1
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Giacomini G, Piquet S, Chevallier O, Dabin J, Bai SK, Kim B, Siddaway R, Raught B, Coyaud E, Shan CM, Reid RJD, Toda T, Rothstein R, Barra V, Wilhelm T, Hamadat S, Bertin C, Crane A, Dubois F, Forne I, Imhof A, Bandopadhayay P, Beroukhim R, Naim V, Jia S, Hawkins C, Rondinelli B, Polo SE. Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors. Nucleic Acids Res 2024; 52:2372-2388. [PMID: 38214234 PMCID: PMC10954481 DOI: 10.1093/nar/gkad1257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
Pediatric high-grade gliomas (pHGG) are devastating and incurable brain tumors with recurrent mutations in histone H3.3. These mutations promote oncogenesis by dysregulating gene expression through alterations of histone modifications. We identify aberrant DNA repair as an independent mechanism, which fosters genome instability in H3.3 mutant pHGG, and opens new therapeutic options. The two most frequent H3.3 mutations in pHGG, K27M and G34R, drive aberrant repair of replication-associated damage by non-homologous end joining (NHEJ). Aberrant NHEJ is mediated by the DNA repair enzyme polynucleotide kinase 3'-phosphatase (PNKP), which shows increased association with mutant H3.3 at damaged replication forks. PNKP sustains the proliferation of cells bearing H3.3 mutations, thus conferring a molecular vulnerability, specific to mutant cells, with potential for therapeutic targeting.
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Affiliation(s)
- Giulia Giacomini
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Sandra Piquet
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Odile Chevallier
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Juliette Dabin
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Siau-Kun Bai
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Byungjin Kim
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Robert Siddaway
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Robert J D Reid
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Viviana Barra
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Therese Wilhelm
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Sabah Hamadat
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Chloé Bertin
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Alexander Crane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Frank Dubois
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Ignasi Forne
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University, Martinsried, Germany
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Valeria Naim
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Cynthia Hawkins
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | | | - Sophie E Polo
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
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2
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Saredi G, Carelli FN, Rolland SGM, Furlan G, Piquet S, Appert A, Sanchez-Pulido L, Price JL, Alcon P, Lampersberger L, Déclais AC, Ramakrishna NB, Toth R, Macartney T, Alabert C, Ponting CP, Polo SE, Miska EA, Gartner A, Ahringer J, Rouse J. The histone chaperone SPT2 regulates chromatin structure and function in Metazoa. Nat Struct Mol Biol 2024; 31:523-535. [PMID: 38238586 PMCID: PMC7615752 DOI: 10.1038/s41594-023-01204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024]
Abstract
Histone chaperones control nucleosome density and chromatin structure. In yeast, the H3-H4 chaperone Spt2 controls histone deposition at active genes but its roles in metazoan chromatin structure and organismal physiology are not known. Here we identify the Caenorhabditis elegans ortholog of SPT2 (CeSPT-2) and show that its ability to bind histones H3-H4 is important for germline development and transgenerational epigenetic gene silencing, and that spt-2 null mutants display signatures of a global stress response. Genome-wide profiling showed that CeSPT-2 binds to a range of highly expressed genes, and we find that spt-2 mutants have increased chromatin accessibility at a subset of these loci. We also show that SPT2 influences chromatin structure and controls the levels of soluble and chromatin-bound H3.3 in human cells. Our work reveals roles for SPT2 in controlling chromatin structure and function in Metazoa.
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Affiliation(s)
- Giulia Saredi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Francesco N Carelli
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Stéphane G M Rolland
- IBS Centre for Genomic Integrity at Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Giulia Furlan
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Transine Therapeutics, Babraham Hall, Cambridge, UK
| | - Sandra Piquet
- Laboratory of Epigenome Integrity, Epigenetics and Cell Fate Centre, UMR 7216 CNRS - Université Paris Cité, Paris, France
| | - Alex Appert
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Jonathan L Price
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pablo Alcon
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Lisa Lampersberger
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Unity Campus, Cambridge, UK
| | - Anne-Cécile Déclais
- Molecular Cell and Developmental Biology Division, School of Life Sciences, University of Dundee, Dundee, UK
| | - Navin B Ramakrishna
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Constance Alabert
- Molecular Cell and Developmental Biology Division, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sophie E Polo
- Laboratory of Epigenome Integrity, Epigenetics and Cell Fate Centre, UMR 7216 CNRS - Université Paris Cité, Paris, France
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Anton Gartner
- IBS Centre for Genomic Integrity at Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Julie Ahringer
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
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3
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Ferrand J, Dabin J, Chevallier O, Kupai A, Rothbart SB, Polo SE. Mitotic chromatin marking governs asymmetric segregation of DNA damage. bioRxiv 2023:2023.09.04.556166. [PMID: 37732208 PMCID: PMC10508772 DOI: 10.1101/2023.09.04.556166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The faithful segregation of intact genetic material and the perpetuation of chromatin states through mitotic cell divisions are pivotal for maintaining cell function and identity across cell generations. However, most exogenous mutagens generate long-lasting DNA lesions that are segregated during mitosis. How this segregation is controlled is unknown. Here, we uncover a mitotic chromatin-marking pathway that governs the segregation of UV-induced damage in human cells. Our mechanistic analyses reveal two layers of control: histone ADP-ribosylation, and the incorporation of newly synthesized histones at UV damage sites, that both prevent local mitotic phosphorylations on histone H3 serines. Functionally, this chromatin-marking pathway drives the asymmetric segregation of UV damage in the cell progeny with potential consequences on daughter cell fate. We propose that this mechanism may help preserve the integrity of stem cell compartments during asymmetric cell divisions.
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Affiliation(s)
- Juliette Ferrand
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
| | - Juliette Dabin
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
| | - Odile Chevallier
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
| | - Ariana Kupai
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Sophie E. Polo
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
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4
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Dabin J, Mori M, Polo SE. The DNA damage response in the chromatin context: A coordinated process. Curr Opin Cell Biol 2023; 82:102176. [PMID: 37301060 DOI: 10.1016/j.ceb.2023.102176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
In the cell nucleus, DNA damage signaling and repair machineries operate on a chromatin substrate, the integrity of which is critical for cell function and viability. Here, we review recent advances in deciphering the tight coordination between chromatin maintenance and the DNA damage response (DDR). We discuss how the DDR impacts chromatin marks, organization and mobility, and, in turn, how chromatin alterations actively contribute to the DDR, providing additional levels of regulation. We present our current knowledge of the molecular bases of these critical processes in physiological and pathological conditions, and also highlight open questions that emerge in this expanding field.
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Affiliation(s)
- Juliette Dabin
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Margherita Mori
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France.
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5
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Chansard A, Pobega E, Caron P, Polo SE. Imaging the Response to DNA Damage in Heterochromatin Domains. Front Cell Dev Biol 2022; 10:920267. [PMID: 35721488 PMCID: PMC9201110 DOI: 10.3389/fcell.2022.920267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic genome is assembled in a nucleoprotein complex called chromatin, whose organization markedly influences the repair of DNA lesions. For instance, compact chromatin states, broadly categorized as heterochromatin, present a challenging environment for DNA damage repair. Through transcriptional silencing, heterochromatin also plays a vital role in the maintenance of genomic integrity and cellular homeostasis. It is thus of critical importance to decipher whether and how heterochromatin affects the DNA damage response (DDR) to understand how this chromatin state is preserved after DNA damage. Here, we present two laser micro-irradiation-based methods for imaging the DDR in heterochromatin domains in mammalian cells. These methods allow DNA damage targeting to specific subnuclear compartments, direct visualization of the DDR and image-based quantification of the repair response. We apply them to study DNA double-strand break repair pathways in facultative heterochromatin and the repair of UV photoproducts in constitutive heterochromatin. We discuss the advantages and limitations of these methods compared to other targeted approaches for DNA damage induction.
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6
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Abstract
In response to DNA double-strand breaks (DSBs), chromatin modifications orchestrate DNA repair pathways thus safeguarding genome integrity. Recent studies have uncovered a key role for heterochromatin marks and associated factors in shaping DSB repair within the nucleus. In this review, we present our current knowledge of the interplay between heterochromatin marks and DSB repair. We discuss the impact of heterochromatin features, either pre-existing in heterochromatin domains or de novo established in euchromatin, on DSB repair pathway choice. We emphasize how heterochromatin decompaction and mobility further support DSB repair, focusing on recent mechanistic insights into these processes. Finally, we speculate about potential molecular players involved in the maintenance or the erasure of heterochromatin marks following DSB repair, and their implications for restoring epigenome function and integrity.
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Affiliation(s)
- Pierre Caron
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Enrico Pobega
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
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7
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Bouvier D, Ferrand J, Chevallier O, Paulsen MT, Ljungman M, Polo SE. Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA. Nat Commun 2021; 12:3835. [PMID: 34158510 PMCID: PMC8219801 DOI: 10.1038/s41467-021-24153-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
Transcription restart after a genotoxic challenge is a fundamental yet poorly understood process. Here, we dissect the interplay between transcription and chromatin restoration after DNA damage by focusing on the human histone chaperone complex HIRA, which is required for transcription recovery post UV. We demonstrate that HIRA is recruited to UV-damaged chromatin via the ubiquitin-dependent segregase VCP to deposit new H3.3 histones. However, this local activity of HIRA is dispensable for transcription recovery. Instead, we reveal a genome-wide function of HIRA in transcription restart that is independent of new H3.3 and not restricted to UV-damaged loci. HIRA coordinates with ASF1B to control transcription restart by two independent pathways: by stabilising the associated subunit UBN2 and by reducing the expression of the transcription repressor ATF3. Thus, HIRA primes UV-damaged chromatin for transcription restart at least in part by relieving transcription inhibition rather than by depositing new H3.3 as an activating bookmark.
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Affiliation(s)
- Déborah Bouvier
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Juliette Ferrand
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Odile Chevallier
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Sophie E Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France.
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8
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Caron P, Pobega E, Polo SE. A molecular Rosetta Stone to decipher the impact of chromatin features on the repair of Cas9-mediated DNA double-strand breaks. Mol Cell 2021; 81:2059-2060. [PMID: 34019786 DOI: 10.1016/j.molcel.2021.04.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Using a barcoded reporter introduced within a thousand different chromatin locations in human cells, (Schep et al., 2021) characterize repair outcomes of Cas9-induced DNA double-strand breaks (DSBs) and the relative use of DSB repair pathways depending on the local chromatin context.
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Affiliation(s)
- Pierre Caron
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR 7216 CNRS - University of Paris, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Enrico Pobega
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR 7216 CNRS - University of Paris, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Sophie E Polo
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR 7216 CNRS - University of Paris, 35 rue Hélène Brion, 75205 Paris Cedex 13, France.
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9
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Fortuny A, Chansard A, Caron P, Chevallier O, Leroy O, Renaud O, Polo SE. Imaging the response to DNA damage in heterochromatin domains reveals core principles of heterochromatin maintenance. Nat Commun 2021; 12:2428. [PMID: 33893291 PMCID: PMC8065061 DOI: 10.1038/s41467-021-22575-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023] Open
Abstract
Heterochromatin is a critical chromatin compartment, whose integrity governs genome stability and cell fate transitions. How heterochromatin features, including higher-order chromatin folding and histone modifications associated with transcriptional silencing, are maintained following a genotoxic stress challenge is unknown. Here, we establish a system for targeting UV damage to pericentric heterochromatin in mammalian cells and for tracking the heterochromatin response to UV in real time. We uncover profound heterochromatin compaction changes during repair, orchestrated by the UV damage sensor DDB2, which stimulates linker histone displacement from chromatin. Despite massive heterochromatin unfolding, heterochromatin-specific histone modifications and transcriptional silencing are maintained. We unveil a central role for the methyltransferase SETDB1 in the maintenance of heterochromatic histone marks after UV. SETDB1 coordinates histone methylation with new histone deposition in damaged heterochromatin, thus protecting cells from genome instability. Our data shed light on fundamental molecular mechanisms safeguarding higher-order chromatin integrity following DNA damage.
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Affiliation(s)
- Anna Fortuny
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Audrey Chansard
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Pierre Caron
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Odile Chevallier
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Olivier Leroy
- Cell and Tissue Imaging Facility, UMR3215 PICT-IBiSA, Institut Curie, Paris, France
| | - Olivier Renaud
- Cell and Tissue Imaging Facility, UMR3215 PICT-IBiSA, Institut Curie, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France.
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10
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Abstract
Chromatin integrity is key for cell homeostasis and for preventing pathological development. Alterations in core chromatin components, histone proteins, recently came into the spotlight through the discovery of their driving role in cancer. Building on these findings, in this review, we discuss how histone variants and their associated chaperones safeguard genome stability and protect against tumorigenesis. Accumulating evidence supports the contribution of histone variants and their chaperones to the maintenance of chromosomal integrity and to various steps of the DNA damage response, including damaged chromatin dynamics, DNA damage repair, and damage-dependent transcription regulation. We present our current knowledge on these topics and review recent advances in deciphering how alterations in histone variant sequence, expression, and deposition into chromatin fuel oncogenic transformation by impacting cell proliferation and cell fate transitions. We also highlight open questions and upcoming challenges in this rapidly growing field.
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Affiliation(s)
| | | | - Sophie E. Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, 75013 Paris, France; (J.F.); (B.R.)
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11
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Abstract
DNA double-strand breaks (DSBs) elicit major chromatin changes. Using super-resolution microscopy in human cells, Ochs et al. unveil that the DSB response protein 53BP1 and its effector RIF1 organize DSB-flanking chromatin into circular micro-domains. These structures control the spatial distribution of DSB repair factors safeguarding genome integrity.
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Affiliation(s)
- Pierre Caron
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013, Paris, France.
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12
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Abstract
In eukaryotic cell nuclei, all DNA transactions, including DNA damage repair, take place on a chromatin substrate, the integrity of which is central to gene expression programs and cell identity. However, substantial chromatin rearrangements accompany the repair response, culminating in the deposition of new histones. How the original epigenetic information conveyed by chromatin may be preserved in this context is a burning question. Elucidating the fate of parental histones, which characterize the pre-damage chromatin state, is a key step forward in deciphering the mechanisms that safeguard epigenome stability. Here, we present an in vivo approach for tracking parental histone H3 variant dynamics in real time after UVC laser-induced damage in human cells.
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Affiliation(s)
- Juliette Dabin
- Epigenetics and Cell Fate Centre, UMR7216 CNRS/Paris Diderot University, Paris, France
| | - Anna Fortuny
- Epigenetics and Cell Fate Centre, UMR7216 CNRS/Paris Diderot University, Paris, France
| | - Sandra Piquet
- Epigenetics and Cell Fate Centre, UMR7216 CNRS/Paris Diderot University, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS/Paris Diderot University, Paris, France.
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13
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Abstract
Eukaryotic genomes are organized into chromatin, divided into structurally and functionally distinct euchromatin and heterochromatin compartments. The high level of compaction and the abundance of repeated sequences in heterochromatin pose multiple challenges for the maintenance of genome stability. Cells have evolved sophisticated and highly controlled mechanisms to overcome these constraints. Here, we summarize recent findings on how the heterochromatic state influences DNA damage formation, signaling, and repair. By focusing on distinct heterochromatin domains in different eukaryotic species, we highlight the heterochromatin contribution to the compartmentalization of DNA damage repair in the cell nucleus and to the repair pathway choice. We also describe the diverse chromatin alterations associated with the DNA damage response in heterochromatin domains and present our current understanding of their regulatory mechanisms. Finally, we discuss the biological significance and the evolutionary conservation of these processes.
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Affiliation(s)
- Anna Fortuny
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Paris, France.
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14
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Abstract
In this issue of Molecular Cell, Taneja et al. (2017) uncover a dual role for the conserved chromatin remodeler Fft3 in the maintenance of silent heterochromatin and the suppression of replication barriers at euchromatic loci through controlled histone turnover.
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Affiliation(s)
- Anna Fortuny
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR 7216 CNRS/Université Paris Diderot, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Sophie E Polo
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR 7216 CNRS/Université Paris Diderot, 35 rue Hélène Brion, 75205 Paris Cedex 13, France.
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15
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Abstract
Transcription is tightly regulated in response to DNA damage. Rapid and transient pausing of RNA polymerase II (RNAPII ) is indeed critical to restrict the production of aberrant transcripts from damaged loci and to prevent deleterious collisions between transcription and repair machineries. Yet, how DNA lesions signal to the transcription machinery to coordinate DNA repair with transcriptional silencing is not fully elucidated. In this issue of EMBO Reports , Awwad et al 1 bring a new piece to the puzzle by identifying the negative transcription elongation factor NELF as a critical player in this process. They demonstrate that NELF is recruited to DNA double‐strand breaks (DSB s) near transcriptionally active genes in a poly(ADP ‐ribose)‐ and RNAPII ‐dependent manner to promote transcriptional repression and facilitate DSB repair.
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Affiliation(s)
- Sophie E Polo
- Epigenetics & Cell Fate CentreUMR7216 CNRSSorbonne Paris CitéParis Diderot UniversityParisFrance
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16
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Abstract
In the cell nucleus, DNA repair machineries operate on a chromatin substrate, whose integrity is key for preserving cell functions and identity. Yet, it is still unclear how the epigenetic information conveyed by chromatin is maintained during the DNA repair process. We recently characterized the dynamics of parental histones coupled to UV-C damage repair in human cells, providing insights into how the pre-damage chromatin state may be restored. Here, we summarize our main findings and discuss them in the context of epigenome maintenance following DNA damage. We further address the mechanistic aspects of repair-coupled histone dynamics and develop working hypotheses regarding their functional relevance in the cellular response to genotoxic stress.
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Affiliation(s)
- Juliette Dabin
- a Epigenetics & Cell Fate Centre, UMR7216 CNRS , Paris Diderot University, Sorbonne Paris Cité , Paris , France
| | - Sophie E Polo
- a Epigenetics & Cell Fate Centre, UMR7216 CNRS , Paris Diderot University, Sorbonne Paris Cité , Paris , France
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17
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Adam S, Dabin J, Chevallier O, Leroy O, Baldeyron C, Corpet A, Lomonte P, Renaud O, Almouzni G, Polo SE. Real-Time Tracking of Parental Histones Reveals Their Contribution to Chromatin Integrity Following DNA Damage. Mol Cell 2016; 64:65-78. [PMID: 27642047 PMCID: PMC5065526 DOI: 10.1016/j.molcel.2016.08.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/20/2016] [Accepted: 08/11/2016] [Indexed: 12/22/2022]
Abstract
Chromatin integrity is critical for cell function and identity but is challenged by DNA damage. To understand how chromatin architecture and the information that it conveys are preserved or altered following genotoxic stress, we established a system for real-time tracking of parental histones, which characterize the pre-damage chromatin state. Focusing on histone H3 dynamics after local UVC irradiation in human cells, we demonstrate that parental histones rapidly redistribute around damaged regions by a dual mechanism combining chromatin opening and histone mobilization on chromatin. Importantly, parental histones almost entirely recover and mix with new histones in repairing chromatin. Our data further define a close coordination of parental histone dynamics with DNA repair progression through the damage sensor DDB2 (DNA damage-binding protein 2). We speculate that this mechanism may contribute to maintaining a memory of the original chromatin landscape and may help preserve epigenome stability in response to DNA damage. Parental H3 histones redistribute to the periphery of UVC-damaged regions The redistribution involves histone mobilization on chromatin and chromatin opening Parental histones recover massively during repair progression Parental histone dynamics may help coordinate DNA repair with epigenome integrity
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Affiliation(s)
- Salomé Adam
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France; Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Juliette Dabin
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France
| | - Odile Chevallier
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France
| | - Olivier Leroy
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie, UMR3215 CNRS/U934 INSERM, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Céline Baldeyron
- Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Armelle Corpet
- Team Chromatin Assembly, Nuclear Domains, Virus, Institut NeuroMyoGène, LabEx DEVweCAN, Université Claude Bernard Lyon 1, UMR5310 CNRS/U1217 INSERM, F-69100 Lyon, France
| | - Patrick Lomonte
- Team Chromatin Assembly, Nuclear Domains, Virus, Institut NeuroMyoGène, LabEx DEVweCAN, Université Claude Bernard Lyon 1, UMR5310 CNRS/U1217 INSERM, F-69100 Lyon, France
| | - Olivier Renaud
- Plateforme Imagerie Cellulaire et Tissulaire-Infrastructure en Biologie Santé et Agronomie, UMR3215 CNRS/U934 INSERM, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Geneviève Almouzni
- Laboratory of Nuclear Dynamics, UMR3664 CNRS, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Sophie E Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, F-75013 Paris, France.
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18
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Abstract
Organism viability relies on the stable maintenance of specific chromatin landscapes, established during development, that shape cell functions and identities by driving distinct gene expression programs. Yet epigenome maintenance is challenged during transcription, replication, and repair of DNA damage, all of which elicit dynamic changes in chromatin organization. Here, we review recent advances that have shed light on the specialized mechanisms contributing to the restoration of epigenome structure and function after DNA damage in the mammalian cell nucleus. By drawing a parallel with epigenome maintenance during replication, we explore emerging concepts and highlight open issues in this rapidly growing field. In particular, we present our current knowledge of molecular players that support the coordinated maintenance of genome and epigenome integrity in response to DNA damage, and we highlight how nuclear organization impacts genome stability. Finally, we discuss possible functional implications of epigenome plasticity in response to genotoxic stress.
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Affiliation(s)
- Juliette Dabin
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Anna Fortuny
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Sophie E Polo
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France.
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19
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Abstract
DNA damage not only jeopardizes genome integrity but also challenges the well-organized association of DNA with histone proteins into chromatin, which is key for regulating gene expression and cell functions. The extent to which the original chromatin structure is altered after repair of DNA lesions is thus a critical issue. Dissecting histone dynamics at sites of DNA damage has provided mechanistic insights into chromatin plasticity in response to genotoxic stress. Here, we present an experimental protocol for visualizing the deposition of newly synthesized histone H3 variants at sites of UVC damage in human cells that couples SNAP-tag based labeling of new histones with local UVC irradiation of cells through micropore filters.
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Affiliation(s)
- Salomé Adam
- Epigenetics and Cell Fate Centre, UMR7216 CNRS/Paris Diderot University, Bâtiment Lamarck (4ème étage) Case 7042, 35 rue Hélène Brion, Paris, 75205, France
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20
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Abstract
DNA damage signaling and repair machineries operate in a nuclear environment where DNA is wrapped around histone proteins and packaged into chromatin. Understanding how chromatin structure is restored together with the DNA sequence during DNA damage repair has been a topic of intense research. Indeed, chromatin integrity is central to cell functions and identity. However, chromatin shows remarkable plasticity in response to DNA damage. This review presents our current knowledge of chromatin dynamics in the mammalian cell nucleus in response to DNA double strand breaks and UV lesions. I provide an overview of the key players involved in regulating histone dynamics in damaged chromatin regions, focusing on histone chaperones and their concerted action with histone modifiers, chromatin remodelers and repair factors. I also discuss how these dynamics contribute to reshaping chromatin and, by altering the chromatin landscape, may affect the maintenance of epigenetic information.
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Affiliation(s)
- Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, 75205 Paris Cedex 13, France.
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21
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Adam S, Polo SE, Almouzni G. How to restore chromatin structure and function in response to DNA damage--let the chaperones play: delivered on 9 July 2013 at the 38th FEBS Congress in St Petersburg, Russia. FEBS J 2014; 281:2315-23. [PMID: 24673849 DOI: 10.1111/febs.12793] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/25/2014] [Indexed: 01/07/2023]
Abstract
Histone deposition onto DNA assisted by specific chaperones forms the chromatin basic unit and serves to package the genome within the cell nucleus. The resulting chromatin organization, often referred to as the epigenome, contributes to a unique transcriptional program that defines cell identity. Importantly, during cellular life, substantial alterations in chromatin structure may arise due to cell stress, including DNA damage, which not only challenges the integrity of the genome but also threatens the epigenome. Considerable efforts have been made to decipher chromatin dynamics in response to genotoxic stress, and to assess how it affects both genome and epigenome stability. Here, we review recent advances in understanding the mechanisms of DNA damage-induced chromatin plasticity in mammalian cells. We focus specifically on the dynamics of histone H3 variants in response to UV irradiation, and highlight the role of their dedicated chaperones in restoring both chromatin structure and function. Finally, we discuss how, in addition to restoring chromatin integrity, the cellular networks that signal and repair DNA damage may also provide a window of opportunity for modulating the information conveyed by chromatin.
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Affiliation(s)
- Salomé Adam
- Institut Curie, Centre de Recherche, Paris, France; Centre National de la Recherche Scientifique, UMR3664, Paris, France; Equipe Labellisée Ligue Contre le Cancer, Paris, France; Institut de Formation Doctorale, University Pierre & Marie Curie, Paris, France; Sorbonne University, PSL*, Paris, France; Epigenetics and Cell Fate Centre, UMR7216, Centre National de la Recherche Scientifique/Paris Diderot University, Paris, France
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22
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Adam S, Polo SE, Almouzni G. Transcription recovery after DNA damage requires chromatin priming by the H3.3 histone chaperone HIRA. Cell 2013; 155:94-106. [PMID: 24074863 DOI: 10.1016/j.cell.2013.08.029] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/17/2013] [Accepted: 08/16/2013] [Indexed: 10/26/2022]
Abstract
Understanding how to recover fully functional and transcriptionally active chromatin when its integrity has been challenged by genotoxic stress is a critical issue. Here, by investigating how chromatin dynamics regulate transcriptional activity in response to DNA damage in human cells, we identify a pathway involving the histone chaperone histone regulator A (HIRA) to promote transcription restart after UVC damage. Our mechanistic studies reveal that HIRA accumulates at sites of UVC irradiation upon detection of DNA damage prior to repair and deposits newly synthesized H3.3 histones. This local action of HIRA depends on ubiquitylation events associated with damage recognition. Furthermore, we demonstrate that the early and transient function of HIRA in response to DNA damage primes chromatin for later reactivation of transcription. We propose that HIRA-dependent histone deposition serves as a chromatin bookmarking system to facilitate transcription recovery after genotoxic stress.
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Affiliation(s)
- Salomé Adam
- Chromatin Dynamics, Institut Curie Research Centre, 75248 Paris Cedex 5, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 218, 75248 Paris Cedex 5, France
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23
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Polo SE. Fine-tuning the p53 response to DNA damage: a new piece in the puzzle. Cell Cycle 2013; 12:1337-8. [PMID: 23588075 PMCID: PMC3674060 DOI: 10.4161/cc.24669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Paris Diderot University, Paris, France.
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24
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Soria G, Polo SE, Almouzni G. Prime, repair, restore: the active role of chromatin in the DNA damage response. Mol Cell 2012; 46:722-34. [PMID: 22749398 DOI: 10.1016/j.molcel.2012.06.002] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/21/2012] [Accepted: 06/08/2012] [Indexed: 11/24/2022]
Abstract
The view of DNA packaging into chromatin as a mere obstacle to DNA repair is evolving. In this review, we focus on histone variants and heterochromatin proteins as chromatin components involved in distinct levels of chromatin organization to integrate them as real players in the DNA damage response (DDR). Based on recent data, we highlight how some of these chromatin components play active roles in the DDR and contribute to the fine-tuning of damage signaling, DNA and chromatin repair. To take into account this integrated view, we revisit the existing access-repair-restore model and propose a new working model involving priming chromatin for repair and restoration as a concerted process. We discuss how this impacts on both genomic and epigenomic stability and plasticity.
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Affiliation(s)
- Gaston Soria
- Laboratory of Chromatin Dynamics, Institut Curie Section Recherche, 75248 Paris Cedex 5, France
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25
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Adam S, Polo SE. Chromatin dynamics during nucleotide excision repair: histones on the move. Int J Mol Sci 2012; 13:11895-11911. [PMID: 23109890 PMCID: PMC3472782 DOI: 10.3390/ijms130911895] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/16/2022] Open
Abstract
It has been a long-standing question how DNA damage repair proceeds in a nuclear environment where DNA is packaged into chromatin. Several decades of analysis combining in vitro and in vivo studies in various model organisms ranging from yeast to human have markedly increased our understanding of the mechanisms underlying chromatin disorganization upon damage detection and re-assembly after repair. Here, we review the methods that have been developed over the years to delineate chromatin alterations in response to DNA damage by focusing on the well-characterized Nucleotide Excision Repair (NER) pathway. We also highlight how these methods have provided key mechanistic insight into histone dynamics coupled to repair in mammals, raising new issues about the maintenance of chromatin integrity. In particular, we discuss how NER factors and central players in chromatin dynamics such as histone modifiers, nucleosome remodeling factors, and histone chaperones function to mobilize histones during repair.
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Affiliation(s)
- Salomé Adam
- Laboratory of Chromatin Dynamics, Curie Institute Research Centre, 75248 Paris Cedex 5, France; E-Mail:
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 218, 75248 Paris Cedex 5, France
| | - Sophie E. Polo
- Laboratory of Chromatin Dynamics, Curie Institute Research Centre, 75248 Paris Cedex 5, France; E-Mail:
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 218, 75248 Paris Cedex 5, France
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-1-5624-6721; Fax: +33-1-4633-3016
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26
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Polo SE, Blackford AN, Chapman JR, Baskcomb L, Gravel S, Rusch A, Thomas A, Blundred R, Smith P, Kzhyshkowska J, Dobner T, Taylor AMR, Turnell AS, Stewart GS, Grand RJ, Jackson SP. Regulation of DNA-end resection by hnRNPU-like proteins promotes DNA double-strand break signaling and repair. Mol Cell 2012; 45:505-16. [PMID: 22365830 PMCID: PMC3550743 DOI: 10.1016/j.molcel.2011.12.035] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 08/26/2011] [Accepted: 12/13/2011] [Indexed: 01/19/2023]
Abstract
DNA double-strand break (DSB) signaling and repair are critical for cell viability, and rely on highly coordinated pathways whose molecular organization is still incompletely understood. Here, we show that heterogeneous nuclear ribonucleoprotein U-like (hnRNPUL) proteins 1 and 2 play key roles in cellular responses to DSBs. We identify human hnRNPUL1 and -2 as binding partners for the DSB sensor complex MRE11-RAD50-NBS1 (MRN) and demonstrate that hnRNPUL1 and -2 are recruited to DNA damage in an interdependent manner that requires MRN. Moreover, we show that hnRNPUL1 and -2 stimulate DNA-end resection and promote ATR-dependent signaling and DSB repair by homologous recombination, thereby contributing to cell survival upon exposure to DSB-inducing agents. Finally, we establish that hnRNPUL1 and -2 function downstream of MRN and CtBP-interacting protein (CtIP) to promote recruitment of the BLM helicase to DNA breaks. Collectively, these results provide insights into how mammalian cells respond to DSBs.
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Affiliation(s)
- Sophie E. Polo
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
| | - Andrew N. Blackford
- Cancer Research UK School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - J. Ross Chapman
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
| | - Linda Baskcomb
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
| | - Serge Gravel
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
| | - Andre Rusch
- Heinrich Pette Institute for Experimental Virology and Immunology, 20251 Hamburg, Germany
| | - Anoushka Thomas
- Cancer Research UK School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Rachel Blundred
- Cancer Research UK School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Philippa Smith
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
| | - Julia Kzhyshkowska
- Medical Faculty Mannheim, Ruprecht-Karls University of Heidelberg, 68167 Mannheim, Germany, and Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125 315 Moscow, Russia
| | - Thomas Dobner
- Heinrich Pette Institute for Experimental Virology and Immunology, 20251 Hamburg, Germany
| | - A. Malcolm R. Taylor
- Cancer Research UK School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew S. Turnell
- Cancer Research UK School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Grant S. Stewart
- Cancer Research UK School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Roger J. Grand
- Cancer Research UK School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Stephen P. Jackson
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
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27
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Abstract
Genome integrity is constantly monitored by sophisticated cellular networks, collectively termed the DNA damage response (DDR). A common feature of DDR proteins is their mobilization in response to genotoxic stress. Here, we outline how the development of various complementary methodologies has provided valuable insights into the spatiotemporal dynamics of DDR protein assembly/disassembly at sites of DNA strand breaks in eukaryotic cells. Considerable advances have also been made in understanding the underlying molecular mechanisms for these events, with post-translational modifications of DDR factors being shown to play prominent roles in controlling the formation of foci in response to DNA-damaging agents. We review these regulatory mechanisms and discuss their biological significance to the DDR.
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Affiliation(s)
- Sophie E Polo
- The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB21QN, United Kingdom
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28
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Harrigan JA, Belotserkovskaya R, Coates J, Dimitrova DS, Polo SE, Bradshaw CR, Fraser P, Jackson SP. Replication stress induces 53BP1-containing OPT domains in G1 cells. ACTA ACUST UNITED AC 2011; 193:97-108. [PMID: 21444690 PMCID: PMC3082192 DOI: 10.1083/jcb.201011083] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
53BP1-OPT domains, nuclear bodies that arise in G1 cells at sites of DNA damage induced by incomplete DNA replication, preferentially localize to chromosomal common fragile sites. Chromosomal deletions and rearrangements in tumors are often associated with common fragile sites, which are specific genomic loci prone to gaps and breaks in metaphase chromosomes. Common fragile sites appear to arise through incomplete DNA replication because they are induced after partial replication inhibition by agents such as aphidicolin. Here, we show that in G1 cells, large nuclear bodies arise that contain p53 binding protein 1 (53BP1), phosphorylated H2AX (γH2AX), and mediator of DNA damage checkpoint 1 (MDC1), as well as components of previously characterized OPT (Oct-1, PTF, transcription) domains. Notably, we find that incubating cells with low aphidicolin doses increases the incidence and number of 53BP1-OPT domains in G1 cells, and by chromatin immunoprecipitation and massively parallel sequencing analysis of γH2AX, we demonstrate that OPT domains are enriched at common fragile sites. These findings invoke a model wherein incomplete DNA synthesis during S phase leads to a DNA damage response and formation of 53BP1-OPT domains in the subsequent G1.
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Affiliation(s)
- Jeanine A Harrigan
- The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, England, UK
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29
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Polo SE, Theocharis SE, Grandin L, Gambotti L, Antoni G, Savignoni A, Asselain B, Patsouris E, Almouzni G. Clinical significance and prognostic value of chromatin assembly factor-1 overexpression in human solid tumours. Histopathology 2011; 57:716-24. [PMID: 21083601 DOI: 10.1111/j.1365-2559.2010.03681.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AIMS Chromatin assembly factor-1 (CAF-1), whose function is critical for maintaining chromatin stability during DNA replication and repair, has been identified as a proliferation marker in breast cancer. The aim was to investigate CAF-1 as a proliferation marker in a wide variety of solid tumours, and to assess its potential value in predicting clinical outcome. METHODS AND RESULTS Using immunocytochemistry on paraffin-embedded tissue sections, the CAF-1 labelling index was compared with known proliferation markers Ki-67 and minichromosome maintenance (MCM), and its association with clinicopathological data and patients' outcome analysed. CAF-1 expression showed a strong positive correlation with Ki-67, used routinely to detect proliferating cells, while it generally displayed weaker correlations with MCM markers, known to label cells with replicative potential. CAF-1 expression was associated significantly with histological grade in breast, cervical, endometrial and renal cell carcinomas, and with disease stage in endometrial and renal carcinomas. Furthermore, high expression of CAF-1 was an independent predictor of adverse clinical outcome in renal, endometrial and cervical carcinomas. CONCLUSIONS CAF-1 is a proliferation marker in various malignant tumours with prognostic value in renal, endometrial and cervical carcinomas, which supports the value of CAF-1 as a clinical marker of cancer progression.
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30
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Miller KM, Tjeertes JV, Coates J, Legube G, Polo SE, Britton S, Jackson SP. Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining. Nat Struct Mol Biol 2010; 17:1144-51. [PMID: 20802485 DOI: 10.1038/nsmb.1899] [Citation(s) in RCA: 477] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 07/20/2010] [Indexed: 12/18/2022]
Abstract
DNA double-strand break (DSB) repair occurs within chromatin and can be modulated by chromatin-modifying enzymes. Here we identify the related human histone deacetylases HDAC1 and HDAC2 as two participants in the DNA-damage response. We show that acetylation of histone H3 Lys56 (H3K56) was regulated by HDAC1 and HDAC2 and that HDAC1 and HDAC2 were rapidly recruited to DNA-damage sites to promote hypoacetylation of H3K56. Furthermore, HDAC1- and 2-depleted cells were hypersensitive to DNA-damaging agents and showed sustained DNA-damage signaling, phenotypes that reflect defective DSB repair, particularly by nonhomologous end-joining (NHEJ). Collectively, these results show that HDAC1 and HDAC2 function in the DNA-damage response by promoting DSB repair and thus provide important insights into the radio-sensitizing effects of HDAC inhibitors that are being developed as cancer therapies.
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Affiliation(s)
- Kyle M Miller
- The Gurdon Institute, University of Cambridge, Cambridge, UK
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31
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Ahel D, Horejsí Z, Wiechens N, Polo SE, Garcia-Wilson E, Ahel I, Flynn H, Skehel M, West SC, Jackson SP, Owen-Hughes T, Boulton SJ. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 2009; 325:1240-3. [PMID: 19661379 DOI: 10.1126/science.1177321] [Citation(s) in RCA: 450] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Posttranslational modifications play key roles in regulating chromatin plasticity. Although various chromatin-remodeling enzymes have been described that respond to specific histone modifications, little is known about the role of poly[adenosine 5'-diphosphate (ADP)-ribose] in chromatin remodeling. Here, we identify a chromatin-remodeling enzyme, ALC1 (Amplified in Liver Cancer 1, also known as CHD1L), that interacts with poly(ADP-ribose) and catalyzes PARP1-stimulated nucleosome sliding. Our results define ALC1 as a DNA damage-response protein whose role in this process is sustained by its association with known DNA repair factors and its rapid poly(ADP-ribose)-dependent recruitment to DNA damage sites. Furthermore, we show that depletion or overexpression of ALC1 results in sensitivity to DNA-damaging agents. Collectively, these results provide new insights into the mechanisms by which poly(ADP-ribose) regulates DNA repair.
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Affiliation(s)
- Dragana Ahel
- DNA Damage Response Laboratory, Clare Hall, London Research Institute, South Mimms EN6 3LD, UK
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32
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Abstract
DNA organization into chromatin has a major influence on the cellular response to DNA damage. Recent studies in various systems ranging from yeast to human cells stress the importance of chromatin not simply as a barrier to DNA repair processes but also as an active contributor to the DNA damage response. Indeed, modulations of chromatin organization involving various degrees of rearrangements, such as histone modifications and even nucleosome displacement, can promote efficient repair and also participate in checkpoint signaling. Here, we survey recent progress in delineating how chromatin rearrangements provide crosstalk with the DNA damage response. In particular, we highlight new data on histone dynamics at damage sites and discuss their functional importance for the stable propagation of specific chromatin states.
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Affiliation(s)
- Sophie E Polo
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
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33
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Affiliation(s)
- Sophie E Polo
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK.
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34
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Polo SE, Roche D, Almouzni G. New histone incorporation marks sites of UV repair in human cells. Cell 2006; 127:481-93. [PMID: 17081972 DOI: 10.1016/j.cell.2006.08.049] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 07/11/2006] [Accepted: 08/22/2006] [Indexed: 10/24/2022]
Abstract
Chromatin organization is compromised during the repair of DNA damage. It remains unknown how and to what extent epigenetic information is preserved in vivo. A central question is whether chromatin reorganization involves recycling of parental histones or new histone incorporation. Here, we devise an approach to follow new histone deposition upon UV irradiation in human cells. We show that new H3.1 histones get incorporated in vivo at repair sites. Remarkably we find that H3.1, which is deposited during S phase, is also incorporated outside of S phase. Histone deposition is dependent on nucleotide excision repair (NER), indicating that it occurs at a postrepair stage. The histone chaperone chromatin assembly factor 1 (CAF-1) is directly involved in the histone deposition process in vivo. We conclude that chromatin restoration after damage cannot rely simply on histone recycling. New histone incorporation at repair sites both challenges epigenetic stability and possibly contributes to damage memory.
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Affiliation(s)
- Sophie E Polo
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR 218 CNRS/Institut Curie, 26 rue d'Ulm, 75248 Paris cedex 5, France
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35
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Abstract
Packaging of eukaryotic genomes into chromatin is a hierarchical mechanism, starting with histone deposition onto DNA to produce nucleosome arrays, which then further fold and ultimately form functional domains. Recent studies provide interesting insight into how nucleosome assembly is coordinated with histone and DNA metabolism and underline the combined contribution of histone chaperones and chromatin remodelers. How these factors operate at a molecular level is a matter of current investigation. New data highlight the importance of histone dimers as deposition entities for de novo nucleosome assembly and identify dedicated machineries involved in histone variant deposition.
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Affiliation(s)
- Sophie E Polo
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR 218 CNRS/Institut Curie, 26 rue d'Ulm, 75248 Paris cedex 5, France
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36
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Abstract
In the eukaryotic nucleus, the DNA repair machinery operates on chromatin-embedded DNA substrates. Currently, a favored model for DNA repair into chromatin involves the transient disruption of chromatin organization to facilitate access of the repair machinery to DNA lesions. Importantly, this model implies that, in addition to DNA repair, a subsequent step is necessary to restore a proper chromatin structure. To study this latter step, we describe here methods for simultaneously analyzing chromatin assembly and DNA repair both in vitro and in vivo. Several cell-free systems have been developed that reproduce both DNA repair and nucleosome assembly. These in vitro systems are based on the use of defined damaged DNA. Two complementary assays are routinely used: (i) with circular DNA molecules, one can monitor in a combined analysis both repair synthesis and plasmid supercoiling; (ii) with immobilized damaged DNA, one follows specific protein interactions including histone deposition. In addition, in vivo assays have been designed to monitor the recruitment of chromatin assembly factors onto damaged chromatin either at a global level over the whole cell nucleus or locally at sites of DNA damage. Combination of these approaches provides powerful tools to gain insights into the mechanism by which chromatin organization can be restored after repair of DNA lesions.
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Affiliation(s)
- Annabelle Gérard
- Laboratory of Nuclear Dynamics and Genome Plasticity, Institut Curie, UMR 218, CNRS, Paris, France
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37
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Abstract
The structural organization of DNA into chromatin is of key importance to regulate genome function and stability. Maintenance of such an organization is thus crucial to preserve cellular identity. At each cell cycle, during S phase, this is achieved by duplication of chromatin structure in tight coordination with DNA replication. Such a coordinate process requires histone synthesis and their deposition onto DNA by chromatin assembly factors to be efficiently coupled to DNA synthesis. In this review, we highlight the intimate relationship between these chromatin-related events and DNA replication and we show how it is possible to take advantage of this coupling in order to identify cells with high replicative potential such as tumor cells. On the basis of recent data, we discuss the potential use of chromatin-associated factors as new proliferation markers of interest for cancer diagnosis and prognosis.
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Affiliation(s)
- Sophie E Polo
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR 218 CNRS/Institut Curie, 26 rue d'Ulm, 75248 Paris cedex 5, France
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38
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Polo SE, Theocharis SE, Klijanienko J, Savignoni A, Asselain B, Vielh P, Almouzni G. Chromatin assembly factor-1, a marker of clinical value to distinguish quiescent from proliferating cells. Cancer Res 2004; 64:2371-81. [PMID: 15059888 DOI: 10.1158/0008-5472.can-03-2893] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Histone synthesis and chromatin assembly are mainly associated with DNA replication and are thus intimately involved in cell cycle regulation. The expression of key components involved in these events in human cells was studied in relation to cell-proliferative status. Among several chromatin assembly factors, chromatin assembly factor (CAF)-1 stood out as the most discriminating marker of the proliferative state. We show, using both immunofluorescence and Western blot analysis, that the expression of both CAF-1 large subunits, p150 and p60, is massively down-regulated during quiescence in several cell lines. Upon exit from the quiescent state, the CAF-1 subunits are re-expressed early, before DNA replication. The amounts of either total or chromatin-associated pools of CAF-1 proteins correlate directly with cell proliferation. Regulation of CAF-1 expression is partly controlled at the RNA level, as shown by quantitative reverse transcription-PCR and Northern blot experiments. Biological material from benign and malignant human breast tumors analyzed by immunocytochemistry and immunohistochemistry exhibits a strong positive correlation between CAF-1 p60 expression and the following proliferation markers: S-phase fraction (r = 0.84, P < 0.0001); Ki-67 (r = 0.94, P < 0.0001); and proliferating cell nuclear antigen (r = 0.95, P = 0.0001). We discuss the advantages of using CAF-1 to assess cell proliferation. High CAF-1 p60 levels are also shown to be associated with various prognostic factors. Our data highlight the precise association of CAF-1 expression with the proliferative state and validate the use of this factor as a useful proliferation marker and prognostic indicator in malignant and benign breast lesions.
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MESH Headings
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/physiology
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cell Division/physiology
- Cell Line, Tumor
- Chromatin/metabolism
- Chromatin Assembly Factor-1
- Chromosomal Proteins, Non-Histone/biosynthesis
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/physiology
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/physiology
- Female
- Gene Expression Regulation, Neoplastic
- HeLa Cells
- Humans
- Immunohistochemistry
- Middle Aged
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Resting Phase, Cell Cycle/physiology
- S Phase/physiology
- Transcription Factors
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Affiliation(s)
- Sophie E Polo
- Laboratories of Nuclear Dynamics and Genome Plasticity, Curie Institute/CNRS, Paris, France
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