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Muhammad A, Sarkadi Z, van Emden T, Mazumder A, Capella M, Fekete G, Sreechakram VNS, Al-Sady B, Papp B, Barrales RR, Braun S. A systematic quantitative approach comprehensively defines domain-specific functional pathways linked to Schizosaccharomyces pombe heterochromatin regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.579970. [PMID: 38405799 PMCID: PMC10888830 DOI: 10.1101/2024.02.13.579970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Heterochromatin plays a critical role in regulating gene expression and maintaining genome integrity. While structural and enzymatic components have been linked to heterochromatin establishment, a comprehensive view of the underlying pathways at diverse heterochromatin domains remains elusive. Here, we developed a systematic approach to identify factors involved in heterochromatin silencing at pericentromeres, subtelomeres, and the silent mating type locus in Schizosaccharomyces pombe. Using quantitative measures, iterative genetic screening, and domain-specific heterochromatin reporters, we identified 369 mutants with different degrees of reduced or enhanced silencing. As expected, mutations in the core heterochromatin machinery globally decreased silencing. However, most other mutants exhibited distinct qualitative and quantitative profiles that indicate domain-specific functions. For example, decreased mating type silencing was linked to mutations in heterochromatin maintenance genes, while compromised subtelomere silencing was associated with metabolic pathways. Furthermore, similar phenotypic profiles revealed shared functions for subunits within complexes. We also discovered that the uncharacterized protein Dhm2 plays a crucial role in maintaining constitutive and facultative heterochromatin, while its absence caused phenotypes akin to DNA replication-deficient mutants. Collectively, our systematic approach unveiled a landscape of domain-specific heterochromatin regulators controlling distinct states and identified Dhm2 as a previously unknown factor linked to heterochromatin inheritance and replication fidelity.
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Affiliation(s)
- Abubakar Muhammad
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Zsuzsa Sarkadi
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Thomas van Emden
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Agnisrota Mazumder
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Matias Capella
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Present address: Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Vishnu N Suma Sreechakram
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Bassem Al-Sady
- Department of Microbiology & Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Ramón Ramos Barrales
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Present address: Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
| | - Sigurd Braun
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
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2
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Colin L, Reyes C, Berthezene J, Maestroni L, Modolo L, Toselli E, Chanard N, Schaak S, Cuvier O, Gachet Y, Coulon S, Bernard P, Tournier S. Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase. eLife 2023; 12:RP89812. [PMID: 37988290 PMCID: PMC10662949 DOI: 10.7554/elife.89812] [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] [Indexed: 11/23/2023] Open
Abstract
The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here, we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.
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Affiliation(s)
- Léonard Colin
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Celine Reyes
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Julien Berthezene
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Laetitia Maestroni
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Laurent Modolo
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Esther Toselli
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Nicolas Chanard
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Stephane Schaak
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Olivier Cuvier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Yannick Gachet
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Stephane Coulon
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Pascal Bernard
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Sylvie Tournier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
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3
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Vaurs M, Naiman K, Bouabboune C, Rai S, Ptasińska K, Rives M, Matmati S, Carr AM, Géli V, Coulon S. Stn1-Ten1 and Taz1 independently promote replication of subtelomeric fragile sequences in fission yeast. Cell Rep 2023; 42:112537. [PMID: 37243596 DOI: 10.1016/j.celrep.2023.112537] [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: 09/15/2022] [Revised: 03/01/2023] [Accepted: 05/03/2023] [Indexed: 05/29/2023] Open
Abstract
Efficient replication of terminal DNA is crucial to maintain telomere stability. In fission yeast, Taz1 and the Stn1-Ten1 (ST) complex play prominent roles in DNA-ends replication. However, their function remains elusive. Here, we have analyzed genome-wide replication and show that ST does not affect genome-wide replication but is crucial for the efficient replication of a subtelomeric region called STE3-2. We further show that, when ST function is compromised, a homologous recombination (HR)-based fork restart mechanism becomes necessary for STE3-2 stability. While both Taz1 and Stn1 bind to STE3-2, we find that the STE3-2 replication function of ST is independent of Taz1 but relies on its association with the shelterin proteins Pot1-Tpz1-Poz1. Finally, we demonstrate that the firing of an origin normally inhibited by Rif1 can circumvent the replication defect of subtelomeres when ST function is compromised. Our results help illuminate why fission yeast telomeres are terminal fragile sites.
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Affiliation(s)
- Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Karel Naiman
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France; Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Chaïnez Bouabboune
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Sudhir Rai
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Katarzyna Ptasińska
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Marion Rives
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Samah Matmati
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Vincent Géli
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France.
| | - Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France.
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4
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Yaseen I, White SA, Torres-Garcia S, Spanos C, Lafos M, Gaberdiel E, Yeboah R, El Karoui M, Rappsilber J, Pidoux AL, Allshire RC. Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance. Nat Struct Mol Biol 2022; 29:745-758. [PMID: 35879419 PMCID: PMC7613290 DOI: 10.1038/s41594-022-00801-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/06/2022] [Indexed: 12/03/2022]
Abstract
Epe1 histone demethylase restricts H3K9-methylation-dependent heterochromatin, preventing it from spreading over, and silencing, gene-containing regions in fission yeast. External stress induces an adaptive response allowing heterochromatin island formation that confers resistance on surviving wild-type lineages. Here we investigate the mechanism by which Epe1 is regulated in response to stress. Exposure to caffeine or antifungals results in Epe1 ubiquitylation and proteasome-dependent removal of the N-terminal 150 residues from Epe1, generating truncated Epe1 (tEpe1) which accumulates in the cytoplasm. Constitutive tEpe1 expression increases H3K9 methylation over several chromosomal regions, reducing expression of underlying genes and enhancing resistance. Reciprocally, constitutive non-cleavable Epe1 expression decreases resistance. tEpe1-mediated resistance requires a functional JmjC demethylase domain. Moreover, caffeine-induced Epe1-to-tEpe1 cleavage is dependent on an intact cell integrity MAP kinase stress signaling pathway, mutations in which alter resistance. Thus, environmental changes elicit a mechanism that curtails the function of this key epigenetic modifier, allowing heterochromatin to reprogram gene expression, thereby bestowing resistance to some cells within a population. H3K9me-heterochromatin components are conserved in human and crop-plant fungal pathogens for which a limited number of antifungals exist. Our findings reveal how transient heterochromatin-dependent antifungal resistant epimutations develop and thus inform on how they might be countered.
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Affiliation(s)
- Imtiyaz Yaseen
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- CSIR Indian Institute of Integrative Medicine, Jammu, India
| | - Sharon A White
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sito Torres-Garcia
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Marcel Lafos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Elisabeth Gaberdiel
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rebecca Yeboah
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Meriem El Karoui
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Alison L Pidoux
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
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5
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Greenstein RA, Ng H, Barrales RR, Tan C, Braun S, Al-Sady B. Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction. PLoS Genet 2022; 18:e1010201. [PMID: 35584134 PMCID: PMC9154106 DOI: 10.1371/journal.pgen.1010201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/31/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022] Open
Abstract
Heterochromatin spreading, the expansion of repressive chromatin structure from sequence-specific nucleation sites, is critical for stable gene silencing. Spreading re-establishes gene-poor constitutive heterochromatin across cell cycles but can also invade gene-rich euchromatin de novo to steer cell fate decisions. How chromatin context (i.e. euchromatic, heterochromatic) or different nucleation pathways influence heterochromatin spreading remains poorly understood. Previously, we developed a single-cell sensor in fission yeast that can separately record heterochromatic gene silencing at nucleation sequences and distal sites. Here we couple our quantitative assay to a genetic screen to identify genes encoding nuclear factors linked to the regulation of heterochromatin nucleation and the distal spreading of gene silencing. We find that mechanisms underlying gene silencing distal to a nucleation site differ by chromatin context. For example, Clr6 histone deacetylase complexes containing the Fkh2 transcription factor are specifically required for heterochromatin spreading at constitutive sites. Fkh2 recruits Clr6 to nucleation-distal chromatin sites in such contexts. In addition, we find that a number of chromatin remodeling complexes antagonize nucleation-distal gene silencing. Our results separate the regulation of heterochromatic gene silencing at nucleation versus distal sites and show that it is controlled by context-dependent mechanisms. The results of our genetic analysis constitute a broad community resource that will support further analysis of the mechanisms underlying the spread of epigenetic silencing along chromatin. Repressive structures, or heterochromatin, are seeded at specific genome sequences and then “spread” to silence nearby chromosomal regions. While much is known about the factors that seed heterochromatin, the genetic requirements for spreading are less clear. We devised a fission yeast single-cell method to examine how gene silencing is propagated by the heterochromatin spreading process specifically. Here we use this platform to ask if specific genes are required for the spreading process and whether the same or different genes direct spreading from different chromosomal seeding sites. We find a significant number of genes that specifically promote or antagonize the heterochromatin spreading process. However, different genes are required to enact spreading from different seeding sites. These results have potential implications for cell fate specification, where genes are newly silenced by heterochromatin spreading from diverse chromosomal sites. In a central finding, we show that the Clr6 protein complex, which removes chromatin marks linked to active genes, associates with the Forkhead 2 transcription factor to promote spreading of silencing structures from seeding sites at numerous chromosomal loci. In contrast, we show that proteins that remodel chromatin antagonize the spreading of gene silencing.
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Affiliation(s)
- R. A. Greenstein
- Department of Microbiology &Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
- TETRAD graduate program, University of California San Francisco, San Francisco, California, United States of America
| | - Henry Ng
- Department of Microbiology &Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
- TETRAD graduate program, University of California San Francisco, San Francisco, California, United States of America
| | - Ramon R. Barrales
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität of Munich, Planegg-Martinsried, Germany
| | - Catherine Tan
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America
- Biomedical Sciences graduate program, University of California San Francisco, San Francisco, California, United States of America
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität of Munich, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Bassem Al-Sady
- Department of Microbiology &Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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6
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Wang L, Wu B, Ma Y, Ren Z, Li W. The blooming of an old story on the bouquet. Biol Reprod 2022; 107:289-300. [PMID: 35470849 DOI: 10.1093/biolre/ioac075] [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: 12/27/2021] [Revised: 03/09/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
As an evolutionarily conserved process, the bouquet stage during meiosis was discovered over a century ago, and active research on this important stage continues. Since the discovery of the first bouquet-related protein Taz1p in 1998, several bouquet formation-related proteins have been identified in various eukaryotes. These proteins are involved in the interaction between telomeres and the inner nuclear membrane (INM), and once these interactions are disrupted, meiotic progression is arrested, leading to infertility. Recent studies have provided significant insights into the relationships and interactions among bouquet formation-related proteins. In this review, we summarize the components involved in telomere-INM interactions and focus on their roles in bouquet formation and telomere homeostasis maintenance. In addition, we examined bouquet-related proteins in different species from an evolutionary viewpoint, highlighting the potential interactions among them.
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Affiliation(s)
- Lina Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Department of Respiratory, China National Clinical Research Center of Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Bingbing Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjie Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengxing Ren
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,Institute of Reproductive Health and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
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7
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Feng S, Ma S, Li K, Gao S, Ning S, Shang J, Guo R, Chen Y, Blumenfeld B, Simon I, Li Q, Guo R, Xu D. RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity. Nat Commun 2022; 13:957. [PMID: 35177609 PMCID: PMC8854732 DOI: 10.1038/s41467-022-28588-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 02/01/2022] [Indexed: 11/12/2022] Open
Abstract
The 53BP1-RIF1 pathway antagonizes resection of DNA broken ends and confers PARP inhibitor sensitivity on BRCA1-mutated tumors. However, it is unclear how this pathway suppresses initiation of resection. Here, we identify ASF1 as a partner of RIF1 via an interacting manner similar to its interactions with histone chaperones CAF-1 and HIRA. ASF1 is recruited to distal chromatin flanking DNA breaks by 53BP1-RIF1 and promotes non-homologous end joining (NHEJ) using its histone chaperone activity. Epistasis analysis shows that ASF1 acts in the same NHEJ pathway as RIF1, but via a parallel pathway with the shieldin complex, which suppresses resection after initiation. Moreover, defects in end resection and homologous recombination (HR) in BRCA1-deficient cells are largely suppressed by ASF1 deficiency. Mechanistically, ASF1 compacts adjacent chromatin by heterochromatinization to protect broken DNA ends from BRCA1-mediated resection. Taken together, our findings identify a RIF1-ASF1 histone chaperone complex that promotes changes in high-order chromatin structure to stimulate the NHEJ pathway for DSB repair. The 53BP1-RIF1 pathway is important for DNA repair. Here, the authors identified the histone chaperone ASF1, which functions as a suppressor of DNA end resection through changing high-order chromatin structure, as a partner of RIF1. This finding links DNA repair and dynamic changes of high-order chromatin structure.
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Affiliation(s)
- Sumin Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Sai Ma
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Kejiao Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Shengxian Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Shaokai Ning
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Jinfeng Shang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Ruiyuan Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Yingying Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Rong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China.
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8
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Faber MW, Vo TV. Long RNA-Mediated Chromatin Regulation in Fission Yeast and Mammals. Int J Mol Sci 2022; 23:968. [PMID: 35055152 PMCID: PMC8778201 DOI: 10.3390/ijms23020968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
As part of a complex network of genome control, long regulatory RNAs exert significant influences on chromatin dynamics. Understanding how this occurs could illuminate new avenues for disease treatment and lead to new hypotheses that would advance gene regulatory research. Recent studies using the model fission yeast Schizosaccharomyces pombe (S. pombe) and powerful parallel sequencing technologies have provided many insights in this area. This review will give an overview of key findings in S. pombe that relate long RNAs to multiple levels of chromatin regulation: histone modifications, gene neighborhood regulation in cis and higher-order chromosomal ordering. Moreover, we discuss parallels recently found in mammals to help bridge the knowledge gap between the study systems.
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Affiliation(s)
| | - Tommy V. Vo
- Department of Biochemistry and Molecular Biology, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA;
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9
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Enervald E, Powell LM, Boteva L, Foti R, Blanes Ruiz N, Kibar G, Piszczek A, Cavaleri F, Vingron M, Cerase A, Buonomo SBC. RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes. EMBO J 2021; 40:e105862. [PMID: 34786738 DOI: 10.15252/embj.2020105862] [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: 06/07/2020] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/09/2022] Open
Abstract
The onset of random X chromosome inactivation in mouse requires the switch from a symmetric to an asymmetric state, where the identities of the future inactive and active X chromosomes are assigned. This process is known as X chromosome choice. Here, we show that RIF1 and KAP1 are two fundamental factors for the definition of this transcriptional asymmetry. We found that at the onset of differentiation of mouse embryonic stem cells (mESCs), biallelic up-regulation of the long non-coding RNA Tsix weakens the symmetric association of RIF1 with the Xist promoter. The Xist allele maintaining the association with RIF1 goes on to up-regulate Xist RNA expression in a RIF1-dependent manner. Conversely, the promoter that loses RIF1 gains binding of KAP1, and KAP1 is required for the increase in Tsix levels preceding the choice. We propose that the mutual exclusion of Tsix and RIF1, and of RIF1 and KAP1, at the Xist promoters establish a self-sustaining loop that transforms an initially stochastic event into a stably inherited asymmetric X-chromosome state.
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Affiliation(s)
- Elin Enervald
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Lynn Marie Powell
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Lora Boteva
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rossana Foti
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Nerea Blanes Ruiz
- Blizard Institute, Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Gözde Kibar
- Max-Planck-Institut fuer molekulare Genetik, Berlin, Germany
| | - Agnieszka Piszczek
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Fatima Cavaleri
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
| | - Martin Vingron
- Max-Planck-Institut fuer molekulare Genetik, Berlin, Germany
| | - Andrea Cerase
- Blizard Institute, Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sara B C Buonomo
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy
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10
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Subtelomeric Chromatin in the Fission Yeast S. pombe. Microorganisms 2021; 9:microorganisms9091977. [PMID: 34576871 PMCID: PMC8466458 DOI: 10.3390/microorganisms9091977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 01/15/2023] Open
Abstract
Telomeres play important roles in safeguarding the genome. The specialized repressive chromatin that assembles at telomeres and subtelomeric domains is key to this protective role. However, in many organisms, the repetitive nature of telomeric and subtelomeric sequences has hindered research efforts. The fission yeast S. pombe has provided an important model system for dissection of chromatin biology due to the relative ease of genetic manipulation and strong conservation of important regulatory proteins with higher eukaryotes. Telomeres and the telomere-binding shelterin complex are highly conserved with mammals, as is the assembly of constitutive heterochromatin at subtelomeres. In this review, we seek to summarize recent work detailing the assembly of distinct chromatin structures within subtelomeric domains in fission yeast. These include the heterochromatic SH subtelomeric domains, the telomere-associated sequences (TAS), and ST chromatin domains that assemble highly condensed chromatin clusters called knobs. Specifically, we review new insights into the sequence of subtelomeric domains, the distinct types of chromatin that assemble on these sequences and how histone H3 K36 modifications influence these chromatin structures. We address the interplay between the subdomains of chromatin structure and how subtelomeric chromatin is influenced by both the telomere-bound shelterin complexes and by euchromatic chromatin regulators internal to the subtelomeric domain. Finally, we demonstrate that telomere clustering, which is mediated via the condensed ST chromatin knob domains, does not depend on knob assembly within these domains but on Set2, which mediates H3K36 methylation.
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11
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Liu J, Hu X, Bao K, Kim JK, Zhang C, Jia S, Qiao F. The cooperative assembly of shelterin bridge provides a kinetic gateway that controls telomere length homeostasis. Nucleic Acids Res 2021; 49:8110-8119. [PMID: 34255844 PMCID: PMC8373121 DOI: 10.1093/nar/gkab550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 11/14/2022] Open
Abstract
Shelterin is a six-protein complex that coats chromosome ends to ensure their proper protection and maintenance. Similar to the human shelterin, fission yeast shelterin is composed of telomeric double- and single-stranded DNA-binding proteins, Taz1 and Pot1, respectively, bridged by Rap1, Poz1 and Tpz1. The assembly of the proteinaceous Tpz1-Poz1-Rap1 complex occurs cooperatively and disruption of this shelterin bridge leads to unregulated telomere elongation. However, how this biophysical property of bridge assembly is integrated into shelterin function is not known. Here, utilizing synthetic bridges with a range of binding properties, we find that synthetic shelterin bridge lacking cooperativity requires a linker pair that matches the native bridge in complex lifespan but has dramatically higher affinity. We find that cooperative assembly confers kinetic properties on the shelterin bridge allowing disassembly to function as a molecular timer, regulating the duration of the telomere open state, and consequently telomere lengthening to achieve a defined species-specific length range.
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Affiliation(s)
- Jinqiang Liu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Xichan Hu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Kehan Bao
- Department of Biological Sciences, Columbia University, New York City, NY 92697-4560, USA
| | - Jin-Kwang Kim
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Catherine Zhang
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York City, NY 92697-4560, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
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12
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Repair pathway choice for double-strand breaks. Essays Biochem 2021; 64:765-777. [PMID: 32648897 DOI: 10.1042/ebc20200007] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) is at a constant risk of damage from endogenous substances, environmental radiation, and chemical stressors. DNA double-strand breaks (DSBs) pose a significant threat to genomic integrity and cell survival. There are two major pathways for DSB repair: nonhomologous end-joining (NHEJ) and homologous recombination (HR). The extent of DNA end resection, which determines the length of the 3' single-stranded DNA (ssDNA) overhang, is the primary factor that determines whether repair is carried out via NHEJ or HR. NHEJ, which does not require a 3' ssDNA tail, occurs throughout the cell cycle. 53BP1 and the cofactors PTIP or RIF1-shieldin protect the broken DNA end, inhibit long-range end resection and thus promote NHEJ. In contrast, HR mainly occurs during the S/G2 phase and requires DNA end processing to create a 3' tail that can invade a homologous region, ensuring faithful gene repair. BRCA1 and the cofactors CtIP, EXO1, BLM/DNA2, and the MRE11-RAD50-NBS1 (MRN) complex promote DNA end resection and thus HR. DNA resection is influenced by the cell cycle, the chromatin environment, and the complexity of the DNA end break. Herein, we summarize the key factors involved in repair pathway selection for DSBs and discuss recent related publications.
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13
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Spreading and epigenetic inheritance of heterochromatin require a critical density of histone H3 lysine 9 tri-methylation. Proc Natl Acad Sci U S A 2021; 118:2100699118. [PMID: 34035174 PMCID: PMC8179192 DOI: 10.1073/pnas.2100699118] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In multicellular organisms, a single genome gives rise to a multitude of cell types by enforcing appropriate gene expression patterns. Epigenetic mechanisms involving modification of histones, including tri-methylation of histone H3 lysine 9 (H3K9me3), assemble and propagate repressive heterochromatin to prevent untimely gene expression. Dysregulation of epigenetic gene-silencing mechanisms is a hallmark of a variety of diseases including cancer. However, the requirements for epigenetic transmission of heterochromatin are not well understood. This study reveals the mechanism by which methylated histones provide an epigenetic template for heterochromatin propagation. We discover that a critical threshold of H3K9me3 is required for effective chromatin-association of the histone methyltransferase, which binds to and catalyzes additional H3K9me to propagate heterochromatin and enforce stable gene silencing. Heterochromatin assembly requires methylation of histone H3 lysine 9 (H3K9me) and serves as a paradigm for understanding the importance of histone modifications in epigenetic genome control. Heterochromatin is nucleated at specific genomic sites and spreads across extended chromosomal domains to promote gene silencing. Moreover, heterochromatic structures can be epigenetically inherited in a self-templating manner, which is critical for stable gene repression. The spreading and inheritance of heterochromatin are believed to be dependent on preexisting H3K9 tri-methylation (H3K9me3), which is recognized by the histone methyltransferase Clr4/Suv39h via its chromodomain, to promote further deposition of H3K9me. However, the process involving the coupling of the “read” and “write” capabilities of histone methyltransferases is poorly understood. From an unbiased genetic screen, we characterize a dominant-negative mutation in histone H3 (H3G13D) that impairs the propagation of endogenous and ectopic heterochromatin domains in the fission yeast genome. H3G13D blocks methylation of H3K9 by the Clr4/Suv39h methyltransferase and acts in a dosage-dependent manner to interfere with the spreading and maintenance of heterochromatin. Our analyses show that the incorporation of unmethylatable histone H3G13D into chromatin decreases H3K9me3 density and thereby compromises the read-write capability of Clr4/Suv39h. Consistently, enhancing the affinity of Clr4/Suv39h for methylated H3K9 is sufficient to overcome the defects in heterochromatin assembly caused by H3G13D. Our work directly implicates methylated histones in the transmission of epigenetic memory and shows that a critical density threshold of H3K9me3 is required to promote epigenetic inheritance of heterochromatin through the read-write mechanism.
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14
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Gnan S, Flyamer IM, Klein KN, Castelli E, Rapp A, Maiser A, Chen N, Weber P, Enervald E, Cardoso MC, Bickmore WA, Gilbert DM, Buonomo SCB. Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction. Nat Commun 2021; 12:2910. [PMID: 34006872 PMCID: PMC8131703 DOI: 10.1038/s41467-021-22899-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing programme and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. The role of RIF1 in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing programme and nuclear architecture.
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Affiliation(s)
- Stefano Gnan
- grid.418924.20000 0004 0627 3632Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy ,grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK ,grid.462584.90000 0004 0367 1475Present Address: Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Ilya M. Flyamer
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kyle N. Klein
- grid.255986.50000 0004 0472 0419Department of Biological Science, Florida State University, Tallahassee, FL USA
| | - Eleonora Castelli
- grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Alexander Rapp
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Andreas Maiser
- grid.5252.00000 0004 1936 973XDepartment of Biology II, LMU Munich, Munich, Germany
| | - Naiming Chen
- grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK
| | - Patrick Weber
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Elin Enervald
- grid.418924.20000 0004 0627 3632Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy ,grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK ,grid.10548.380000 0004 1936 9377Present Address: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - M. Cristina Cardoso
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Wendy A. Bickmore
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David M. Gilbert
- grid.255986.50000 0004 0472 0419Department of Biological Science, Florida State University, Tallahassee, FL USA
| | - Sara C. B. Buonomo
- grid.418924.20000 0004 0627 3632Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy ,grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK
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15
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Bauwens S, Lototska L, Koundrioukoff S, Debatisse M, Ye J, Gilson E, Mendez-Bermudez A. The Telomeric Protein TRF2 Regulates Replication Origin Activity within Pericentromeric Heterochromatin. Life (Basel) 2021; 11:life11040267. [PMID: 33804994 PMCID: PMC8063955 DOI: 10.3390/life11040267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Heterochromatic regions render the replication process particularly difficult due to the high level of chromatin compaction and the presence of repeated DNA sequences. In humans, replication through pericentromeric heterochromatin requires the binding of a complex formed by the telomeric factor TRF2 and the helicase RTEL1 in order to relieve topological barriers blocking fork progression. Since TRF2 is known to bind the Origin Replication Complex (ORC), we hypothesized that this factor could also play a role at the replication origins (ORI) of these heterochromatin regions. By performing DNA combing analysis, we found that the ORI density is higher within pericentromeric satellite DNA repeats than within bulk genomic DNA and decreased upon TRF2 downregulation. Moreover, we showed that TRF2 and ORC2 interact in pericentromeric DNA, providing a mechanism by which TRF2 is involved in ORI activity. Altogether, our findings reveal an essential role for TRF2 in pericentromeric heterochromatin replication by regulating both replication initiation and elongation.
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Affiliation(s)
- Serge Bauwens
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
| | - Liudmyla Lototska
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
| | - Stephane Koundrioukoff
- Institut Gustave Roussy, Sorbonne Université, UPMC University, 94805 Villejuif, France; (S.K.); (M.D.)
| | - Michelle Debatisse
- Institut Gustave Roussy, Sorbonne Université, UPMC University, 94805 Villejuif, France; (S.K.); (M.D.)
| | - Jing Ye
- International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| | - Eric Gilson
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
- International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
- Correspondence: (E.G.); (A.M.-B.)
| | - Aaron Mendez-Bermudez
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
- International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
- Correspondence: (E.G.); (A.M.-B.)
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16
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Weigt M, Gao Q, Ban H, He H, Mastrobuoni G, Kempa S, Chen W, Li F. Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex. Epigenetics Chromatin 2021; 14:8. [PMID: 33468217 PMCID: PMC7816512 DOI: 10.1186/s13072-021-00382-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/08/2021] [Indexed: 01/13/2023] Open
Abstract
Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses indicated that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodelers known to be important for heterochromatin silencing. Deletion of Rbm10 results in significant reduction of Clr6 in heterochromatin. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation.
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Affiliation(s)
- Martina Weigt
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Hyoju Ban
- Department of Biology, New York University, New York, NY, 10003-6688, USA
| | - Haijin He
- Department of Biology, New York University, New York, NY, 10003-6688, USA
| | - Guido Mastrobuoni
- Integrative Metabolomics and Proteomics, Berlin Institute of Medical Systems Biology, Max-Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Stefan Kempa
- Integrative Metabolomics and Proteomics, Berlin Institute of Medical Systems Biology, Max-Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Wei Chen
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany. .,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China. .,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Fei Li
- Department of Biology, New York University, New York, NY, 10003-6688, USA.
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17
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Epigenetic gene silencing by heterochromatin primes fungal resistance. Nature 2020; 585:453-458. [PMID: 32908306 PMCID: PMC7116710 DOI: 10.1038/s41586-020-2706-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 06/12/2020] [Indexed: 12/27/2022]
Abstract
Heterochromatin that depends on histone H3 lysine 9 methylation (H3K9me) renders embedded genes transcriptionally silent1-3. In the fission yeast Schizosaccharomyces pombe, H3K9me heterochromatin can be transmitted through cell division provided the counteracting demethylase Epe1 is absent4,5. Heterochromatin heritability might allow wild-type cells under certain conditions to acquire epimutations, which could influence phenotype through unstable gene silencing rather than DNA change6,7. Here we show that heterochromatin-dependent epimutants resistant to caffeine arise in fission yeast grown with threshold levels of caffeine. Isolates with unstable resistance have distinct heterochromatin islands with reduced expression of embedded genes, including some whose mutation confers caffeine resistance. Forced heterochromatin formation at implicated loci confirms that resistance results from heterochromatin-mediated silencing. Our analyses reveal that epigenetic processes promote phenotypic plasticity, letting wild-type cells adapt to unfavourable environments without genetic alteration. In some isolates, subsequent or coincident gene-amplification events augment resistance. Caffeine affects two anti-silencing factors: Epe1 is downregulated, reducing its chromatin association, and a shortened isoform of Mst2 histone acetyltransferase is expressed. Thus, heterochromatin-dependent epimutation provides a bet-hedging strategy allowing cells to adapt transiently to insults while remaining genetically wild type. Isolates with unstable caffeine resistance show cross-resistance to antifungal agents, suggesting that related heterochromatin-dependent processes may contribute to resistance of plant and human fungal pathogens to such agents.
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18
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Vo TV, Dhakshnamoorthy J, Larkin M, Zofall M, Thillainadesan G, Balachandran V, Holla S, Wheeler D, Grewal SIS. CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing. Cell Rep 2020; 28:267-281.e5. [PMID: 31269446 DOI: 10.1016/j.celrep.2019.05.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/16/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic genomes, heterochromatin is targeted by RNAi machinery and/or by pathways requiring RNA elimination and transcription termination factors. However, a direct connection between termination machinery and RNA polymerase II (RNAPII) transcriptional activity at heterochromatic loci has remained elusive. Here, we show that, in fission yeast, the conserved cleavage and polyadenylation factor (CPF) is a key component involved in RNAi-independent assembly of constitutive and facultative heterochromatin domains and that CPF is broadly required to silence genes regulated by Clr4SUV39H. Remarkably, CPF is recruited to non-canonical termination sites within the body of genes by the YTH family RNA-binding protein Mmi1 and is required for RNAPII transcription termination and facultative heterochromatin assembly. CPF loading by Mmi1 also promotes the selective termination of long non-coding RNAs that regulate gene expression in cis. These analyses delineate a mechanism in which CPF loaded onto non-canonical termination sites specifies targets of heterochromatin assembly and gene silencing.
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Affiliation(s)
- Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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19
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Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D. Trends Genet 2020; 36:967-980. [PMID: 32713597 DOI: 10.1016/j.tig.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication is regulated in time and space through DNA-associated trans-acting factors, diffusible limiting replication initiation factors, higher-order chromatin folding, dynamic origin localization, and specific nuclear microenvironments. We present an integrated model for the regulation of DNA replication in 3D and highlight the importance of accurate spatio-temporal regulation of DNA replication in physiology and disease.
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20
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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin. Sci Rep 2020; 10:6055. [PMID: 32269268 PMCID: PMC7142091 DOI: 10.1038/s41598-020-63209-y] [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: 07/05/2019] [Accepted: 03/26/2020] [Indexed: 01/24/2023] Open
Abstract
Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
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Mendez-Bermudez A, Giraud-Panis MJ, Ye J, Gilson E. Heterochromatin replication goes hand in hand with telomere protection. Nat Struct Mol Biol 2020; 27:313-318. [PMID: 32231287 DOI: 10.1038/s41594-020-0400-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/21/2020] [Indexed: 12/25/2022]
Abstract
Telomeres arose from the need to stabilize natural chromosome ends, resulting in terminal chromatin structures with specific protective functions. Their constituent proteins also execute general functions within heterochromatin, mediating late replication and facilitating fork progression. Emerging insights into the mechanisms governing heterochromatin replication suggest telomeres and heterochromatin act in concert during development and aging. They also suggest a common evolutionary origin for these two chromosome regions that arose during eukaryogenesis.
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Affiliation(s)
- Aaron Mendez-Bermudez
- School of Medicine, CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France.,International Research Laboratory for Hematology, Cancer and Aging, Shanghai Ruijin Hospital, Shanghai Jiaotong University and Côte-d'Azur University, Shanghai, China
| | | | - Jing Ye
- International Research Laboratory for Hematology, Cancer and Aging, Shanghai Ruijin Hospital, Shanghai Jiaotong University and Côte-d'Azur University, Shanghai, China.
| | - Eric Gilson
- School of Medicine, CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France. .,International Research Laboratory for Hematology, Cancer and Aging, Shanghai Ruijin Hospital, Shanghai Jiaotong University and Côte-d'Azur University, Shanghai, China. .,Department of Genetics, CHU Nice, Nice, France.
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Mutation in histone deacetylase clr6 promotes the survival of S. pombe cds1 null mutant in response to hydroxyurea. Mol Genet Genomics 2020; 295:695-703. [PMID: 32124033 DOI: 10.1007/s00438-020-01655-z] [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: 09/26/2019] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
Abstract
Fission yeast Cds1 is responsible for the replication checkpoint activation and helps to protect replication fork collapse in response to hydroxyurea (HU). Here, we investigated the role of histone deacetylase in response to replication fork arrest and observed that in the presence of HU, the survival of cds1Δ cells was improved when the cells were simultaneously treated with histone deacetylase inhibitors. Furthermore, a mutation in the histone deacetylase gene, clr6, also suppresses the growth defect of cds1Δ cells in response to HU indicating a suppressive role of clr6-1 mutation in cds1 deletion background upon HU treatment. Interestingly, in response to HU, phosphorylation of Chk1 kinase and the number of Rad52YFP foci was reduced in cds1Δ clr6-1 double mutant as compared to cds1Δ single mutant indicating a decrease in the level of DNA damage in response to HU. Accordingly, the single-cell gel electrophoresis assay revealed a drastic reduction in the tail length of cds1Δ clr6-1 double mutant as compared to cds1Δ cells in the presence of HU suggesting the suppression of chromosomal defects in the double mutant. Taken together, we proposed that there could be transient suppression of fork collapse in cds1Δ clr6-1 double mutant upon HU treatment due to the delay in mitotic progression that leads to the facilitation of cell growth.
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Sorida M, Murakami Y. Unprogrammed epigenetic variation mediated by stochastic formation of ectopic heterochromatin. Curr Genet 2019; 66:319-325. [PMID: 31598751 DOI: 10.1007/s00294-019-01031-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/09/2023]
Abstract
Changes in gene expression via chromatin-mediated mechanisms are important for reprogramming and differentiation, but uncontrolled changes can potentially lead to harmful or adaptive phenotypic alteration. Thus, diversification of the genome-wide chromatin state must be strictly limited, but the underlying mechanism of this regulation is largely unknown. In this review, we focused on distribution of heterochromatin, a tight chromatin structure that negatively regulates gene expression. Heterochromatin is characterized by methylation of histone H3 at lysine 9, and its formation and spreading are controlled by H3K9-specific methyltransferases and reversal factors such as histone demethylases. We summarize recent findings and discuss how variability in the heterochromatin distribution is controlled in the unicellular eukaryote fission yeast. In this context, we recently found that the anti-silencing factor Epe1 plays a key role in the formation of the individual-specific heterochromatin distribution. In conclusion, recent studies revealed that there are many potential heterochromatin formation sites in the fission yeast genome, and several proteins contribute to suppression of spreading and genome-wide dispersal of heterochromatin; knowledge from fission yeast studies may provide insights into the mechanisms regulating epigenetic diversification in multicellular eukaryotes.
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Affiliation(s)
- Masato Sorida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yota Murakami
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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Folco HD, McCue A, Balachandran V, Grewal SIS. Cohesin Impedes Heterochromatin Assembly in Fission Yeast Cells Lacking Pds5. Genetics 2019; 213:127-141. [PMID: 31278118 PMCID: PMC6727797 DOI: 10.1534/genetics.119.302256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/24/2019] [Indexed: 01/05/2023] Open
Abstract
The fission yeast Schizosaccharomyces pombe is a powerful genetic model system for uncovering fundamental principles of heterochromatin assembly and epigenetic inheritance of chromatin states. Heterochromatin defined by histone H3 lysine 9 methylation and HP1 proteins coats large chromosomal domains at centromeres, telomeres, and the mating-type (mat) locus. Although genetic and biochemical studies have provided valuable insights into heterochromatin assembly, many key mechanistic details remain unclear. Here, we use a sensitized reporter system at the mat locus to screen for factors affecting heterochromatic silencing. In addition to known components of heterochromatin assembly pathways, our screen identified eight new factors including the cohesin-associated protein Pds5. We find that Pds5 enriched throughout heterochromatin domains is required for proper maintenance of heterochromatin. This function of Pds5 requires its associated Eso1 acetyltransferase, which is implicated in the acetylation of cohesin. Indeed, introducing an acetylation-mimicking mutation in a cohesin subunit suppresses defects in heterochromatin assembly in pds5∆ and eso1∆ cells. Our results show that in cells lacking Pds5, cohesin interferes with heterochromatin assembly. Supporting this, eliminating cohesin from the mat locus in the pds5∆ mutant restores both heterochromatin assembly and gene silencing. These analyses highlight an unexpected requirement for Pds5 in ensuring proper coordination between cohesin and heterochromatin factors to effectively maintain gene silencing.
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Affiliation(s)
- H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrea McCue
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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Cubiles MD, Barroso S, Vaquero-Sedas MI, Enguix A, Aguilera A, Vega-Palas MA. Epigenetic features of human telomeres. Nucleic Acids Res 2019; 46:2347-2355. [PMID: 29361030 PMCID: PMC5861411 DOI: 10.1093/nar/gky006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/09/2018] [Indexed: 01/02/2023] Open
Abstract
Although subtelomeric regions in humans are heterochromatic, the epigenetic nature of human telomeres remains controversial. This controversy might have been influenced by the confounding effect of subtelomeric regions and interstitial telomeric sequences (ITSs) on telomeric chromatin structure analyses. In addition, different human cell lines might carry diverse epigenetic marks at telomeres. We have developed a reliable procedure to study the chromatin structure of human telomeres independently of subtelomeres and ITSs. This procedure is based on the statistical analysis of multiple ChIP-seq experiments. We have found that human telomeres are not enriched in the heterochromatic H3K9me3 mark in most of the common laboratory cell lines, including embryonic stem cells. Instead, they are labeled with H4K20me1 and H3K27ac, which might be established by p300. These results together with previously published data argue that subtelomeric heterochromatin might control human telomere functions. Interestingly, U2OS cells that exhibit alternative lengthening of telomeres have heterochromatic levels of H3K9me3 in their telomeres.
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Affiliation(s)
- María D Cubiles
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, 41012 Seville, Spain
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avd. Américo Vespucio s/n, 41092 Seville, Spain
| | - María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Avd. Américo Vespucio n° 49, 41092 Seville, Spain
| | - Alicia Enguix
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avd. Américo Vespucio s/n, 41092 Seville, Spain
| | - Miguel A Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Avd. Américo Vespucio n° 49, 41092 Seville, Spain
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Telomere DNA length-dependent regulation of DNA replication timing at internal late replication origins. Sci Rep 2019; 9:9946. [PMID: 31289327 PMCID: PMC6617677 DOI: 10.1038/s41598-019-46229-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
DNA replication is initiated at replication origins on chromosomes at their scheduled time during S phase of the cell cycle. Replication timing control is highly conserved among eukaryotes but the underlying mechanisms are not fully understood. Recent studies have revealed that some telomere-binding proteins regulate replication timing at late-replicating origins throughout the genome. To investigate the molecular basis of this process, we analyzed the effects of excessive elongation of telomere DNA on replication timing by deleting telomere-associated shelterin proteins in Schizosaccharomyces pombe. We found that rap1∆ and poz1∆ cells showed abnormally accelerated replication at internal late origins but not at subtelomere regions. These defects were suppressed by removal of telomere DNA and by deletion of the telomere-binding protein Taz1. Furthermore, Sds21—a counter protein phosphatase against Dbf4-dependent kinase (DDK)—accumulated at elongated telomeres in a Taz1-dependent manner but was depleted at internal late origins, indicating that highly elongated telomeres sequester Sds21 at telomeres and perturb replication timing at internal regions. These results demonstrate that telomere DNA length is an important determinant of replication timing at internal regions of chromosomes in eukaryotes.
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Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1. PLoS Genet 2019; 15:e1008129. [PMID: 31206516 PMCID: PMC6576747 DOI: 10.1371/journal.pgen.1008129] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 04/09/2019] [Indexed: 01/28/2023] Open
Abstract
H3K9 methylation (H3K9me) is a conserved marker of heterochromatin, a transcriptionally silent chromatin structure. Knowledge of the mechanisms for regulating heterochromatin distribution is limited. The fission yeast JmjC domain-containing protein Epe1 localizes to heterochromatin mainly through its interaction with Swi6, a homologue of heterochromatin protein 1 (HP1), and directs JmjC-mediated H3K9me demethylation in vivo. Here, we found that loss of epe1 (epe1Δ) induced a red-white variegated phenotype in a red-pigment accumulation background that generated uniform red colonies. Analysis of isolated red and white colonies revealed that silencing of genes involved in pigment accumulation by stochastic ectopic heterochromatin formation led to white colony formation. In addition, genome-wide analysis of red- and white-isolated clones revealed that epe1Δ resulted in a heterogeneous heterochromatin distribution among clones. We found that Epe1 had an N-terminal domain distinct from its JmjC domain, which activated transcription in both fission and budding yeasts. The N-terminal transcriptional activation (NTA) domain was involved in suppression of ectopic heterochromatin-mediated red-white variegation. We introduced a single copy of Epe1 into epe1Δ clones harboring ectopic heterochromatin, and found that Epe1 could reduce H3K9me from ectopic heterochromatin but some of the heterochromatin persisted. This persistence was due to a latent H3K9me source embedded in ectopic heterochromatin. Epe1H297A, a canonical JmjC mutant, suppressed red-white variegation, but entirely failed to remove already-established ectopic heterochromatin, suggesting that Epe1 prevented stochastic de novo deposition of ectopic H3K9me in an NTA-dependent but JmjC-independent manner, while its JmjC domain mediated removal of H3K9me from established ectopic heterochromatin. Our results suggest that Epe1 not only limits the distribution of heterochromatin but also controls the balance between suppression and retention of heterochromatin-mediated epigenetic diversification. Suppression of unscheduled epigenetic alterations is important for maintenance of homogeneity among clones, while emergence of epigenetic differences is also important for adaptation or differentiation. The mechanisms that balance both processes warrant further investigation. Epe1, a fission yeast JmjC domain-containing protein, is thought to be an H3K9me demethylase that targets ectopic heterochromatin via its JmjC-dependent demethylation function. Here we found that loss of epe1 induced stochastic ectopic heterochromatin formation genome-wide, suggesting that the fission yeast genome had multiple potential heterochromatin formation sites, which were protected by Epe1. We found that Epe1 prevented deposition of ectopic H3K9me independently of its JmjC-mediated demethylation before heterochromatin establishment. By contrast, Epe1 could attack already-established ectopic heterochromatin via its JmjC domain, but demethylation was not 100% effective, which provided a basis for epigenetic variation. Together, our findings indicate that Epe1 is involved in both maintenance and alteration of heterochromatin distribution, and shed light on the mechanisms controlling individual-specific epigenome profiles.
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28
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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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29
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TASks for subtelomeres: when nucleosome loss and genome instability are favored. Curr Genet 2019; 65:1153-1160. [DOI: 10.1007/s00294-019-00986-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022]
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van Emden TS, Forn M, Forné I, Sarkadi Z, Capella M, Martín Caballero L, Fischer-Burkart S, Brönner C, Simonetta M, Toczyski D, Halic M, Imhof A, Braun S. Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability. EMBO Rep 2018; 20:embr.201847181. [PMID: 30420521 DOI: 10.15252/embr.201847181] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/03/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Telomeres and the shelterin complex cap and protect the ends of chromosomes. Telomeres are flanked by the subtelomeric sequences that have also been implicated in telomere regulation, although their role is not well defined. Here, we show that, in Schizosaccharomyces pombe, the telomere-associated sequences (TAS) present on most subtelomeres are hyper-recombinogenic, have metastable nucleosomes, and unusual low levels of H3K9 methylation. Ccq1, a subunit of shelterin, protects TAS from nucleosome loss by recruiting the heterochromatic repressor complexes CLRC and SHREC, thereby linking nucleosome stability to gene silencing. Nucleosome instability at TAS is independent of telomeric repeats and can be transmitted to an intrachromosomal locus containing an ectopic TAS fragment, indicating that this is an intrinsic property of the underlying DNA sequence. When telomerase recruitment is compromised in cells lacking Ccq1, DNA sequences present in the TAS promote recombination between chromosomal ends, independent of nucleosome abundance, implying an active function of these sequences in telomere maintenance. We propose that Ccq1 and fragile subtelomeres co-evolved to regulate telomere plasticity by controlling nucleosome occupancy and genome stability.
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Affiliation(s)
- Thomas S van Emden
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, Martinsried, Germany
| | - Marta Forn
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Ignasi Forné
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Zsuzsa Sarkadi
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Matías Capella
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Lucía Martín Caballero
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, Martinsried, Germany
| | - Sabine Fischer-Burkart
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Cornelia Brönner
- Department of Biochemistry, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany
| | - Marco Simonetta
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - David Toczyski
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Mario Halic
- Department of Biochemistry, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit (ZfP), BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Sigurd Braun
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig Maximilians University of Munich, Martinsried, Germany .,International Max Planck Research School for Molecular and Cellular Life Sciences, Martinsried, Germany
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Ogawa S, Kido S, Handa T, Ogawa H, Asakawa H, Takahashi TS, Nakagawa T, Hiraoka Y, Masukata H. Shelterin promotes tethering of late replication origins to telomeres for replication-timing control. EMBO J 2018; 37:embj.201898997. [PMID: 29997179 DOI: 10.15252/embj.201898997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/19/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
DNA replication initiates at many discrete loci on eukaryotic chromosomes, and individual replication origins are regulated under a spatiotemporal program. However, the underlying mechanisms of this regulation remain largely unknown. In the fission yeast Schizosaccharomyces pombe, the telomere-binding protein Taz1, ortholog of human TRF1/TRF2, regulates a subset of late replication origins by binding to the telomere-like sequence near the origins. Here, we showed using a lacO/LacI-GFP system that Taz1-dependent late origins were predominantly localized at the nuclear periphery throughout interphase, and were localized adjacent to the telomeres in the G1/S phase. The peripheral localization that depended on the nuclear membrane protein Bqt4 was not necessary for telomeric association and replication-timing control of the replication origins. Interestingly, the shelterin components Rap1 and Poz1 were required for replication-timing control and telomeric association of Taz1-dependent late origins, and this requirement was bypassed by a minishelterin Tpz1-Taz1 fusion protein. Our results suggest that Taz1 suppresses replication initiation through shelterin-mediated telomeric association of the origins at the onset of S phase.
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Affiliation(s)
- Shiho Ogawa
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Sayuri Kido
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Tetsuya Handa
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Hidesato Ogawa
- Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
| | | | - Takuro Nakagawa
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
| | - Hisao Masukata
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan .,Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
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Seller CA, O’Farrell PH. Rif1 prolongs the embryonic S phase at the Drosophila mid-blastula transition. PLoS Biol 2018; 16:e2005687. [PMID: 29746464 PMCID: PMC5963817 DOI: 10.1371/journal.pbio.2005687] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/22/2018] [Accepted: 04/23/2018] [Indexed: 01/09/2023] Open
Abstract
In preparation for dramatic morphogenetic events of gastrulation, rapid embryonic cell cycles slow at the mid-blastula transition (MBT). In Drosophila melanogaster embryos, down-regulation of cyclin-dependent kinase 1 (Cdk1) activity initiates this slowing by delaying replication of heterochromatic satellite sequences and extending S phase. We found that Cdk1 activity inhibited the chromatin association of Rap1 interacting factor 1 (Rif1), a candidate repressor of replication. Furthermore, Rif1 bound selectively to satellite sequences following Cdk1 down-regulation at the MBT. In the next S phase, Rif1 dissociated from different satellites in an orderly schedule that anticipated their replication. Rif1 lacking potential phosphorylation sites failed to dissociate and dominantly prevented completion of replication. Loss of Rif1 in mutant embryos shortened the post-MBT S phase and rescued embryonic cell cycles disrupted by depletion of the S phase–promoting kinase, cell division cycle 7 (Cdc7). Our work shows that Rif1 and S phase kinases compose a replication timer controlling first the developmental onset of late replication and then the precise schedule of replication within S phase. In addition, we describe how onset of late replication fits into the progressive maturation of heterochromatin during development. Cells divide rapidly in the early embryos of most animals. However, during a conserved period of development known as the mid-blastula transition (MBT), the cell cycle slows down dramatically. In Drosophila embryos, genome duplication abruptly slows to initiate this cell cycle prolongation. This is achieved through the onset of late replication, a well-recognized phenomenon in which specific sequences of the genome await replication until long after other sequences have finished. Even though this temporal program of replication is a major determinant of the duration of S phase, the factors involved in this process remain unknown. Here, we use genetics and real-time microscopy to visualize replication in developing fly embryos and show that the protein Rap1 interacting factor 1 (Rif1) mediates the introduction of late replication at the MBT. We find that at this stage, Rif1 binds to and selectively delays the replication of large blocks of repetitive DNA known as satellite sequences. During the rapid cell cycles before the MBT, we show that the cyclin-dependent kinase 1 (Cdk1) prevents Rif1 from slowing down DNA replication by driving its removal from the chromatin. The developmental down-regulation of Cdk1 at the MBT allows Rif1 to associate with the satellite sequences and initiate cell cycle slowing. Our work provides new insights into the temporal programming of S phase and into the embryonic origin of late replication.
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Affiliation(s)
- Charles A. Seller
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Patrick H. O’Farrell
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Fukuda K, Okuda A, Yusa K, Shinkai Y. A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells. Genome Res 2018; 28:846-858. [PMID: 29728365 PMCID: PMC5991520 DOI: 10.1101/gr.227280.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 04/26/2018] [Indexed: 12/16/2022]
Abstract
In mouse embryonic stem cells (mESCs), the expression of provirus and endogenous retroelements is epigenetically repressed. Although many cellular factors involved in retroelement silencing have been identified, the complete molecular mechanism remains elusive. In this study, we performed a genome-wide CRISPR screen to advance our understanding of retroelement silencing in mESCs. The Moloney murine leukemia virus (MLV)–based retroviral vector MSCV-GFP, which is repressed by the SETDB1/TRIM28 pathway in mESCs, was used as a reporter provirus, and we identified more than 80 genes involved in this process. In particular, ATF7IP and the BAF complex components are linked with the repression of most of the SETDB1 targets. We characterized two factors, MORC2A and RESF1, of which RESF1 is a novel molecule in retroelement silencing. Although both factors are recruited to repress provirus, their roles in repression are different. MORC2A appears to function dependent on repressive epigenetic modifications, while RESF1 regulates repressive epigenetic modifications associated with SETDB1. Our genome-wide CRISPR screen cataloged genes which function at different levels in silencing of SETDB1-target retroelements and provides a useful resource for further molecular studies.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane Hidaka Saitama 350-1241, Japan
| | - Kosuke Yusa
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Yoichi Shinkai
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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LARP7-like protein Pof8 regulates telomerase assembly and poly(A)+TERRA expression in fission yeast. Nat Commun 2018; 9:586. [PMID: 29422503 PMCID: PMC5805695 DOI: 10.1038/s41467-018-02874-0] [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: 07/28/2017] [Accepted: 01/05/2018] [Indexed: 02/06/2023] Open
Abstract
Telomerase is a reverse transcriptase complex that ensures stable maintenance of linear eukaryotic chromosome ends by overcoming the end replication problem, posed by the inability of replicative DNA polymerases to fully replicate linear DNA. The catalytic subunit TERT must be assembled properly with its telomerase RNA for telomerase to function, and studies in Tetrahymena have established that p65, a La-related protein 7 (LARP7) family protein, utilizes its C-terminal xRRM domain to promote assembly of the telomerase ribonucleoprotein (RNP) complex. However, LARP7-dependent telomerase complex assembly has been considered as unique to ciliates that utilize RNA polymerase III to transcribe telomerase RNA. Here we show evidence that fission yeast Schizosaccharomyces pombe utilizes the p65-related protein Pof8 and its xRRM domain to promote assembly of RNA polymerase II-encoded telomerase RNA with TERT. Furthermore, we show that Pof8 contributes to repression of the transcription of noncoding RNAs at telomeres. A functional telomerase complex requires that the catalytic TERT subunit be assembled with the template RNA TER1. Here the authors show that Pof8, a possible LARP7 family protein, is required for assembly of the telomerase complex, and repression of lncRNA transcripts at telomeres in S. pombe.
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35
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Jahn LJ, Mason B, Brøgger P, Toteva T, Nielsen DK, Thon G. Dependency of Heterochromatin Domains on Replication Factors. G3 (BETHESDA, MD.) 2018; 8:477-489. [PMID: 29187422 PMCID: PMC5919735 DOI: 10.1534/g3.117.300341] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/20/2017] [Indexed: 01/26/2023]
Abstract
Chromatin structure regulates both genome expression and dynamics in eukaryotes, where large heterochromatic regions are epigenetically silenced through the methylation of histone H3K9, histone deacetylation, and the assembly of repressive complexes. Previous genetic screens with the fission yeast Schizosaccharomyces pombe have led to the identification of key enzymatic activities and structural constituents of heterochromatin. We report here on additional factors discovered by screening a library of deletion mutants for silencing defects at the edge of a heterochromatic domain bound by its natural boundary-the IR-R+ element-or by ectopic boundaries. We found that several components of the DNA replication progression complex (RPC), including Mrc1/Claspin, Mcl1/Ctf4, Swi1/Timeless, Swi3/Tipin, and the FACT subunit Pob3, are essential for robust heterochromatic silencing, as are the ubiquitin ligase components Pof3 and Def1, which have been implicated in the removal of stalled DNA and RNA polymerases from chromatin. Moreover, the search identified the cohesin release factor Wpl1 and the forkhead protein Fkh2, both likely to function through genome organization, the Ssz1 chaperone, the Fkbp39 proline cis-trans isomerase, which acts on histone H3P30 and P38 in Saccharomyces cerevisiae, and the chromatin remodeler Fft3. In addition to their effects in the mating-type region, to varying extents, these factors take part in heterochromatic silencing in pericentromeric regions and telomeres, revealing for many a general effect in heterochromatin. This list of factors provides precious new clues with which to study the spatiotemporal organization and dynamics of heterochromatic regions in connection with DNA replication.
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Affiliation(s)
| | - Bethany Mason
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Peter Brøgger
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Tea Toteva
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Dennis Kim Nielsen
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
| | - Genevieve Thon
- Department of Biology, University of Copenhagen, BioCenter, 2200, Denmark
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36
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Li P, Wang L, Bennett BD, Wang J, Li J, Qin Y, Takaku M, Wade PA, Wong J, Hu G. Rif1 promotes a repressive chromatin state to safeguard against endogenous retrovirus activation. Nucleic Acids Res 2018; 45:12723-12738. [PMID: 29040764 PMCID: PMC5727408 DOI: 10.1093/nar/gkx884] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 10/05/2017] [Indexed: 12/29/2022] Open
Abstract
Transposable elements, including endogenous retroviruses (ERVs), constitute a large fraction of the mammalian genome. They are transcriptionally silenced during early development to protect genome integrity and aberrant transcription. However, the mechanisms that control their repression are not fully understood. To systematically study ERV repression, we carried out an RNAi screen in mouse embryonic stem cells (ESCs) and identified a list of novel regulators. Among them, Rif1 displays the strongest effect. Rif1 depletion by RNAi or gene deletion led to increased transcription and increased chromatin accessibility at ERV regions and their neighboring genes. This transcriptional de-repression becomes more severe when DNA methylation is lost. On the mechanistic level, Rif1 directly occupies ERVs and is required for repressive histone mark H3K9me3 and H3K27me3 assembly and DNA methylation. It interacts with histone methyltransferases and facilitates their recruitment to ERV regions. Importantly, Rif1 represses ERVs in human ESCs as well, and the evolutionally-conserved HEAT-like domain is essential for its function. Finally, Rif1 acts as a barrier during somatic cell reprogramming, and its depletion significantly enhances reprogramming efficiency. Together, our study uncovered many previously uncharacterized repressors of ERVs, and defined an essential role of Rif1 in the epigenetic defense against ERV activation.
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Affiliation(s)
- Pishun Li
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Brian D. Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
| | - Jiajia Wang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
| | - Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yufeng Qin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
| | - Motoki Takaku
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
| | - Paul A. Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
- To whom correspondence should be addressed. Tel: +1 919 541 4755; Fax: +1 919 541 0146;
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37
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Jamieson K, McNaught KJ, Ormsby T, Leggett NA, Honda S, Selker EU. Telomere repeats induce domains of H3K27 methylation in Neurospora. eLife 2018; 7:31216. [PMID: 29297465 PMCID: PMC5752202 DOI: 10.7554/elife.31216] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022] Open
Abstract
Development in higher organisms requires selective gene silencing, directed in part by di-/trimethylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungus Neurospora crassa to elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. We found that proximity to chromosome ends is necessary to maintain, and sufficient to induce, transcriptionally repressive, subtelomeric H3K27me2/3. We ascertained that such telomere-proximal facultative heterochromatin requires native telomere repeats and found that a short array of ectopic telomere repeats, (TTAGGG)17, can induce a large domain (~225 kb) of H3K27me2/3. This provides an example of a cis-acting sequence that directs H3K27 methylation. Our findings provide new insight into the relationship between genome organization and control of heterochromatin formation.
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Affiliation(s)
- Kirsty Jamieson
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Kevin J McNaught
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Tereza Ormsby
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Neena A Leggett
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, United States
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38
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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39
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Wang Y, Khan A, Marks AB, Smith OK, Giri S, Lin YC, Creager R, MacAlpine DM, Prasanth KV, Aladjem MI, Prasanth SG. Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization. Nucleic Acids Res 2017; 45:2490-2502. [PMID: 27924004 PMCID: PMC5389698 DOI: 10.1093/nar/gkw1211] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/23/2016] [Indexed: 12/19/2022] Open
Abstract
DNA replication requires the recruitment of a pre-replication complex facilitated by Origin Recognition Complex (ORC) onto the chromatin during G1 phase of the cell cycle. The ORC-associated protein (ORCA/LRWD1) stabilizes ORC on chromatin. Here, we evaluated the genome-wide distribution of ORCA using ChIP-seq during specific time points of G1. ORCA binding sites on the G1 chromatin are dynamic and temporally regulated. ORCA association to specific genomic sites decreases as the cells progressed towards S-phase. The majority of the ORCA-bound sites represent replication origins that also associate with the repressive chromatin marks H3K9me3 and methylated-CpGs, consistent with ORCA-bound origins initiating DNA replication late in S-phase. Further, ORCA directly associates with the repressive marks and interacts with the enzymes that catalyze these marks. Regions that associate with both ORCA and H3K9me3, exhibit diminished H3K9 methylation in ORCA-depleted cells, suggesting a role for ORCA in recruiting the H3K9me3 mark at certain genomic loci. Similarly, DNA methylation is altered at ORCA-occupied sites in cells lacking ORCA. Furthermore, repressive chromatin marks influence ORCA's binding on chromatin. We propose that ORCA coordinates with the histone and DNA methylation machinery to establish a repressive chromatin environment at a subset of origins, which primes them for late replication.
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Affiliation(s)
- Yating Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Abid Khan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Anna B Marks
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Sumanprava Giri
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Rachel Creager
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
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40
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Erlendson AA, Friedman S, Freitag M. A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0054-2017. [PMID: 28752814 PMCID: PMC5536859 DOI: 10.1128/microbiolspec.funk-0054-2017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 02/06/2023] Open
Abstract
Chromatin and chromosomes of fungi are highly diverse and dynamic, even within species. Much of what we know about histone modification enzymes, RNA interference, DNA methylation, and cell cycle control was first addressed in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Neurospora crassa. Here, we examine the three landmark regions that are required for maintenance of stable chromosomes and their faithful inheritance, namely, origins of DNA replication, telomeres and centromeres. We summarize the state of recent chromatin research that explains what is required for normal function of these specialized chromosomal regions in different fungi, with an emphasis on the silencing mechanism associated with subtelomeric regions, initiated by sirtuin histone deacetylases and histone H3 lysine 27 (H3K27) methyltransferases. We explore mechanisms for the appearance of "accessory" or "conditionally dispensable" chromosomes and contrast what has been learned from studies on genome-wide chromosome conformation capture in S. cerevisiae, S. pombe, N. crassa, and Trichoderma reesei. While most of the current knowledge is based on work in a handful of genetically and biochemically tractable model organisms, we suggest where major knowledge gaps remain to be closed. Fungi will continue to serve as facile organisms to uncover the basic processes of life because they make excellent model organisms for genetics, biochemistry, cell biology, and evolutionary biology.
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Affiliation(s)
- Allyson A. Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Steven Friedman
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
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41
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Shelterin components mediate genome reorganization in response to replication stress. Proc Natl Acad Sci U S A 2017; 114:5479-5484. [PMID: 28490498 DOI: 10.1073/pnas.1705527114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The dynamic nature of genome organization impacts critical nuclear functions including the regulation of gene expression, replication, and DNA damage repair. Despite significant progress, the mechanisms responsible for reorganization of the genome in response to cellular stress, such as aberrant DNA replication, are poorly understood. Here, we show that fission yeast cells carrying a mutation in the DNA-binding protein Sap1 show defects in DNA replication progression and genome stability and display extensive changes in genome organization. Chromosomal regions such as subtelomeres that show defects in replication progression associate with the nuclear envelope in sap1 mutant cells. Moreover, high-resolution, genome-wide chromosome conformation capture (Hi-C) analysis revealed prominent contacts between telomeres and chromosomal arm regions containing replication origins proximal to binding sites for Taz1, a component of the Shelterin telomere protection complex. Strikingly, we find that Shelterin components are required for interactions between Taz1-associated chromosomal arm regions and telomeres. These analyses reveal an unexpected role for Shelterin components in genome reorganization in cells experiencing replication stress, with important implications for understanding the mechanisms governing replication and genome stability.
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42
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Taneja N, Zofall M, Balachandran V, Thillainadesan G, Sugiyama T, Wheeler D, Zhou M, Grewal SIS. SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication. Mol Cell 2017; 66:50-62.e6. [PMID: 28318821 DOI: 10.1016/j.molcel.2017.02.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/13/2017] [Accepted: 02/08/2017] [Indexed: 02/05/2023]
Abstract
Heterochromatin can be epigenetically inherited in cis, leading to stable gene silencing. However, the mechanisms underlying heterochromatin inheritance remain unclear. Here, we identify Fft3, a fission yeast homolog of the mammalian SMARCAD1 SNF2 chromatin remodeler, as a factor uniquely required for heterochromatin inheritance, rather than for de novo assembly. Importantly, we find that Fft3 suppresses turnover of histones at heterochromatic loci to facilitate epigenetic transmission of heterochromatin in cycling cells. Moreover, Fft3 also precludes nucleosome turnover at several euchromatic loci to prevent R-loop formation, ensuring proper replication progression. Our analyses show that overexpression of Clr4/Suv39h, which is also required for efficient replication through these loci, suppresses phenotypes associated with the loss of Fft3. This work uncovers a conserved factor critical for epigenetic inheritance of heterochromatin and describes a mechanism in which suppression of nucleosome turnover prevents formation of structural barriers that impede replication at fragile regions in the genome.
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Affiliation(s)
- Nitika Taneja
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tomoyasu Sugiyama
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhou
- Laboratory of Proteomics and Analytical Technologies, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Aladjem MI, Redon CE. Order from clutter: selective interactions at mammalian replication origins. Nat Rev Genet 2017; 18:101-116. [PMID: 27867195 PMCID: PMC6596300 DOI: 10.1038/nrg.2016.141] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian chromosome duplication progresses in a precise order and is subject to constraints that are often relaxed in developmental disorders and malignancies. Molecular information about the regulation of DNA replication at the chromatin level is lacking because protein complexes that initiate replication seem to bind chromatin indiscriminately. High-throughput sequencing and mathematical modelling have yielded detailed genome-wide replication initiation maps. Combining these maps and models with functional genetic analyses suggests that distinct DNA-protein interactions at subgroups of replication initiation sites (replication origins) modulate the ubiquitous replication machinery and supports an emerging model that delineates how indiscriminate DNA-binding patterns translate into a consistent, organized replication programme.
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Affiliation(s)
- Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
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44
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Toteva T, Mason B, Kanoh Y, Brøgger P, Green D, Verhein-Hansen J, Masai H, Thon G. Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast. Proc Natl Acad Sci U S A 2017; 114:1093-1098. [PMID: 28096402 PMCID: PMC5293076 DOI: 10.1073/pnas.1614837114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identify cis- and trans-acting factors capable of creating heterochromatin-euchromatin boundaries in fission yeast. The preponderance of cis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1. Boundary formation and gene silencing by these elements required Taz1 and Rif1 and coincided with altered replication timing in the region. Thus, small chromosomal elements sensitive to Taz1 and Rif1 (STAR) could simultaneously regulate gene expression and DNA replication over a large domain, at the edge of which they established a heterochromatin-euchromatin boundary. Taz1, Rif1, and Rif1-associated protein phosphatases Sds21 and Dis2 were each sufficient to establish a boundary when tethered to DNA. Moreover, efficient boundary formation required the amino-terminal domain of the Mcm4 replicative helicase onto which the antagonistic activities of the replication-promoting Dbf4-dependent kinase and Rif1-recruited phosphatases are believed to converge to control replication origin firing. Altogether these observations provide an insight into a coordinated control of DNA replication and organization of the genome into expression domains.
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Affiliation(s)
- Tea Toteva
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bethany Mason
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Yutaka Kanoh
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamkitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Peter Brøgger
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Daniel Green
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Janne Verhein-Hansen
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamkitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Geneviève Thon
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark;
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45
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Moriyama K, Lai MS, Masai H. Interaction of Rif1 Protein with G-Quadruplex in Control of Chromosome Transactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:287-310. [PMID: 29357064 DOI: 10.1007/978-981-10-6955-0_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent studies on G-quadruplex (G4) revealed crucial and conserved functions of G4 in various biological systems. We recently showed that Rif1, a conserved nuclear factor, binds to G4 present in the intergenic regions and plays a major role in spatiotemporal regulation of DNA replication. Rif1 may tether chromatin fibers through binding to G4, generating specific chromatin domains that dictate the replication timing. G4 and its various binding partners are now implicated in many other chromosome regulations, including transcription, replication initiation, recombination, gene rearrangement, and transposition.
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Affiliation(s)
- Kenji Moriyama
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Mong Sing Lai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
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46
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Liu L. Linking Telomere Regulation to Stem Cell Pluripotency. Trends Genet 2016; 33:16-33. [PMID: 27889084 DOI: 10.1016/j.tig.2016.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/18/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022]
Abstract
Embryonic stem cells (ESCs), somatic cell nuclear transfer ESCs, and induced pluripotent stem cells (iPSCs) represent the most studied group of PSCs. Unlimited self-renewal without incurring chromosomal instability and pluripotency are essential for the potential use of PSCs in regenerative therapy. Telomere length maintenance is critical for the unlimited self-renewal, pluripotency, and chromosomal stability of PSCs. While telomerase has a primary role in telomere maintenance, alternative lengthening of telomere pathways involving recombination and epigenetic modifications are also required for telomere length regulation, notably in mouse PSCs. Telomere rejuvenation is part of epigenetic reprogramming to pluripotency. Insights into telomere reprogramming and maintenance in PSCs may have implications for understanding of aging and tumorigenesis. Here, I discuss the link between telomere elongation and homeostasis to the acquisition and maintenance of stem cell pluripotency, and their regulatory mechanisms by epigenetic modifications.
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Affiliation(s)
- Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin 300071, China.
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