51
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Kallimasioti-Pazi EM, Thelakkad Chathoth K, Taylor GC, Meynert A, Ballinger T, Kelder MJE, Lalevée S, Sanli I, Feil R, Wood AJ. Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair. PLoS Biol 2018; 16:e2005595. [PMID: 30540740 PMCID: PMC6306241 DOI: 10.1371/journal.pbio.2005595] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 12/26/2018] [Accepted: 11/21/2018] [Indexed: 11/18/2022] Open
Abstract
Genome editing occurs in the context of chromatin, which is heterogeneous in structure and function across the genome. Chromatin heterogeneity is thought to affect genome editing efficiency, but this has been challenging to quantify due to the presence of confounding variables. Here, we develop a method that exploits the allele-specific chromatin status of imprinted genes in order to address this problem in cycling mouse embryonic stem cells (mESCs). Because maternal and paternal alleles of imprinted genes have identical DNA sequence and are situated in the same nucleus, allele-specific differences in the frequency and spectrum of mutations induced by CRISPR-Cas9 can be unequivocally attributed to epigenetic mechanisms. We found that heterochromatin can impede mutagenesis, but to a degree that depends on other key experimental parameters. Mutagenesis was impeded by up to 7-fold when Cas9 exposure was brief and when intracellular Cas9 expression was low. In contrast, the outcome of mutagenic DNA repair was unaffected by chromatin state, with similar efficiencies of homology-directed repair (HDR) and deletion spectra on maternal and paternal chromosomes. Combined, our data show that heterochromatin imposes a permeable barrier that influences the kinetics, but not the endpoint, of CRISPR-Cas9 genome editing and suggest that therapeutic applications involving low-level Cas9 exposure will be particularly affected by chromatin status.
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Affiliation(s)
- Eirini M. Kallimasioti-Pazi
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Keerthi Thelakkad Chathoth
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Gillian C. Taylor
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Tracy Ballinger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Martijn J. E. Kelder
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sébastien Lalevée
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and University of Montpellier, Montpellier, France
| | - Ildem Sanli
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and University of Montpellier, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and University of Montpellier, Montpellier, France
| | - Andrew J. Wood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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52
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Clouaire T, Rocher V, Lashgari A, Arnould C, Aguirrebengoa M, Biernacka A, Skrzypczak M, Aymard F, Fongang B, Dojer N, Iacovoni JS, Rowicka M, Ginalski K, Côté J, Legube G. Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures. Mol Cell 2018; 72:250-262.e6. [PMID: 30270107 PMCID: PMC6202423 DOI: 10.1016/j.molcel.2018.08.020] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/13/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
Double-strand breaks (DSBs) are extremely detrimental DNA lesions that can lead to cancer-driving mutations and translocations. Non-homologous end joining (NHEJ) and homologous recombination (HR) represent the two main repair pathways operating in the context of chromatin to ensure genome stability. Despite extensive efforts, our knowledge of DSB-induced chromatin still remains fragmented. Here, we describe the distribution of 20 chromatin features at multiple DSBs spread throughout the human genome using ChIP-seq. We provide the most comprehensive picture of the chromatin landscape set up at DSBs and identify NHEJ- and HR-specific chromatin events. This study revealed the existence of a DSB-induced monoubiquitination-to-acetylation switch on histone H2B lysine 120, likely mediated by the SAGA complex, as well as higher-order signaling at HR-repaired DSBs whereby histone H1 is evicted while ubiquitin and 53BP1 accumulate over the entire γH2AX domains. DSB-chromatin landscape and HR/NHEJ chromatin signatures uncovered by ChIP-seq H2BK120 undergoes a switch from ubiquitination to acetylation at a local scale H1 is removed and ubiquitin accumulates on entire γH2AX domains, mainly at HR DSB 53BP1 spreads over megabase-sized domains, mostly in G1 at HR-prone DSBs
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France.
| | - Vincent Rocher
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Anahita Lashgari
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Coline Arnould
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Marion Aguirrebengoa
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Anna Biernacka
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - François Aymard
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Bernard Fongang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA
| | - Norbert Dojer
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA; Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM and University of Toulouse, Toulouse 31062, France
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-0615, USA
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury Warsaw 93, 02-089, Poland
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France.
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53
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Rodriguez-Berriguete G, Granata G, Puliyadi R, Tiwana G, Prevo R, Wilson RS, Yu S, Buffa F, Humphrey TC, McKenna WG, Higgins GS. Nucleoporin 54 contributes to homologous recombination repair and post-replicative DNA integrity. Nucleic Acids Res 2018; 46:7731-7746. [PMID: 29986057 PMCID: PMC6125679 DOI: 10.1093/nar/gky569] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/25/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
The nuclear pore complex (NPC) machinery is emerging as an important determinant in the maintenance of genome integrity and sensitivity to DNA double-strand break (DSB)-inducing agents, such as ionising radiation (IR). In this study, using a high-throughput siRNA screen, we identified the central channel NPC protein Nup54, and concomitantly its molecular partners Nup62 and Nup58, as novel factors implicated in radiosensitivity. Nup54 depletion caused an increase in cell death by mitotic catastrophe after IR, and specifically enhanced both the duration of the G2 arrest and the radiosensitivity of cells that contained replicated DNA at the time of IR exposure. Nup54-depleted cells also exhibited increased formation of chromosome aberrations arisen from replicated DNA. Interestingly, we found that Nup54 is epistatic with the homologous recombination (HR) factor Rad51. Moreover, using specific DNA damage repair reporters, we observed a decreased HR repair activity upon Nup54 knockdown. In agreement with a role in HR repair, we also demonstrated a decreased formation of HR-linked DNA synthesis foci and sister chromatid exchanges after IR in cells depleted of Nup54. Our study reveals a novel role for Nup54 in the response to IR and the maintenance of HR-mediated genome integrity.
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Affiliation(s)
- Gonzalo Rodriguez-Berriguete
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Giovanna Granata
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Rathi Puliyadi
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Gaganpreet Tiwana
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Remko Prevo
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Rhodri S Wilson
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Sheng Yu
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Francesca Buffa
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Timothy C Humphrey
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - W Gillies McKenna
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Geoff S Higgins
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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54
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Abstract
53BP1 restrains DNA end resection, and its dosage imbalance upsets DNA double-strand break (DSB) repair pathway choice. Here, by monitoring 53BP1 distribution on DSB-flanking chromatin, we have established a dose-dependent role of the RING finger protein RNF169 in limiting 53BP1 DSB deposition. Moreover, we found that forced expression of RNF169 overcomes 53BP1 activity and stimulates mutagenic DSB repair via the single-strand annealing pathway. Our findings suggest that aberrant expression of RNF169 may represent a deleterious factor in DSB repair control and in maintenance of genome stability. Unrestrained 53BP1 activity at DNA double-strand breaks (DSBs) hampers DNA end resection and upsets DSB repair pathway choice. RNF169 acts as a molecular rheostat to limit 53BP1 deposition at DSBs, but how this fine balance translates to DSB repair control remains undefined. In striking contrast to 53BP1, ChIP analyses of AsiSI-induced DSBs unveiled that RNF169 exhibits robust accumulation at DNA end-proximal regions and preferentially targets resected, RPA-bound DSBs. Accordingly, we found that RNF169 promotes CtIP-dependent DSB resection and favors homology-mediated DSB repair, and further showed that RNF169 dose-dependently stimulates single-strand annealing repair, in part, by alleviating the 53BP1-imposed barrier to DSB end resection. Our results highlight the interplay of RNF169 with 53BP1 in fine-tuning choice of DSB repair pathways.
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55
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Abstract
During meiosis, maternal and paternal chromosomes undergo exchanges by homologous recombination. This is essential for fertility and contributes to genome evolution. In many eukaryotes, sites of meiotic recombination, also called hotspots, are regions of accessible chromatin, but in many vertebrates, their location follows a distinct pattern and is specified by PR domain-containing protein 9 (PRDM9). The specification of meiotic recombination hotspots is achieved by the different activities of PRDM9: DNA binding, histone methyltransferase, and interaction with other proteins. Remarkably, PRDM9 activity leads to the erosion of its own binding sites and the rapid evolution of its DNA-binding domain. PRDM9 may also contribute to reproductive isolation, as it is involved in hybrid sterility potentially due to a reduction of its activity in specific heterozygous contexts.
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Affiliation(s)
- Corinne Grey
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Bernard de Massy
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
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56
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Lukaszewicz A, Lange J, Keeney S, Jasin M. Control of meiotic double-strand-break formation by ATM: local and global views. Cell Cycle 2018; 17:1155-1172. [PMID: 29963942 PMCID: PMC6110601 DOI: 10.1080/15384101.2018.1464847] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/19/2018] [Accepted: 04/08/2018] [Indexed: 10/28/2022] Open
Abstract
DNA double-strand breaks (DSBs) generated by the SPO11 protein initiate meiotic recombination, an essential process for successful chromosome segregation during gametogenesis. The activity of SPO11 is controlled by multiple factors and regulatory mechanisms, such that the number of DSBs is limited and DSBs form at distinct positions in the genome and at the right time. Loss of this control can affect genome integrity or cause meiotic arrest by mechanisms that are not fully understood. Here we focus on the DSB-responsive kinase ATM and its functions in regulating meiotic DSB numbers and distribution. We review the recently discovered roles of ATM in this context, discuss their evolutionary conservation, and examine future research perspectives.
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Affiliation(s)
- Agnieszka Lukaszewicz
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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57
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Geel TM, Ruiters MHJ, Cool RH, Halby L, Voshart DC, Andrade Ruiz L, Niezen-Koning KE, Arimondo PB, Rots MG. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170077. [PMID: 29685979 PMCID: PMC5915719 DOI: 10.1098/rstb.2017.0077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- T M Geel
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - M H J Ruiters
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - R H Cool
- Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - L Halby
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - D C Voshart
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - L Andrade Ruiz
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - K E Niezen-Koning
- Laboratory of Metabolic Diseases, Dept Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - P B Arimondo
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - M G Rots
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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58
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Wei S, Li C, Yin Z, Wen J, Meng H, Xue L, Wang J. Histone methylation in DNA repair and clinical practice: new findings during the past 5-years. J Cancer 2018; 9:2072-2081. [PMID: 29937925 PMCID: PMC6010677 DOI: 10.7150/jca.23427] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 03/31/2018] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can impair cellular homeostasis and genome stability to result in tumorigenesis for inappropriate repair. Although DSBs are repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ), the related mechanisms are still incompletely unclear. Indeed, more and more evidences indicate that the methylation of histone lysine has an important role in choosing the pathways of DNA repair. For example, tri-methylated H3K36 is required for HR repair, while di-methylated H4K20 can recruit 53BP1 for NHEJ repair. Here, we reviewed the recent progress in the molecular mechanisms by which histone methylation functions in DNA double-strand breaks repair (DSBR). The insight into the mechanisms of histone methylation repairing DNA damage will supply important cues for clinical cancer treatment.
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Affiliation(s)
- Shuhua Wei
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Chunxiao Li
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Zhongnan Yin
- Medical Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Jie Wen
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Hui Meng
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
| | - Lixiang Xue
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China.,Medical Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Junjie Wang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing 100191, China
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59
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Sengupta A, Haldar D. Human sirtuin 3 (SIRT3) deacetylates histone H3 lysine 56 to promote nonhomologous end joining repair. DNA Repair (Amst) 2017; 61:1-16. [PMID: 29136592 DOI: 10.1016/j.dnarep.2017.11.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/20/2017] [Accepted: 11/07/2017] [Indexed: 01/28/2023]
Abstract
Human sirtuin 3 (SIRT3) is a conserved NAD+ dependent deacetylase, which functions in important cellular processes including transcription, metabolism, oxidative stress response. It is a robust mitochondrial deacetylase; however, few studies have indicated its nuclear functions. Here we report interaction of SIRT3 with core histones and identified acetylated histone H3 lysine 56 (H3K56ac) as its novel substrate, in addition to known substrates acetylated H4K16 and H3K9. Further, we showed in response to DNA damage SIRT3 localizes to the repair foci colocalizing with γH2AX and nonhomologous end joining (NHEJ) marker p53-binding protein 1 (53BP1). However, it does not colocalize with homologous repair (HR) marker BRCA1. By ChIP break assay, we demonstrated the recruitment of SIRT3 at the double strand-break site in response to DNA damage. Additionally, the relocalization of SIRT3 to the nucleus on MMS treatment led to concurrent decrease in H3K56ac, which is an important step in NHEJ. Depletion of SIRT3 by si-RNA mediated knock down affected recruitment of 53BP1, resulting in compromised NHEJ efficiency, and survival defect as seen by colony formation assay. Altogether, our results demonstrated that SIRT3 recruits 53BP1 to the site of damage thereby plays a significant role in NHEJ pathway.
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Affiliation(s)
- Amrita Sengupta
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, Ranga Reddy District, India; Graduate studies, Manipal University, Manipal, Karnataka 576104, India
| | - Devyani Haldar
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, Ranga Reddy District, India.
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60
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Zaki-Dizaji M, Akrami SM, Abolhassani H, Rezaei N, Aghamohammadi A. Ataxia telangiectasia syndrome: moonlighting ATM. Expert Rev Clin Immunol 2017; 13:1155-1172. [PMID: 29034753 DOI: 10.1080/1744666x.2017.1392856] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Ataxia-telangiectasia (A-T) a multisystem disorder primarily characterized by cerebellar degeneration, telangiectasia, immunodeficiency, cancer susceptibility and radiation sensitivity. Identification of the gene defective in this syndrome, ataxia-telangiectasia mutated gene (ATM), and further characterization of the disorder together with a greater insight into the function of the ATM protein have expanded our knowledge about the molecular pathogenesis of this disease. Area covered: In this review, we have attempted to summarize the different roles of ATM signaling that have provided new insights into the diverse clinical phenotypes exhibited by A-T patients. Expert commentary: ATM, in addition to DNA repair response, is involved in many cytoplasmic roles that explain diverse phenotypes of A-T patients. It seems accumulation of DNA damage, persistent DNA damage response signaling, and chronic oxidative stress are the main players in the pathogenesis of this disease.
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Affiliation(s)
- Majid Zaki-Dizaji
- a Department of Medical Genetics, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran.,b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran
| | - Seyed Mohammad Akrami
- a Department of Medical Genetics, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Hassan Abolhassani
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran.,c Division of Clinical Immunology, Department of Laboratory Medicine , Karolinska Institute at Karolinska University Hospital Huddinge , Stockholm , Sweden.,d Primary Immunodeficiency Diseases Network (PIDNet ), Universal Scientific Education and Research Network (USERN) , Stockholm , Sweden
| | - Nima Rezaei
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran.,e Department of Immunology and Biology, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran.,f Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
| | - Asghar Aghamohammadi
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Science , Tehran , Iran
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61
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Jeggo PA, Downs JA, Gasser SM. Chromatin modifiers and remodellers in DNA repair and signalling. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160279. [PMID: 28847816 PMCID: PMC5577457 DOI: 10.1098/rstb.2016.0279] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2017] [Indexed: 12/15/2022] Open
Affiliation(s)
- Penny A Jeggo
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton BN71TL, UK
| | - Jessica A Downs
- Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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62
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Abstract
Ataxia Telangiectasia Mutated (ATM) has been known for decades as the main kinase mediating the DNA Double-Strand Break Response (DDR). Extensive studies have revealed its dual role in locally promoting detection and repair of DSBs as well as in activating global DNA damage checkpoints. However, recent studies pinpoint additional unanticipated functions for ATM in modifying both the local chromatin landscape and the global chromosome organization, more particularly at persistent breaks. Given the emergence of a novel and unexpected class of DSBs prevalently arising in transcriptionally active genes and intrinsically difficult to repair, a specific role of ATM at refractory DSBs could be an important and so far overlooked feature of Ataxia Telangiectasia (A-T) a severe disorder associated with ATM mutations.
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France.
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63
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Menoni H, Di Mascio P, Cadet J, Dimitrov S, Angelov D. Chromatin associated mechanisms in base excision repair - nucleosome remodeling and DNA transcription, two key players. Free Radic Biol Med 2017; 107:159-169. [PMID: 28011149 DOI: 10.1016/j.freeradbiomed.2016.12.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022]
Abstract
Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health. Although the enzymology of BER mechanisms has been largely elucidated using chemically defined DNA damage substrates and purified proteins, the complex interplay of BER with another vital process like transcription or when DNA is in its natural state (i.e. wrapped in nucleosome and assembled in chromatin fiber is largely unexplored. Cells use chromatin remodeling factors to overcome the general repression associated with the nucleosomal organization. It is broadly accepted that energy-dependent nucleosome remodeling factors disrupt histones-DNA interactions at the expense of ATP hydrolysis to favor transcription as well as DNA repair. Importantly, unlike transcription, BER is not part of a regulated developmental process but represents a maintenance system that should be efficient anytime and anywhere in the genome. In this review we will discuss how BER can deal with chromatin organization to maintain genetic information. Emphasis will be placed on the following challenging question: how BER is initiated within chromatin?
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Affiliation(s)
- Hervé Menoni
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL UMR 5239 and Institut NeuroMyoGène - INMG CNRS/UCBL UMR 5310, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon, France; Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France.
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000 São Paulo, SP, Brazil
| | - Jean Cadet
- Département de Médecine Nucléaire et de Radiobiologie, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Stefan Dimitrov
- Université de Grenoble Alpes/INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS/ENSL/UCBL UMR 5239 and Institut NeuroMyoGène - INMG CNRS/UCBL UMR 5310, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon, France.
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64
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Marnef A, Cohen S, Legube G. Transcription-Coupled DNA Double-Strand Break Repair: Active Genes Need Special Care. J Mol Biol 2017; 429:1277-1288. [PMID: 28363678 DOI: 10.1016/j.jmb.2017.03.024] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/22/2022]
Abstract
For decades, it has been speculated that specific loci on eukaryotic chromosomes are inherently susceptible to breakage. The advent of high-throughput genomic technologies has now paved the way to their identification. A wealth of data suggests that transcriptionally active loci are particularly fragile and that a specific DNA damage response is activated and dedicated to their repair. Here, we review current understanding of the crosstalk between transcription and double-strand break repair, from the reasons underlying the intrinsic fragility of genes to the mechanisms that restore the integrity of damaged transcription units.
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Affiliation(s)
- Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France
| | - Sarah Cohen
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France.
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65
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Grey C, Clément JAJ, Buard J, Leblanc B, Gut I, Gut M, Duret L, de Massy B. In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites. Genome Res 2017; 27:580-590. [PMID: 28336543 PMCID: PMC5378176 DOI: 10.1101/gr.217240.116] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/23/2017] [Indexed: 02/02/2023]
Abstract
In mouse and human meiosis, DNA double-strand breaks (DSBs) initiate homologous recombination and occur at specific sites called hotspots. The localization of these sites is determined by the sequence-specific DNA binding domain of the PRDM9 histone methyl transferase. Here, we performed an extensive analysis of PRDM9 binding in mouse spermatocytes. Unexpectedly, we identified a noncanonical recruitment of PRDM9 to sites that lack recombination activity and the PRDM9 binding consensus motif. These sites include gene promoters, where PRDM9 is recruited in a DSB-dependent manner. Another subset reveals DSB-independent interactions between PRDM9 and genomic sites, such as the binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot-bound PRDM9 and genomic sequences located on the chromosome axis.
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Affiliation(s)
- Corinne Grey
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396 Montpellier Cedex 05, France
| | - Julie A J Clément
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396 Montpellier Cedex 05, France
| | - Jérôme Buard
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396 Montpellier Cedex 05, France
| | - Benjamin Leblanc
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Laurent Duret
- Université de Lyon, Université Claude Bernard, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69100, Villeurbanne, France
| | - Bernard de Massy
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396 Montpellier Cedex 05, France
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66
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Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes. Nat Struct Mol Biol 2017; 24:353-361. [PMID: 28263325 PMCID: PMC5385132 DOI: 10.1038/nsmb.3387] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/07/2017] [Indexed: 12/29/2022]
Abstract
The ability of DNA Double Strand Breaks (DSBs) to cluster in mammalian cells has been subjected to intense debate over the past few years. Here we used a high throughput chromosome conformation capture assay (Capture Hi-C) to investigate clustering of DSBs induced at defined loci in the human genome. We unambiguously found that DSBs do cluster but only when induced in transcriptionally active genes. Clustering of damaged genes mainly occurs during the G1 cell cycle phase and coincides with delayed repair. Moreover DSB clustering depends on the MRN complex, as well as the Formin 2 (FMN2) nuclear actin organizer and the LINC (LInker of Nuclear and Cytoplasmic skeleton) complex, suggesting that active mechanisms promote DSB clustering. This work reveals that when damaged, active genes exhibit a very peculiar behavior compared to the rest of the genome, being mostly left unrepaired and clustered in G1 while being repaired by homologous recombination in post-replicative cells.
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67
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Marnef A, Legube G. Organizing DNA repair in the nucleus: DSBs hit the road. Curr Opin Cell Biol 2017; 46:1-8. [PMID: 28068556 DOI: 10.1016/j.ceb.2016.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/30/2016] [Accepted: 12/12/2016] [Indexed: 10/20/2022]
Abstract
In the past decade, large-scale movements of DNA double strand breaks (DSBs) have repeatedly been identified following DNA damage. These mobility events include clustering, anchoring or peripheral movement at subnuclear structures. Recent work suggests roles for motion in homology search and in break sequestration to preclude deleterious outcomes. Yet, the precise functions of these movements still remain relatively obscure, and the same holds true for the determinants. Here we review recent advances in this exciting area of research, and highlight that a recurrent characteristic of mobile DSBs may lie in their inability to undergo rapid repair. A major future challenge remains to understand how DSB mobility impacts on genome integrity.
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Affiliation(s)
- Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France.
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68
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Chanut P, Britton S, Coates J, Jackson SP, Calsou P. Coordinated nuclease activities counteract Ku at single-ended DNA double-strand breaks. Nat Commun 2016; 7:12889. [PMID: 27641979 PMCID: PMC5031800 DOI: 10.1038/ncomms12889] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/12/2016] [Indexed: 12/16/2022] Open
Abstract
Repair of single-ended DNA double-strand breaks (seDSBs) by homologous recombination (HR) requires the generation of a 3' single-strand DNA overhang by exonuclease activities in a process called DNA resection. However, it is anticipated that the highly abundant DNA end-binding protein Ku sequesters seDSBs and shields them from exonuclease activities. Despite pioneering works in yeast, it is unclear how mammalian cells counteract Ku at seDSBs to allow HR to proceed. Here we show that in human cells, ATM-dependent phosphorylation of CtIP and the epistatic and coordinated actions of MRE11 and CtIP nuclease activities are required to limit the stable loading of Ku on seDSBs. We also provide evidence for a hitherto unsuspected additional mechanism that contributes to prevent Ku accumulation at seDSBs, acting downstream of MRE11 endonuclease activity and in parallel with MRE11 exonuclease activity. Finally, we show that Ku persistence at seDSBs compromises Rad51 focus assembly but not DNA resection.
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Affiliation(s)
- Pauline Chanut
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
- Equipe labellisée Ligue Nationale Contre le Cancer
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
- Equipe labellisée Ligue Nationale Contre le Cancer
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Stephen P. Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
- Equipe labellisée Ligue Nationale Contre le Cancer
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69
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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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70
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DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: Cell cycle and proliferation-dependent regulation. Semin Cancer Biol 2016; 37-38:51-64. [DOI: 10.1016/j.semcancer.2016.03.003] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 12/18/2022]
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71
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Complex interactions between the DNA-damage response and mammalian telomeres. Nat Struct Mol Biol 2016; 22:859-66. [PMID: 26581520 DOI: 10.1038/nsmb.3092] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/23/2015] [Indexed: 12/28/2022]
Abstract
Natural chromosome ends resemble double-stranded DNA breaks, but they do not activate a damage response in healthy cells. Telomeres therefore have evolved to solve the 'end-protection problem' by inhibiting multiple DNA damage-response pathways. During the past decade, the view of telomeres has progressed from simple caps that hide chromosome ends to complex machineries that have an active role in organizing the genome. Here we focus on mammalian telomeres and summarize and interpret recent discoveries in detail, focusing on how repair pathways are inhibited, how resection and replication are controlled and how these mechanisms govern cell fate during senescence, crisis and transformation.
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72
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Caron P, Choudjaye J, Clouaire T, Bugler B, Daburon V, Aguirrebengoa M, Mangeat T, Iacovoni JS, Álvarez-Quilón A, Cortés-Ledesma F, Legube G. Non-redundant Functions of ATM and DNA-PKcs in Response to DNA Double-Strand Breaks. Cell Rep 2015; 13:1598-609. [PMID: 26586426 PMCID: PMC4670905 DOI: 10.1016/j.celrep.2015.10.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 09/04/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022] Open
Abstract
DNA double-strand breaks (DSBs) elicit the so-called DNA damage response (DDR), largely relying on ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PKcs), two members of the PI3K-like kinase family, whose respective functions during the sequential steps of the DDR remains controversial. Using the DIvA system (DSB inducible via AsiSI) combined with high-resolution mapping and advanced microscopy, we uncovered that both ATM and DNA-PKcs spread in cis on a confined region surrounding DSBs, independently of the pathway used for repair. However, once recruited, these kinases exhibit non-overlapping functions on end joining and γH2AX domain establishment. More specifically, we found that ATM is required to ensure the association of multiple DSBs within "repair foci." Our results suggest that ATM acts not only on chromatin marks but also on higher-order chromatin organization to ensure repair accuracy and survival.
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Affiliation(s)
- Pierre Caron
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Jonathan Choudjaye
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Thomas Clouaire
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Béatrix Bugler
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Virginie Daburon
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Marion Aguirrebengoa
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Thomas Mangeat
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM and University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse Cedex 4, France
| | - Alejandro Álvarez-Quilón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
| | - Gaëlle Legube
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France.
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73
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Lavin MF, Kozlov S, Gatei M, Kijas AW. ATM-Dependent Phosphorylation of All Three Members of the MRN Complex: From Sensor to Adaptor. Biomolecules 2015; 5:2877-902. [PMID: 26512707 PMCID: PMC4693261 DOI: 10.3390/biom5042877] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/16/2022] Open
Abstract
The recognition, signalling and repair of DNA double strand breaks (DSB) involves the participation of a multitude of proteins and post-translational events that ensure maintenance of genome integrity. Amongst the proteins involved are several which when mutated give rise to genetic disorders characterised by chromosomal abnormalities, cancer predisposition, neurodegeneration and other pathologies. ATM (mutated in ataxia-telangiectasia (A-T) and members of the Mre11/Rad50/Nbs1 (MRN complex) play key roles in this process. The MRN complex rapidly recognises and locates to DNA DSB where it acts to recruit and assist in ATM activation. ATM, in the company of several other DNA damage response proteins, in turn phosphorylates all three members of the MRN complex to initiate downstream signalling. While ATM has hundreds of substrates, members of the MRN complex play a pivotal role in mediating the downstream signalling events that give rise to cell cycle control, DNA repair and ultimately cell survival or apoptosis. Here we focus on the interplay between ATM and the MRN complex in initiating signaling of breaks and more specifically on the adaptor role of the MRN complex in mediating ATM signalling to downstream substrates to control different cellular processes.
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Affiliation(s)
- Martin F Lavin
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
| | - Sergei Kozlov
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
| | - Magtouf Gatei
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
| | - Amanda W Kijas
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
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74
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Gravells P, Ahrabi S, Vangala RK, Tomita K, Brash JT, Brustle LA, Chung C, Hong JM, Kaloudi A, Humphrey TC, Porter ACG. Use of the HPRT gene to study nuclease-induced DNA double-strand break repair. Hum Mol Genet 2015; 24:7097-110. [PMID: 26423459 PMCID: PMC4654060 DOI: 10.1093/hmg/ddv409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/23/2015] [Indexed: 12/17/2022] Open
Abstract
Understanding the mechanisms of chromosomal double-strand break repair (DSBR) provides insight into genome instability, oncogenesis and genome engineering, including disease gene correction. Research into DSBR exploits rare-cutting endonucleases to cleave exogenous reporter constructs integrated into the genome. Multiple reporter constructs have been developed to detect various DSBR pathways. Here, using a single endogenous reporter gene, the X-chromosomal disease gene encoding hypoxanthine phosphoribosyltransferase (HPRT), we monitor the relative utilization of three DSBR pathways following cleavage by I-SceI or CRISPR/Cas9 nucleases. For I-SceI, our estimated frequencies of accurate or mutagenic non-homologous end-joining and gene correction by homologous recombination are 4.1, 1.5 and 0.16%, respectively. Unexpectedly, I-SceI and Cas9 induced markedly different DSBR profiles. Also, using an I-SceI-sensitive HPRT minigene, we show that gene correction is more efficient when using long double-stranded DNA than single- or double-stranded oligonucleotides. Finally, using both endogenous HPRT and exogenous reporters, we validate novel cell cycle phase-specific I-SceI derivatives for investigating cell cycle variations in DSBR. The results obtained using these novel approaches provide new insights into template design for gene correction and the relationships between multiple DSBR pathways at a single endogenous disease gene.
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Affiliation(s)
- Polly Gravells
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - Sara Ahrabi
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Rajani K Vangala
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - Kazunori Tomita
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - James T Brash
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - Lena A Brustle
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - Christopher Chung
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - Julia M Hong
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - Aikaterini Kaloudi
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
| | - Timothy C Humphrey
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W120NN, UK and
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