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Lesage E, Clouaire T, Legube G. Repair of DNA double-strand breaks in RNAPI- and RNAPII-transcribed loci. DNA Repair (Amst) 2021; 104:103139. [PMID: 34111758 DOI: 10.1016/j.dnarep.2021.103139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
DNA double-strand breaks (DSBs) are toxic lesions triggered not only by environmental sources, but also by a large number of physiological processes. Of importance, endogenous DSBs frequently occur in genomic loci that are transcriptionally active. Recent work suggests that DSBs occurring in transcribed loci are handled by specific pathway(s) that entail local transcriptional repression, chromatin signaling, the involvement of RNA species and DSB mobility. In this Graphical Review we provide an updated view of the "Transcription-Coupled DSB Repair" (TC-DSBR) pathway(s) that are mounted at DSBs occurring in loci transcribed by RNA Polymerase I (RNAPI) or RNA Polymerase II (RNAPII), highlighting differences and common features, as well as yet unanswered questions.
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Affiliation(s)
- E Lesage
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - T Clouaire
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France
| | - G Legube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), UPS, CNRS, Toulouse, France.
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2
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Liddiard K, Grimstead JW, Cleal K, Evans A, Baird DM. Tracking telomere fusions through crisis reveals conflict between DNA transcription and the DNA damage response. NAR Cancer 2021; 3:zcaa044. [PMID: 33447828 PMCID: PMC7787266 DOI: 10.1093/narcan/zcaa044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/02/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Identifying attributes that distinguish pre-malignant from senescent cells provides opportunities for targeted disease eradication and revival of anti-tumour immunity. We modelled a telomere-driven crisis in four human fibroblast lines, sampling at multiple time points to delineate genomic rearrangements and transcriptome developments that characterize the transition from dynamic proliferation into replicative crisis. Progression through crisis was associated with abundant intra-chromosomal telomere fusions with increasing asymmetry and reduced microhomology usage, suggesting shifts in DNA repair capacity. Eroded telomeres also fused with genomic loci actively engaged in transcription, with particular enrichment in long genes. Both gross copy number alterations and transcriptional responses to crisis likely underpin the elevated frequencies of telomere fusion with chromosomes 9, 16, 17, 19 and most exceptionally, chromosome 12. Juxtaposition of crisis-regulated genes with loci undergoing de novo recombination exposes the collusive contributions of cellular stress responses to the evolving cancer genome.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Julia W Grimstead
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Kez Cleal
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Anna Evans
- Wales Gene Park, Institute of Medical Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
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Pentzold C, Kokal M, Pentzold S, Weise A. Sites of chromosomal instability in the context of nuclear architecture and function. Cell Mol Life Sci 2020; 78:2095-2103. [PMID: 33219838 PMCID: PMC7966619 DOI: 10.1007/s00018-020-03698-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/02/2020] [Accepted: 10/31/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal fragile sites are described as areas within the tightly packed mitotic chromatin that appear as breaks or gaps mostly tracing back to a loosened structure and not a real nicked break within the DNA molecule. Most facts about fragile sites result from studies in mitotic cells, mainly during metaphase and mainly in lymphocytes. Here, we synthesize facts about the genomic regions that are prone to form gaps and breaks on metaphase chromosomes in the context of interphase. We conclude that nuclear architecture shapes the activity profile of the cell, i.e. replication timing and transcriptional activity, thereby influencing genomic integrity during interphase with the potential to cause fragility in mitosis. We further propose fragile sites as examples of regions specifically positioned in the interphase nucleus with putative anchoring points at the nuclear lamina to enable a tightly regulated replication–transcription profile and diverse signalling functions in the cell. Consequently, fragility starts before the actual display as chromosomal breakage in metaphase to balance the initial contradiction of cellular overgrowth or malfunctioning and maintaining diversity in molecular evolution.
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Affiliation(s)
- Constanze Pentzold
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany.
| | - Miriam Kokal
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Stefan Pentzold
- Research Center Lobeda, Jena University Hospital, 07747, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
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Miné-Hattab J, Chiolo I. Complex Chromatin Motions for DNA Repair. Front Genet 2020; 11:800. [PMID: 33061931 PMCID: PMC7481375 DOI: 10.3389/fgene.2020.00800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.
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Affiliation(s)
- Judith Miné-Hattab
- UMR 3664, CNRS, Institut Curie, PSL Research University, Paris, France
- UMR 3664, CNRS, Institut Curie, Sorbonne Université, Paris, France
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
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Marnef A, Finoux AL, Arnould C, Guillou E, Daburon V, Rocher V, Mangeat T, Mangeot PE, Ricci EP, Legube G. A cohesin/HUSH- and LINC-dependent pathway controls ribosomal DNA double-strand break repair. Genes Dev 2019; 33:1175-1190. [PMID: 31395742 PMCID: PMC6719620 DOI: 10.1101/gad.324012.119] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/26/2019] [Indexed: 02/01/2023]
Abstract
The ribosomal DNA (rDNA) represents a particularly unstable locus undergoing frequent breakage. DNA double-strand breaks (DSBs) within rDNA induce both rDNA transcriptional repression and nucleolar segregation, but the link between the two events remains unclear. Here we found that DSBs induced on rDNA trigger transcriptional repression in a cohesin- and HUSH (human silencing hub) complex-dependent manner throughout the cell cycle. In S/G2 cells, transcriptional repression is further followed by extended resection within the interior of the nucleolus, DSB mobilization at the nucleolar periphery within nucleolar caps, and repair by homologous recombination. We showed that nuclear envelope invaginations frequently connect the nucleolus and that rDNA DSB mobilization, but not transcriptional repression, involves the nuclear envelope-associated LINC complex and the actin pathway. Altogether, our data indicate that rDNA break localization at the nucleolar periphery is not a direct consequence of transcriptional repression but rather is an active process that shares features with the mobilization of persistent DSB in active genes and heterochromatin.
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Affiliation(s)
- Aline Marnef
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Anne-Laure Finoux
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Coline Arnould
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Emmanuelle Guillou
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Virginie Daburon
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Vincent Rocher
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Thomas Mangeat
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
| | - Philippe E Mangeot
- International Center for Infectiology Research (CIRI), Ecole Normale Supérieure de Lyon (ENS), U1111, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR5308, Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1, Université Lyon, Lyon F-6900, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC), Ecole Normale Supérieure de Lyon (ENS), U1210, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR5239, Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1, Université de Lyon, Lyon F-69007, France
| | - Gaëlle Legube
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse 31062, France
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Arnould C, Legube G. The Secret Life of Chromosome Loops upon DNA Double-Strand Break. J Mol Biol 2019; 432:724-736. [PMID: 31401119 PMCID: PMC7057266 DOI: 10.1016/j.jmb.2019.07.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022]
Abstract
DNA double-strand breaks (DSBs) are harmful lesions that severely challenge genomic integrity, and recent evidence suggests that DSBs occur more frequently on the genome than previously thought. These lesions activate a complex and multilayered response called the DNA damage response, which allows to coordinate their repair with the cell cycle progression. While the mechanistic details of repair processes have been narrowed, thanks to several decades of intense studies, our knowledge of the impact of DSB on chromatin composition and chromosome architecture is still very sparse. However, the recent development of various tools to induce DSB at annotated loci, compatible with next-generation sequencing-based approaches, is opening a new framework to tackle these questions. Here we discuss the influence of initial and DSB-induced chromatin conformation and the strong potential of 3C-based technologies to decipher the contribution of chromosome architecture during DSB repair.
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Affiliation(s)
- Coline Arnould
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
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Bouwman BAM, Crosetto N. Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling. Genes (Basel) 2018; 9:E632. [PMID: 30558210 PMCID: PMC6316733 DOI: 10.3390/genes9120632] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) jeopardize genome integrity and can-when repaired unfaithfully-give rise to structural rearrangements associated with cancer. Exogenous agents such as ionizing radiation or chemotherapy can invoke DSBs, but a vast amount of breakage arises during vital endogenous DNA transactions, such as replication and transcription. Additionally, chromatin looping involved in 3D genome organization and gene regulation is increasingly recognized as a possible contributor to DSB events. In this review, we first discuss insights into the mechanisms of endogenous DSB formation, showcasing the trade-off between essential DNA transactions and the intrinsic challenges that these processes impose on genomic integrity. In the second part, we highlight emerging methods for genome-wide profiling of DSBs, and discuss future directions of research that will help advance our understanding of genome-wide DSB formation and repair.
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Affiliation(s)
- Britta A M Bouwman
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden.
| | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden.
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