressing lineage-inappropriate genes and shielding them from activation by transcription factors. Here we describe the role of H3K9me3 heterochromatin in impeding the reprogramming of cell identity and the mechanisms by which H3K9me3 is reorganized during development and cell fate determination.
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Affiliation(s)
- Justin S Becker
- Institute for Regenerative Medicine, Epigenetics Program, and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Dario Nicetto
- Institute for Regenerative Medicine, Epigenetics Program, and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Epigenetics Program, and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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Linking replication stress with heterochromatin formation. Chromosoma 2015; 125:523-33. [PMID: 26511280 PMCID: PMC4901112 DOI: 10.1007/s00412-015-0545-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 09/27/2015] [Accepted: 09/30/2015] [Indexed: 11/23/2022]
Abstract
The eukaryotic genome can be roughly divided into euchromatin and heterochromatin domains that are structurally and functionally distinct. Heterochromatin is characterized by its high compaction that impedes DNA transactions such as gene transcription, replication, or recombination. Beyond its role in regulating DNA accessibility, heterochromatin plays essential roles in nuclear architecture, chromosome segregation, and genome stability. The formation of heterochromatin involves special histone modifications and the recruitment and spreading of silencing complexes that impact the higher-order structures of chromatin; however, its molecular nature varies between different chromosomal regions and between species. Although heterochromatin has been extensively characterized, its formation and maintenance throughout the cell cycle are not yet fully understood. The biggest challenge for the faithful transmission of chromatin domains is the destabilization of chromatin structures followed by their reassembly on a novel DNA template during genomic replication. This destabilizing event also provides a window of opportunity for the de novo establishment of heterochromatin. In recent years, it has become clear that different types of obstacles such as tight protein-DNA complexes, highly transcribed genes, and secondary DNA structures could impede the normal progression of the replisome and thus have the potential to endanger the integrity of the genome. Multiple studies carried out in different model organisms have demonstrated the capacity of such replisome impediments to favor the formation of heterochromatin. Our review summarizes these reports and discusses the potential role of replication stress in the formation and maintenance of heterochromatin and the role that silencing proteins could play at sites where the integrity of the genome is compromised.
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Cardinale A, Filesi I, Singh PB, Biocca S. Intrabody-mediated diverting of HP1β to the cytoplasm induces co-aggregation of H3-H4 histones and lamin-B receptor. Exp Cell Res 2015; 338:70-81. [PMID: 26364738 DOI: 10.1016/j.yexcr.2015.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 12/12/2022]
Abstract
Diverting a protein from its intracellular location is a unique property of intrabodies. To interfere with the intracellular traffic of heterochromatin protein 1β (HP1β) in living cells, we have generated a cytoplasmic targeted anti-HP1β intrabody, specifically directed against the C-terminal portion of the molecule. HP1β is a conserved component of mouse and human constitutive heterochromatin involved in diverse nuclear functions including gene silencing, DNA repair and nuclear membrane assembly. We found that the anti-HP1β intrabody sequesters HP1β into cytoplasmic aggregates, inhibiting its traffic to the nucleus. Lamin B receptor (LBR) and a subset of core histones (H3/H4) are also specifically co-sequestered in the cytoplasm of anti-HP1β intrabody-expressing cells. Methylated histone H3 at K9 (Me9H3), a marker of constitutive heterochromatin, is not affected by the anti-HP1β intrabody expression. Hyper-acetylating conditions completely dislodge H3 from HP1β:LBR containing aggregates. The expression of anti-HP1β scFv fragments induces apoptosis, associated with an alteration of nuclear morphology. Both these phenotypes are specifically rescued either by overexpression of recombinant full length HP1β or by HP1β mutant containing the chromoshadow domain, but not by recombinant LBR protein. The HP1β-chromodomain mutant, on the other hand, does not rescue the phenotypes, but does compete with LBR for binding to HP1β. These findings provide new insights into the mode of action of cytoplasmic-targeted intrabodies and the interaction between HP1β and its binding partners involved in peripheral heterochromatin organisation.
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Affiliation(s)
- Alessio Cardinale
- Laboratory of Molecular and Cellular Neurobiology, IRCCS San Raffaele Pisana, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Ilaria Filesi
- Department of Systems Medicine, University of Roma Tor Vergata, Via Montpellier 1, 00133 Roma, Italy
| | - Prim B Singh
- Department of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
| | - Silvia Biocca
- Department of Systems Medicine, University of Roma Tor Vergata, Via Montpellier 1, 00133 Roma, Italy.
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48
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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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Mishima Y, Jayasinghe CD, Lu K, Otani J, Shirakawa M, Kawakami T, Kimura H, Hojo H, Carlton P, Tajima S, Suetake I. Nucleosome compaction facilitates HP1γ binding to methylated H3K9. Nucleic Acids Res 2015; 43:10200-12. [PMID: 26319017 PMCID: PMC4666388 DOI: 10.1093/nar/gkv841] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/07/2015] [Indexed: 12/15/2022] Open
Abstract
The α, β and γ isoforms of mammalian heterochromatin protein 1 (HP1) selectively bind to methylated lysine 9 of histone H3 via their chromodomains. Although the phenotypes of HP1-knockout mice are distinct for each isoform, the molecular mechanisms underlying HP1 isoform-specific function remain elusive. In the present study, we found that in contrast to HP1α, HP1γ could not bind tri-methylated H3 lysine 9 in a reconstituted tetra-nucleosomes when the nucleosomes were in an uncompacted state. The hinge region connecting HP1's chromodomain and chromoshadow domain contributed to the distinct recognition of the nucleosomes by HP1α and HP1γ. HP1γ, but not HP1α, was strongly enhanced in selective binding to tri-methylated lysine 9 in histone H3 by the addition of Mg(2+) or linker histone H1, which are known to induce compaction of nucleosomes. We propose that this novel property of HP1γ recognition of lysine 9 in the histone H3 tail in different nucleosome structures plays a role in reading the histone code.
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Affiliation(s)
- Yuichi Mishima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Chanika D Jayasinghe
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kai Lu
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Junji Otani
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Toru Kawakami
- Laboratory of Organic Chemistry, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Hironobu Kimura
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hironobu Hojo
- Laboratory of Organic Chemistry, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Peter Carlton
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
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50
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Aydin E, Kloos DP, Gay E, Jonker W, Hu L, Bullwinkel J, Brown JP, Manukyan M, Giera M, Singh PB, Fundele R. A hypomorphic Cbx3 allele causes prenatal growth restriction and perinatal energy homeostasis defects. J Biosci 2015; 40:325-38. [DOI: 10.1007/s12038-015-9520-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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