1
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Bedir M, Outwin E, Colnaghi R, Bassett L, Abramowicz I, O'Driscoll M. A novel role for the peptidyl-prolyl cis-trans isomerase Cyclophilin A in DNA-repair following replication fork stalling via the MRE11-RAD50-NBS1 complex. EMBO Rep 2024:10.1038/s44319-024-00184-9. [PMID: 38943005 DOI: 10.1038/s44319-024-00184-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024] Open
Abstract
Cyclosporin A (CsA) induces DNA double-strand breaks in LIG4 syndrome fibroblasts, specifically upon transit through S-phase. The basis underlying this has not been described. CsA-induced genomic instability may reflect a direct role of Cyclophilin A (CYPA) in DNA repair. CYPA is a peptidyl-prolyl cis-trans isomerase (PPI). CsA inhibits the PPI activity of CYPA. Using an integrated approach involving CRISPR/Cas9-engineering, siRNA, BioID, co-immunoprecipitation, pathway-specific DNA repair investigations as well as protein expression interaction analysis, we describe novel impacts of CYPA loss and inhibition on DNA repair. We characterise a direct CYPA interaction with the NBS1 component of the MRE11-RAD50-NBS1 complex, providing evidence that CYPA influences DNA repair at the level of DNA end resection. We define a set of genetic vulnerabilities associated with CYPA loss and inhibition, identifying DNA replication fork protection as an important determinant of viability. We explore examples of how CYPA inhibition may be exploited to selectively kill cancers sharing characteristic genomic instability profiles, including MYCN-driven Neuroblastoma, Multiple Myeloma and Chronic Myelogenous Leukaemia. These findings propose a repurposing strategy for Cyclophilin inhibitors.
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Affiliation(s)
- Marisa Bedir
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Emily Outwin
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Lydia Bassett
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Iga Abramowicz
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK
| | - Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, University of Sussex, Brighton, BN1 9RQ, UK.
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2
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Técher H, Gopaul D, Heuzé J, Bouzalmad N, Leray B, Vernet A, Mettling C, Moreaux J, Pasero P, Lin YL. MRE11 and TREX1 control senescence by coordinating replication stress and interferon signaling. Nat Commun 2024; 15:5423. [PMID: 38926338 PMCID: PMC11208572 DOI: 10.1038/s41467-024-49740-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Oncogene-induced senescence (OIS) arrests cell proliferation in response to replication stress (RS) induced by oncogenes. OIS depends on the DNA damage response (DDR), but also on the cGAS-STING pathway, which detects cytosolic DNA and induces type I interferons (IFNs). Whether and how RS and IFN responses cooperate to promote OIS remains unknown. Here, we show that the induction of OIS by the H-RASV12 oncogene in immortalized human fibroblasts depends on the MRE11 nuclease. Indeed, treatment with the MRE11 inhibitor Mirin prevented RS, micronuclei formation and IFN response induced by RASV12. Overexpression of the cytosolic nuclease TREX1 also prevented OIS. Conversely, overexpression of a dominant negative mutant of TREX1 or treatment with IFN-β was sufficient to induce RS and DNA damage, independent of RASV12 induction. These data suggest that the IFN response acts as a positive feedback loop to amplify DDR in OIS through a process regulated by MRE11 and TREX1.
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Affiliation(s)
- Hervé Técher
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
- Institute for Research on Cancer and Aging of Nice (IRCAN), Université Côte d'Azur, CNRS UMR7284 - INSERM U1081, Nice, France
| | - Diyavarshini Gopaul
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
- Biotech Research and Innovation Centre, University of Copenhagen, 2200 N, Copenhagen, Denmark
| | - Jonathan Heuzé
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Nail Bouzalmad
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Baptiste Leray
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Audrey Vernet
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Clément Mettling
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | - Jérôme Moreaux
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- University of Montpellier, UFR Medicine, Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
| | - Yea-Lih Lin
- Institut de Génétique Humaine, University of Montpellier, CNRS, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
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3
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Bosart K, Petreaca RC, Bouley RA. In silico analysis of several frequent SLX4 mutations appearing in human cancers. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001216. [PMID: 38828439 PMCID: PMC11143449 DOI: 10.17912/micropub.biology.001216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
SLX4 is an interactor and activator of structure-specific exonuclease that helps resolve tangled recombination intermediates arising at stalled replication forks. It is one of the many factors that assist with homologous recombination, the major mechanism for restarting replication. SLX4 mutations have been reported in many cancers but a pan cancer map of all the mutations has not been undertaken. Here, using data from the Catalogue of Somatic Mutations in Cancers (COSMIC), we show that mutations occur in almost every cancer and many of them truncate the protein which should severely alter the function of the enzyme. We identified a frequent R1779W point mutation that occurs in the SLX4 domain required for heterodimerization with its partner, SLX1. In silico protein structure analysis of this mutation shows that it significantly alters the protein structure and is likely to destabilize the interaction with SLX1. Although this brief communication is limited to only in silico analysis, it identifies certain high frequency SLX4 mutations in human cancers that would warrant further in vivo studies. Additionally, these mutations may be potentially actionable for drug therapies.
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Affiliation(s)
- Korey Bosart
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States
| | - Ruben C Petreaca
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States
- Molecular Genetics, The Ohio State University at Marion, Marion, Ohio, United States
| | - Renee A Bouley
- Chemistry and Biochemistry, The Ohio State University at Marion, Marion, Ohio, United States
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4
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Muñoz S, Blanco-Romero E, González-Acosta D, Rodriguez-Acebes S, Megías D, Lopes M, Méndez J. RAD51 restricts DNA over-replication from re-activated origins. EMBO J 2024; 43:1043-1064. [PMID: 38360996 PMCID: PMC10942984 DOI: 10.1038/s44318-024-00038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
Eukaryotic cells rely on several mechanisms to ensure that the genome is duplicated precisely once in each cell division cycle, preventing DNA over-replication and genomic instability. Most of these mechanisms limit the activity of origin licensing proteins to prevent the reactivation of origins that have already been used. Here, we have investigated whether additional controls restrict the extension of re-replicated DNA in the event of origin re-activation. In a genetic screening in cells forced to re-activate origins, we found that re-replication is limited by RAD51 and enhanced by FBH1, a RAD51 antagonist. In the presence of chromatin-bound RAD51, forks stemming from re-fired origins are slowed down, leading to frequent events of fork reversal. Eventual re-initiation of DNA synthesis mediated by PRIMPOL creates ssDNA gaps that facilitate the partial elimination of re-duplicated DNA by MRE11 exonuclease. In the absence of RAD51, these controls are abrogated and re-replication forks progress much longer than in normal conditions. Our study uncovers a safeguard mechanism to protect genome stability in the event of origin reactivation.
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Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Elena Blanco-Romero
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Daniel González-Acosta
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Advanced Optical Microscopy Unit, Central Core Facilities, Instituto de Salud Carlos III, Madrid, Spain
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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5
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Guo L, Bao Y, Zhao Y, Ren Z, Bi L, Zhang X, Liu C, Hou X, Wang MD, Sun B. Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G-Quadruplex. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307696. [PMID: 38126671 PMCID: PMC10916570 DOI: 10.1002/advs.202307696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/28/2023] [Indexed: 12/23/2023]
Abstract
G-quadruplex (G4) is a four-stranded noncanonical DNA structure that has long been recognized as a potential hindrance to DNA replication. However, how replisomes effectively deal with G4s to avoid replication failure is still obscure. Here, using single-molecule and ensemble approaches, the consequence of the collision between bacteriophage T7 replisome and an intramolecular G4 located on either the leading or lagging strand is examined. It is found that the adjacent fork junctions induced by G4 formation incur the binding of T7 DNA polymerase (DNAP). In addition to G4, these inactive DNAPs present insuperable obstacles, impeding the progression of DNA synthesis. Nevertheless, T7 helicase can dismantle them and resolve lagging-strand G4s, paving the way for the advancement of the replication fork. Moreover, with the assistance of the single-stranded DNA binding protein (SSB) gp2.5, T7 helicase is also capable of maintaining a leading-strand G4 structure in an unfolded state, allowing for a fraction of T7 DNAPs to synthesize through without collapse. These findings broaden the functional repertoire of a replicative helicase and underscore the inherent G4 tolerance of a replisome.
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Affiliation(s)
- Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yanling Bao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yilin Zhao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Zhiyun Ren
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai201210China
| | - Xi‐Miao Hou
- College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State PhysicsCornell UniversityIthacaNY14853USA
- Howard Hughes Medical InstituteCornell UniversityIthacaNY14853USA
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
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6
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Khodaverdian V, Sano T, Maggs L, Tomarchio G, Dias A, Clairmont C, Tran M, McVey M. REV1 Coordinates a Multi-Faceted Tolerance Response to DNA Alkylation Damage and Prevents Chromosome Shattering in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580051. [PMID: 38405884 PMCID: PMC10888836 DOI: 10.1101/2024.02.13.580051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
When replication forks encounter damaged DNA, cells utilize DNA damage tolerance mechanisms to allow replication to proceed. These include translesion synthesis at the fork, postreplication gap filling, and template switching via fork reversal or homologous recombination. The extent to which these different damage tolerance mechanisms are utilized depends on cell, tissue, and developmental context-specific cues, the last two of which are poorly understood. To address this gap, we have investigated damage tolerance responses following alkylation damage in Drosophila melanogaster. We report that translesion synthesis, rather than template switching, is the preferred response to alkylation-induced damage in diploid larval tissues. Furthermore, we show that the REV1 protein plays a multi-faceted role in damage tolerance in Drosophila. Drosophila larvae lacking REV1 are hypersensitive to methyl methanesulfonate (MMS) and have highly elevated levels of γ-H2Av foci and chromosome aberrations in MMS-treated tissues. Loss of the REV1 C-terminal domain (CTD), which recruits multiple translesion polymerases to damage sites, sensitizes flies to MMS. In the absence of the REV1 CTD, DNA polymerases eta and zeta become critical for MMS tolerance. In addition, flies lacking REV3, the catalytic subunit of polymerase zeta, require the deoxycytidyl transferase activity of REV1 to tolerate MMS. Together, our results demonstrate that Drosophila prioritize the use of multiple translesion polymerases to tolerate alkylation damage and highlight the critical role of REV1 in the coordination of this response to prevent genome instability.
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Affiliation(s)
- Varandt Khodaverdian
- Department of Biology, Tufts University, Medford, MA 02155
- Current address: Yarrow Biotechnology, New York, NY
| | - Tokio Sano
- Department of Biology, Tufts University, Medford, MA 02155
| | - Lara Maggs
- Department of Biology, Tufts University, Medford, MA 02155
| | - Gina Tomarchio
- Current address: Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ana Dias
- Department of Biology, Tufts University, Medford, MA 02155
| | - Connor Clairmont
- Department of Biology, Tufts University, Medford, MA 02155
- Current address: Vertex Pharmaceuticals, Boston, MA
| | - Mai Tran
- Department of Biology, Tufts University, Medford, MA 02155
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, MA 02155
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7
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Heuzé J, Kemiha S, Barthe A, Vilarrubias AT, Aouadi E, Aiello U, Libri D, Lin Y, Lengronne A, Poli J, Pasero P. RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart. EMBO J 2023; 42:e113104. [PMID: 37855233 PMCID: PMC10690446 DOI: 10.15252/embj.2022113104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.
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Affiliation(s)
- Jonathan Heuzé
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Samira Kemiha
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Antoine Barthe
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Alba Torán Vilarrubias
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Elyès Aouadi
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
- Present address:
Institut de Génétique Moléculaire de MontpellierUniversité de Montpellier, CNRSMontpellierFrance
| | - Yea‐Lih Lin
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Armelle Lengronne
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
| | - Jérôme Poli
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Philippe Pasero
- Institut de Génétique HumaineUniversité de Montpellier, CNRS, Equipe labélisée Ligue contre le CancerMontpellierFrance
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8
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Bai G, Endres T, Kühbacher U, Greer BH, Peacock EM, Crossley MP, Sathirachinda A, Cortez D, Eichman BF, Cimprich KA. HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.563641. [PMID: 37961428 PMCID: PMC10634870 DOI: 10.1101/2023.10.27.563641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
G-quadruplexes (G4s) form throughout the genome and influence important cellular processes, but their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected, dual role for the dsDNA translocase HLTF in G4 metabolism. First, we find that HLTF is enriched at G4s in the human genome and suppresses G4 accumulation throughout the cell cycle using its ATPase activity. This function of HLTF affects telomere maintenance by restricting alternative lengthening of telomeres, a process stimulated by G4s. We also show that HLTF and MSH2, a mismatch repair factor that binds G4s, act in independent pathways to suppress G4s and to promote resistance to G4 stabilization. In a second, distinct role, HLTF restrains DNA synthesis upon G4 stabilization by suppressing PrimPol-dependent repriming. Together, the dual functions of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
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9
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Heuzé J, Lin YL, Lengronne A, Poli J, Pasero P. Impact of R-loops on oncogene-induced replication stress in cancer cells. C R Biol 2023; 346:95-105. [PMID: 37779381 DOI: 10.5802/crbiol.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 10/03/2023]
Abstract
Replication stress is an alteration in the progression of replication forks caused by a variety of events of endogenous or exogenous origin. In precancerous lesions, this stress is exacerbated by the deregulation of oncogenic pathways, which notably disrupts the coordination between replication and transcription, and leads to genetic instability and cancer development. It is now well established that transcription can interfere with genome replication in different ways, such as head-on collisions between polymerases, accumulation of positive DNA supercoils or formation of R-loops. These structures form during transcription when nascent RNA reanneals with DNA behind the RNA polymerase, forming a stable DNA:RNA hybrid. In this review, we discuss how these different cotranscriptional processes disrupt the progression of replication forks and how they contribute to genetic instability in cancer cells.
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10
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Ghaddar N, Corda Y, Luciano P, Galli M, Doksani Y, Géli V. The COMPASS subunit Spp1 protects nascent DNA at the Tus/Ter replication fork barrier by limiting DNA availability to nucleases. Nat Commun 2023; 14:5430. [PMID: 37669924 PMCID: PMC10480214 DOI: 10.1038/s41467-023-41100-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Homologous recombination factors play a crucial role in protecting nascent DNA during DNA replication, but the role of chromatin in this process is largely unknown. Here, we used the bacterial Tus/Ter barrier known to induce a site-specific replication fork stalling in S. cerevisiae. We report that the Set1C subunit Spp1 is recruited behind the stalled replication fork independently of its interaction with Set1. Spp1 chromatin recruitment depends on the interaction of its PHD domain with H3K4me3 parental histones deposited behind the stalled fork. Its recruitment prevents the accumulation of ssDNA at the stalled fork by restricting the access of Exo1. We further show that deleting SPP1 increases the mutation rate upstream of the barrier favoring the accumulation of microdeletions. Finally, we report that Spp1 protects nascent DNA at the Tus/Ter stalled replication fork. We propose that Spp1 limits the remodeling of the fork, which ultimately limits nascent DNA availability to nucleases.
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Affiliation(s)
- Nagham Ghaddar
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix-Marseille University, Institute Paoli-Calmettes, Ligue Nationale Contre le Cancer (Equipe Labellisée), Marseille, France
| | - Yves Corda
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix-Marseille University, Institute Paoli-Calmettes, Ligue Nationale Contre le Cancer (Equipe Labellisée), Marseille, France
| | - Pierre Luciano
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix-Marseille University, Institute Paoli-Calmettes, Ligue Nationale Contre le Cancer (Equipe Labellisée), Marseille, France
| | - Martina Galli
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Ylli Doksani
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix-Marseille University, Institute Paoli-Calmettes, Ligue Nationale Contre le Cancer (Equipe Labellisée), Marseille, France.
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11
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Muellner J, Schmidt KH. Helicase activities of Rad5 and Rrm3 genetically interact in the prevention of recombinogenic DNA lesions in Saccharomyces cerevisiae. DNA Repair (Amst) 2023; 126:103488. [PMID: 37054652 PMCID: PMC10399609 DOI: 10.1016/j.dnarep.2023.103488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/09/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023]
Abstract
The genome must be monitored to ensure its duplication is completed accurately to prevent genome instability. In Saccharomyces cerevisiae, the 5' to 3' DNA helicase Rrm3, a member of the conserved PIF1 family, facilitates replication fork progression through an unknown mechanism. Disruption of Rrm3 helicase activity leads to increased replication fork pausing throughout the yeast genome. Here, we show that Rrm3 contributes to replication stress tolerance in the absence of the fork reversal activity of Rad5, defined by its HIRAN domain and DNA helicase activity, but not in the absence of Rad5's ubiquitin ligase activity. The Rrm3 and Rad5 helicase activities also interact in the prevention of recombinogenic DNA lesions, and DNA lesions that accumulate in their absence need to be salvaged by a Rad59-dependent recombination pathway. Disruption of the structure-specific endonuclease Mus81 leads to accumulation of recombinogenic DNA lesions and chromosomal rearrangements in the absence of Rrm3, but not Rad5. Thus, at least two mechanisms exist to overcome fork stalling at replication barriers, defined by Rad5-mediated fork reversal and Mus81-mediated cleavage, and contribute to the maintenance of chromosome stability in the absence of Rrm3.
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Affiliation(s)
- Julius Muellner
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, United States; Graduate program in Cell and Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Kristina H Schmidt
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, United States; Graduate program in Cell and Molecular Biology, University of South Florida, Tampa, FL 33620, United States; Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States.
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12
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Moore CE, Yalcindag SE, Czeladko H, Ravindranathan R, Wijesekara Hanthi Y, Levy JC, Sannino V, Schindler D, Ciccia A, Costanzo V, Elia AE. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks. J Cell Biol 2023; 222:e202106022. [PMID: 37036693 PMCID: PMC10097976 DOI: 10.1083/jcb.202106022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 04/11/2023] Open
Abstract
Replication fork reversal is an important mechanism to protect the stability of stalled forks and thereby preserve genomic integrity. While multiple enzymes have been identified that can remodel forks, their regulation remains poorly understood. Here, we demonstrate that the ubiquitin ligase RFWD3, whose mutation causes Fanconi Anemia, promotes recruitment of the DNA translocase ZRANB3 to stalled replication forks and ubiquitinated sites of DNA damage. Using electron microscopy, we show that RFWD3 stimulates fork remodeling in a ZRANB3-epistatic manner. Fork reversal is known to promote nascent DNA degradation in BRCA2-deficient cells. Consistent with a role for RFWD3 in fork reversal, inactivation of RFWD3 in these cells rescues fork degradation and collapse, analogous to ZRANB3 inactivation. RFWD3 loss impairs ZRANB3 localization to spontaneous nuclear foci induced by inhibition of the PCNA deubiquitinase USP1. We demonstrate that RFWD3 promotes PCNA ubiquitination and interaction with ZRANB3, providing a mechanism for RFWD3-dependent recruitment of ZRANB3. Together, these results uncover a new role for RFWD3 in regulating ZRANB3-dependent fork remodeling.
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Affiliation(s)
- Chandler E. Moore
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Selin E. Yalcindag
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hanna Czeladko
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramya Ravindranathan
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yodhara Wijesekara Hanthi
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Juliana C. Levy
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Detlev Schindler
- Department of Human Genetics, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Alberto Ciccia
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Andrew E.H. Elia
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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13
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Di Biagi L, Malacaria E, Aiello FA, Valenzisi P, Marozzi G, Franchitto A, Pichierri P. RAD52 prevents accumulation of Polα-dependent replication gaps at perturbed replication forks in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536536. [PMID: 37090680 PMCID: PMC10120653 DOI: 10.1101/2023.04.12.536536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Replication gaps can arise as a consequence of perturbed DNA replication and their accumulation might undermine the stability of the genome. Loss of RAD52, a protein involved in the regulation of fork reversal, promotes accumulation of parental ssDNA gaps during replication perturbation. Here, we demonstrate that this is due to the engagement of Polα downstream of the extensive degradation of perturbed replication forks after their reversal, and is not dependent on PrimPol. Polα is hyper-recruited at parental ssDNA in the absence of RAD52, and this recruitment is dependent on fork reversal enzymes and RAD51. Of note, we report that the interaction between Polα and RAD51 is stimulated by RAD52 inhibition, and Polα-dependent gap accumulation requires nucleation of RAD51 suggesting that it occurs downstream strand invasion. Altogether, our data indicate that RAD51-Polα-dependent repriming is essential to promote fork restart and limit DNA damage accumulation when RAD52 function is disabled.
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Affiliation(s)
- Ludovica Di Biagi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d’Oro 305, 00136 Rome (Italy)
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Francesca Antonella Aiello
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d’Oro 305, 00136 Rome (Italy)
| | - Pasquale Valenzisi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Giorgia Marozzi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d’Oro 305, 00136 Rome (Italy)
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14
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RAD51 paralogs: Expanding roles in replication stress responses and repair. Curr Opin Pharmacol 2022; 67:102313. [PMID: 36343481 DOI: 10.1016/j.coph.2022.102313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022]
Abstract
Mammalian RAD51 paralogs are essential for cell survival and are critical for RAD51-mediated repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the molecular mechanism by which RAD51 paralogs participate in HR is largely unclear. Germline mutations in RAD51 paralogs are associated with breast and ovarian cancers and Fanconi anemia-like disorder, underscoring the crucial roles of RAD51 paralogs in genome maintenance and tumor suppression. Despite their discovery over three decades ago, the essential functions of RAD51 paralogs in cell survival and genome stability remain obscure. Recent studies unravel DSB repair independent functions of RAD51 paralogs in replication stress responses. Here, we highlight the recent findings that uncovered the novel functions of RAD51 paralogs in replication fork progression, its stability, and restart and discuss RAD51 paralogs as a potential therapeutic target for cancer treatment.
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15
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Role of Cockayne Syndrome Group B Protein in Replication Stress: Implications for Cancer Therapy. Int J Mol Sci 2022; 23:ijms231810212. [PMID: 36142121 PMCID: PMC9499456 DOI: 10.3390/ijms231810212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 12/01/2022] Open
Abstract
A variety of endogenous and exogenous insults are capable of impeding replication fork progression, leading to replication stress. Several SNF2 fork remodelers have been shown to play critical roles in resolving this replication stress, utilizing different pathways dependent upon the nature of the DNA lesion, location on the DNA, and the stage of the cell cycle, to complete DNA replication in a manner preserving genetic integrity. Under certain conditions, however, the attempted repair may lead to additional genetic instability. Cockayne syndrome group B (CSB) protein, a SNF2 chromatin remodeler best known for its role in transcription-coupled nucleotide excision repair, has recently been shown to catalyze fork reversal, a pathway that can provide stability of stalled forks and allow resumption of DNA synthesis without chromosome breakage. Prolonged stalling of replication forks may collapse to give rise to DNA double-strand breaks, which are preferentially repaired by homology-directed recombination. CSB plays a role in repairing collapsed forks by promoting break-induced replication in S phase and early mitosis. In this review, we discuss roles of CSB in regulating the sources of replication stress, replication stress response, as well as the implications of CSB for cancer therapy.
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16
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A DNA Replication Fork-centric View of the Budding Yeast DNA Damage Response. DNA Repair (Amst) 2022; 119:103393. [DOI: 10.1016/j.dnarep.2022.103393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022]
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17
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Saxena S, Zou L. Hallmarks of DNA replication stress. Mol Cell 2022; 82:2298-2314. [PMID: 35714587 DOI: 10.1016/j.molcel.2022.05.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/15/2022] [Accepted: 05/04/2022] [Indexed: 12/12/2022]
Abstract
Faithful DNA replication is critical for the maintenance of genomic integrity. Although DNA replication machinery is highly accurate, the process of DNA replication is constantly challenged by DNA damage and other intrinsic and extrinsic stresses throughout the genome. A variety of cellular stresses interfering with DNA replication, which are collectively termed replication stress, pose a threat to genomic stability in both normal and cancer cells. To cope with replication stress and maintain genomic stability, cells have evolved a complex network of cellular responses to alleviate and tolerate replication problems. This review will focus on the major sources of replication stress, the impacts of replication stress in cells, and the assays to detect replication stress, offering an overview of the hallmarks of DNA replication stress.
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Affiliation(s)
- Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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18
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Balasubramanian S, Andreani M, Andrade JG, Saha T, Sundaravinayagam D, Garzón J, Zhang W, Popp O, Hiraga SI, Rahjouei A, Rosen DB, Mertins P, Chait BT, Donaldson AD, Di Virgilio M. Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region. eLife 2022; 11:e75047. [PMID: 35416772 PMCID: PMC9007588 DOI: 10.7554/elife.75047] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/30/2022] [Indexed: 12/22/2022] Open
Abstract
RIF1 is a multifunctional protein that plays key roles in the regulation of DNA processing. During repair of DNA double-strand breaks (DSBs), RIF1 functions in the 53BP1-Shieldin pathway that inhibits resection of DNA ends to modulate the cellular decision on which repair pathway to engage. Under conditions of replication stress, RIF1 protects nascent DNA at stalled replication forks from degradation by the DNA2 nuclease. How these RIF1 activities are regulated at the post-translational level has not yet been elucidated. Here, we identified a cluster of conserved ATM/ATR consensus SQ motifs within the intrinsically disordered region (IDR) of mouse RIF1 that are phosphorylated in proliferating B lymphocytes. We found that phosphorylation of the conserved IDR SQ cluster is dispensable for the inhibition of DSB resection by RIF1, but is essential to counteract DNA2-dependent degradation of nascent DNA at stalled replication forks. Therefore, our study identifies a key molecular feature that enables the genome-protective function of RIF1 during DNA replication stress.
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Affiliation(s)
- Sandhya Balasubramanian
- Laboratory of Genome Diversification & Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Freie Universität BerlinBerlinGermany
| | - Matteo Andreani
- Laboratory of Genome Diversification & Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Freie Universität BerlinBerlinGermany
| | - Júlia Goncalves Andrade
- Laboratory of Genome Diversification & Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Tannishtha Saha
- Laboratory of Genome Diversification & Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Freie Universität BerlinBerlinGermany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification & Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Javier Garzón
- Institute of Medical Sciences, University of Aberdeen, ForesterhillAberdeenUnited Kingdom
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Oliver Popp
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Berlin Institute of HealthBerlinGermany
| | - Shin-ichiro Hiraga
- Institute of Medical Sciences, University of Aberdeen, ForesterhillAberdeenUnited Kingdom
| | - Ali Rahjouei
- Laboratory of Genome Diversification & Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Daniel B Rosen
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Philipp Mertins
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Berlin Institute of HealthBerlinGermany
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, ForesterhillAberdeenUnited Kingdom
| | - Michela Di Virgilio
- Laboratory of Genome Diversification & Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Charité-Universitätsmedizin BerlinBerlinGermany
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19
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Hashimoto Y, Tanaka H. Mre11 exonuclease activity promotes irreversible mitotic progression under replication stress. Life Sci Alliance 2022; 5:5/6/e202101249. [PMID: 35292537 PMCID: PMC8924007 DOI: 10.26508/lsa.202101249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
Mre11 is a versatile exo-/endonuclease involved in multiple aspects of DNA replication and repair, such as DSB end processing and checkpoint activation. We previously demonstrated that forced mitotic entry drives replisome disassembly at stalled replication forks in Xenopus egg extracts. Here, we examined the effects of various chemical inhibitors using this system and discovered a novel role of Mre11 exonuclease activity in promoting mitotic entry under replication stress. Mre11 activity was necessary for the initial progression of mitotic entry in the presence of stalled forks but unnecessary in the absence of stalled forks or after mitotic entry. In the absence of Mre11 activity, mitotic CDK was inactivated by Wee1/Myt1-dependent phosphorylation, causing mitotic exit. An inhibitor of Wee1/Myt1 or a nonphosphorylatable CDK1 mutant was able to partially bypass the requirement of Mre11 for mitotic entry. These results suggest that Mre11 exonuclease activity facilitates the processing of stalled replication forks upon mitotic entry, which attenuates the inhibitory pathways of mitotic CDK activation, leading to irreversible mitotic progression and replisome disassembly.
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Affiliation(s)
- Yoshitami Hashimoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hirofumi Tanaka
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
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20
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Yan S, Gao S, Zhou P. Multi-functions of exonuclease 1 in DNA damage response and cancer susceptibility. RADIATION MEDICINE AND PROTECTION 2021. [DOI: 10.1016/j.radmp.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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21
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Datta A, Biswas K, Sommers JA, Thompson H, Awate S, Nicolae CM, Thakar T, Moldovan GL, Shoemaker RH, Sharan SK, Brosh RM. WRN helicase safeguards deprotected replication forks in BRCA2-mutated cancer cells. Nat Commun 2021; 12:6561. [PMID: 34772932 PMCID: PMC8590011 DOI: 10.1038/s41467-021-26811-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
The tumor suppressor BRCA2 protects stalled forks from degradation to maintain genome stability. However, the molecular mechanism(s) whereby unprotected forks are stabilized remains to be fully characterized. Here, we demonstrate that WRN helicase ensures efficient restart and limits excessive degradation of stalled forks in BRCA2-deficient cancer cells. In vitro, WRN ATPase/helicase catalyzes fork restoration and curtails MRE11 nuclease activity on regressed forks. We show that WRN helicase inhibitor traps WRN on chromatin leading to rapid fork stalling and nucleolytic degradation of unprotected forks by MRE11, resulting in MUS81-dependent double-strand breaks, elevated non-homologous end-joining and chromosomal instability. WRN helicase inhibition reduces viability of BRCA2-deficient cells and potentiates cytotoxicity of a poly (ADP)ribose polymerase (PARP) inhibitor. Furthermore, BRCA2-deficient xenograft tumors in mice exhibited increased DNA damage and growth inhibition when treated with WRN helicase inhibitor. This work provides mechanistic insight into stalled fork stabilization by WRN helicase when BRCA2 is deficient.
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Affiliation(s)
- Arindam Datta
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Joshua A Sommers
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Haley Thompson
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Sanket Awate
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Robert H Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Robert M Brosh
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA.
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22
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Somyajit K, Spies J, Coscia F, Kirik U, Rask MB, Lee JH, Neelsen KJ, Mund A, Jensen LJ, Paull TT, Mann M, Lukas J. Homology-directed repair protects the replicating genome from metabolic assaults. Dev Cell 2021; 56:461-477.e7. [PMID: 33621493 DOI: 10.1016/j.devcel.2021.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/14/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
Homology-directed repair (HDR) safeguards DNA integrity under various forms of stress, but how HDR protects replicating genomes under extensive metabolic alterations remains unclear. Here, we report that besides stalling replication forks, inhibition of ribonucleotide reductase (RNR) triggers metabolic imbalance manifested by the accumulation of increased reactive oxygen species (ROS) in cell nuclei. This leads to a redox-sensitive activation of the ATM kinase followed by phosphorylation of the MRE11 nuclease, which in HDR-deficient settings degrades stalled replication forks. Intriguingly, nascent DNA degradation by the ROS-ATM-MRE11 cascade is also triggered by hypoxia, which elevates signaling-competent ROS and attenuates functional HDR without arresting replication forks. Under these conditions, MRE11 degrades daughter-strand DNA gaps, which accumulate behind active replisomes and attract error-prone DNA polymerases to escalate mutation rates. Thus, HDR safeguards replicating genomes against metabolic assaults by restraining mutagenic repair at aberrantly processed nascent DNA. These findings have implications for cancer evolution and tumor therapy.
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Affiliation(s)
- Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
| | - Julian Spies
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Fabian Coscia
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ufuk Kirik
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein, Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Maj-Britt Rask
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ji-Hoon Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kai John Neelsen
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein, Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Matthias Mann
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
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23
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Nickoloff JA, Sharma N, Allen CP, Taylor L, Allen SJ, Jaiswal AS, Hromas R. Roles of homologous recombination in response to ionizing radiation-induced DNA damage. Int J Radiat Biol 2021; 99:903-914. [PMID: 34283012 PMCID: PMC9629169 DOI: 10.1080/09553002.2021.1956001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/04/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Ionizing radiation induces a vast array of DNA lesions including base damage, and single- and double-strand breaks (SSB, DSB). DSBs are among the most cytotoxic lesions, and mis-repair causes small- and large-scale genome alterations that can contribute to carcinogenesis. Indeed, ionizing radiation is a 'complete' carcinogen. DSBs arise immediately after irradiation, termed 'frank DSBs,' as well as several hours later in a replication-dependent manner, termed 'secondary' or 'replication-dependent DSBs. DSBs resulting from replication fork collapse are single-ended and thus pose a distinct problem from two-ended, frank DSBs. DSBs are repaired by error-prone nonhomologous end-joining (NHEJ), or generally error-free homologous recombination (HR), each with sub-pathways. Clarifying how these pathways operate in normal and tumor cells is critical to increasing tumor control and minimizing side effects during radiotherapy. CONCLUSIONS The choice between NHEJ and HR is regulated during the cell cycle and by other factors. DSB repair pathways are major contributors to cell survival after ionizing radiation, including tumor-resistance to radiotherapy. Several nucleases are important for HR-mediated repair of replication-dependent DSBs and thus replication fork restart. These include three structure-specific nucleases, the 3' MUS81 nuclease, and two 5' nucleases, EEPD1 and Metnase, as well as three end-resection nucleases, MRE11, EXO1, and DNA2. The three structure-specific nucleases evolved at very different times, suggesting incremental acceleration of replication fork restart to limit toxic HR intermediates and genome instability as genomes increased in size during evolution, including the gain of large numbers of HR-prone repetitive elements. Ionizing radiation also induces delayed effects, observed days to weeks after exposure, including delayed cell death and delayed HR. In this review we highlight the roles of HR in cellular responses to ionizing radiation, and discuss the importance of HR as an exploitable target for cancer radiotherapy.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Christopher P. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, Immunology and Pathology, Flow Cytometry and Cell Sorting Facility, Colorado State University, Fort Collins, CO, USA
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sage J. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Aruna S. Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
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24
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Audoynaud C, Vagner S, Lambert S. Non-homologous end-joining at challenged replication forks: an RNA connection? Trends Genet 2021; 37:973-985. [PMID: 34238592 DOI: 10.1016/j.tig.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Defective DNA replication, known as 'replication stress', is a source of DNA damage, a hallmark of numerous human diseases, including cancer, developmental defect, neurological disorders, and premature aging. Recent work indicates that non-homologous end-joining (NHEJ) is unexpectedly active during DNA replication to repair replication-born DNA lesions and to safeguard replication fork integrity. However, erroneous NHEJ events are deleterious to genome stability. RNAs are novel regulators of NHEJ activity through their ability to modulate the assembly of repair complexes in trans. At DNA damage sites, RNAs and DNA-embedded ribonucleotides modulate repair efficiency and fidelity. We discuss here how RNAs and associated proteins, including RNA binding proteins, may regulate NHEJ to sustain genome stability during DNA replication.
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Affiliation(s)
- Charlotte Audoynaud
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Stéphan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
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25
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Checkpoint-mediated DNA polymerase ε exonuclease activity curbing counteracts resection-driven fork collapse. Mol Cell 2021; 81:2778-2792.e4. [PMID: 33932350 PMCID: PMC7612761 DOI: 10.1016/j.molcel.2021.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 02/01/2023]
Abstract
DNA polymerase ε (Polε) carries out high-fidelity leading strand synthesis owing to its exonuclease activity. Polε polymerase and exonuclease activities are balanced, because of partitioning of nascent DNA strands between catalytic sites, so that net resection occurs when synthesis is impaired. In vivo, DNA synthesis stalling activates replication checkpoint kinases, which act to preserve the functional integrity of replication forks. We show that stalled Polε drives nascent strand resection causing fork functional collapse, averted via checkpoint-dependent phosphorylation. Polε catalytic subunit Pol2 is phosphorylated on serine 430, influencing partitioning between polymerase and exonuclease active sites. A phosphormimetic S430D change reduces exonucleolysis in vitro and counteracts fork collapse. Conversely, non-phosphorylatable pol2-S430A expression causes resection-driven stressed fork defects. Our findings reveal that checkpoint kinases switch Polε to an exonuclease-safe mode preventing nascent strand resection and stabilizing stalled replication forks. Elective partitioning suppression has implications for the diverse Polε roles in genome integrity maintenance.
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26
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Técher H, Pasero P. The Replication Stress Response on a Narrow Path Between Genomic Instability and Inflammation. Front Cell Dev Biol 2021; 9:702584. [PMID: 34249949 PMCID: PMC8270677 DOI: 10.3389/fcell.2021.702584] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
The genome of eukaryotic cells is particularly at risk during the S phase of the cell cycle, when megabases of chromosomal DNA are unwound to generate two identical copies of the genome. This daunting task is executed by thousands of micro-machines called replisomes, acting at fragile structures called replication forks. The correct execution of this replication program depends on the coordinated action of hundreds of different enzymes, from the licensing of replication origins to the termination of DNA replication. This review focuses on the mechanisms that ensure the completion of DNA replication under challenging conditions of endogenous or exogenous origin. It also covers new findings connecting the processing of stalled forks to the release of small DNA fragments into the cytoplasm, activating the cGAS-STING pathway. DNA damage and fork repair comes therefore at a price, which is the activation of an inflammatory response that has both positive and negative impacts on the fate of stressed cells. These new findings have broad implications for the etiology of interferonopathies and for cancer treatment.
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Affiliation(s)
- Hervé Técher
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
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27
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Wong RP, Petriukov K, Ulrich HD. Daughter-strand gaps in DNA replication - substrates of lesion processing and initiators of distress signalling. DNA Repair (Amst) 2021; 105:103163. [PMID: 34186497 DOI: 10.1016/j.dnarep.2021.103163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
Dealing with DNA lesions during genome replication is particularly challenging because damaged replication templates interfere with the progression of the replicative DNA polymerases and thereby endanger the stability of the replisome. A variety of mechanisms for the recovery of replication forks exist, but both bacteria and eukaryotic cells also have the option of continuing replication downstream of the lesion, leaving behind a daughter-strand gap in the newly synthesized DNA. In this review, we address the significance of these single-stranded DNA structures as sites of DNA damage sensing and processing at a distance from ongoing genome replication. We describe the factors controlling the emergence of daughter-strand gaps from stalled replication intermediates, the benefits and risks of their expansion and repair via translesion synthesis or recombination-mediated template switching, and the mechanisms by which they activate local as well as global replication stress signals. Our growing understanding of daughter-strand gaps not only identifies them as targets of fundamental genome maintenance mechanisms, but also suggests that proper control over their activities has important practical implications for treatment strategies and resistance mechanisms in cancer therapy.
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Affiliation(s)
- Ronald P Wong
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany
| | - Kirill Petriukov
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany.
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28
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Ishimoto R, Tsuzuki Y, Matsumura T, Kurashige S, Enokitani K, Narimatsu K, Higa M, Sugimoto N, Yoshida K, Fujita M. SLX4-XPF mediates DNA damage responses to replication stress induced by DNA-protein interactions. J Cell Biol 2021; 220:211628. [PMID: 33347546 PMCID: PMC7754685 DOI: 10.1083/jcb.202003148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 10/05/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) has a critical role in the maintenance of genomic integrity during chromosome replication. However, responses to replication stress evoked by tight DNA–protein complexes have not been fully elucidated. Here, we used bacterial LacI protein binding to lacO arrays to make site-specific replication fork barriers on the human chromosome. These barriers induced the accumulation of single-stranded DNA (ssDNA) and various DDR proteins at the lacO site. SLX4–XPF functioned as an upstream factor for the accumulation of DDR proteins, and consequently, ATR and FANCD2 were interdependently recruited. Moreover, LacI binding in S phase caused underreplication and abnormal mitotic segregation of the lacO arrays. Finally, we show that the SLX4–ATR axis represses the anaphase abnormality induced by LacI binding. Our results outline a long-term process by which human cells manage nucleoprotein obstacles ahead of the replication fork to prevent chromosomal instability.
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Affiliation(s)
- Riko Ishimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yota Tsuzuki
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoki Matsumura
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Seiichiro Kurashige
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kouki Enokitani
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Koki Narimatsu
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsunori Higa
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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29
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Segura-Bayona S, Villamor-Payà M, Attolini CSO, Koenig LM, Sanchiz-Calvo M, Boulton SJ, Stracker TH. Tousled-Like Kinases Suppress Innate Immune Signaling Triggered by Alternative Lengthening of Telomeres. Cell Rep 2021; 32:107983. [PMID: 32755577 PMCID: PMC7408502 DOI: 10.1016/j.celrep.2020.107983] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The Tousled-like kinases 1 and 2 (TLK1/2) control histone deposition through the ASF1 histone chaperone and influence cell cycle progression and genome maintenance, yet the mechanisms underlying TLK-mediated genome stability remain uncertain. Here, we show that TLK loss results in severe chromatin decompaction and altered genome accessibility, particularly affecting heterochromatic regions. Failure to maintain heterochromatin increases spurious transcription of repetitive elements and induces features of alternative lengthening of telomeres (ALT). TLK depletion culminates in a cGAS-STING-TBK1-mediated innate immune response that is independent of replication-stress signaling and attenuated by the depletion of factors required to produce extra-telomeric DNA. Analysis of human cancers reveals that chromosomal instability correlates with high TLK2 and low STING levels in many cohorts. Based on these findings, we propose that high TLK levels contribute to immune evasion in chromosomally unstable and ALT+ cancers. TLK-deficient cells have increased accessibility at heterochromatin regions TLK1/2 suppress spurious transcription and telomere hyper-recombination Extra-telomeric DNA generated upon TLK loss promotes innate immune signaling cGAS-STING-TBK1 signaling in TLK-deficient cells is independent of replication stress
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Affiliation(s)
- Sandra Segura-Bayona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Marina Villamor-Payà
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Lars M Koenig
- Division of Clinical Pharmacology, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Maria Sanchiz-Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.
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30
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Maiorano D, El Etri J, Franchet C, Hoffmann JS. Translesion Synthesis or Repair by Specialized DNA Polymerases Limits Excessive Genomic Instability upon Replication Stress. Int J Mol Sci 2021; 22:3924. [PMID: 33920223 PMCID: PMC8069355 DOI: 10.3390/ijms22083924] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
DNA can experience "replication stress", an important source of genome instability, induced by various external or endogenous impediments that slow down or stall DNA synthesis. While genome instability is largely documented to favor both tumor formation and heterogeneity, as well as drug resistance, conversely, excessive instability appears to suppress tumorigenesis and is associated with improved prognosis. These findings support the view that karyotypic diversity, necessary to adapt to selective pressures, may be limited in tumors so as to reduce the risk of excessive instability. This review aims to highlight the contribution of specialized DNA polymerases in limiting extreme genetic instability by allowing DNA replication to occur even in the presence of DNA damage, to either avoid broken forks or favor their repair after collapse. These mechanisms and their key regulators Rad18 and Polθ not only offer diversity and evolutionary advantage by increasing mutagenic events, but also provide cancer cells with a way to escape anti-cancer therapies that target replication forks.
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Affiliation(s)
- Domenico Maiorano
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Jana El Etri
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Camille Franchet
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
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31
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Willaume S, Rass E, Fontanilla-Ramirez P, Moussa A, Wanschoor P, Bertrand P. A Link between Replicative Stress, Lamin Proteins, and Inflammation. Genes (Basel) 2021; 12:genes12040552. [PMID: 33918867 PMCID: PMC8070205 DOI: 10.3390/genes12040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Double-stranded breaks (DSB), the most toxic DNA lesions, are either a consequence of cellular metabolism, programmed as in during V(D)J recombination, or induced by anti-tumoral therapies or accidental genotoxic exposure. One origin of DSB sources is replicative stress, a major source of genome instability, especially when the integrity of the replication forks is not properly guaranteed. To complete stalled replication, restarting the fork requires complex molecular mechanisms, such as protection, remodeling, and processing. Recently, a link has been made between DNA damage accumulation and inflammation. Indeed, defects in DNA repair or in replication can lead to the release of DNA fragments in the cytosol. The recognition of this self-DNA by DNA sensors leads to the production of inflammatory factors. This beneficial response activating an innate immune response and destruction of cells bearing DNA damage may be considered as a novel part of DNA damage response. However, upon accumulation of DNA damage, a chronic inflammatory cellular microenvironment may lead to inflammatory pathologies, aging, and progression of tumor cells. Progress in understanding the molecular mechanisms of DNA damage repair, replication stress, and cytosolic DNA production would allow to propose new therapeutical strategies against cancer or inflammatory diseases associated with aging. In this review, we describe the mechanisms involved in DSB repair, the replicative stress management, and its consequences. We also focus on new emerging links between key components of the nuclear envelope, the lamins, and DNA repair, management of replicative stress, and inflammation.
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32
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Jones MJK, Gelot C, Munk S, Koren A, Kawasoe Y, George KA, Santos RE, Olsen JV, McCarroll SA, Frattini MG, Takahashi TS, Jallepalli PV. Human DDK rescues stalled forks and counteracts checkpoint inhibition at unfired origins to complete DNA replication. Mol Cell 2021; 81:426-441.e8. [PMID: 33545059 DOI: 10.1016/j.molcel.2021.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 09/25/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022]
Abstract
Eukaryotic genomes replicate via spatially and temporally regulated origin firing. Cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK) promote origin firing, whereas the S phase checkpoint limits firing to prevent nucleotide and RPA exhaustion. We used chemical genetics to interrogate human DDK with maximum precision, dissect its relationship with the S phase checkpoint, and identify DDK substrates. We show that DDK inhibition (DDKi) leads to graded suppression of origin firing and fork arrest. S phase checkpoint inhibition rescued origin firing in DDKi cells and DDK-depleted Xenopus egg extracts. DDKi also impairs RPA loading, nascent-strand protection, and fork restart. Via quantitative phosphoproteomics, we identify the BRCA1-associated (BRCA1-A) complex subunit MERIT40 and the cohesin accessory subunit PDS5B as DDK effectors in fork protection and restart. Phosphorylation neutralizes autoinhibition mediated by intrinsically disordered regions in both substrates. Our results reveal mechanisms through which DDK controls the duplication of large vertebrate genomes.
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Affiliation(s)
- Mathew J K Jones
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Camille Gelot
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephanie Munk
- University of Copenhagen and Novo Nordisk Foundation Center for Protein Research, Copenhagen 2200, Denmark
| | - Amnon Koren
- Cornell University, Department of Molecular Biology and Genetics, Ithaca, NY 14853, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yoshitaka Kawasoe
- Graduate School of Science, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kelly A George
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruth E Santos
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jesper V Olsen
- University of Copenhagen and Novo Nordisk Foundation Center for Protein Research, Copenhagen 2200, Denmark
| | | | - Mark G Frattini
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Tatsuro S Takahashi
- Graduate School of Science, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Prasad V Jallepalli
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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33
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Orvain C, Lin YL, Jean-Louis F, Hocini H, Hersant B, Bennasser Y, Ortonne N, Hotz C, Wolkenstein P, Boniotto M, Tisserand P, Lefebvre C, Lelièvre JD, Benkirane M, Pasero P, Lévy Y, Hüe S. Hair follicle stem cell replication stress drives IFI16/STING-dependent inflammation in hidradenitis suppurativa. J Clin Invest 2021; 130:3777-3790. [PMID: 32240121 DOI: 10.1172/jci131180] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 03/31/2020] [Indexed: 12/28/2022] Open
Abstract
Hidradenitis suppurativa (HS) is a chronic, relapsing, inflammatory skin disease. HS appears to be a primary abnormality in the pilosebaceous-apocrine unit. In this work, we characterized hair follicle stem cells (HFSCs) isolated from HS patients and more precisely the outer root sheath cells (ORSCs). We showed that hair follicle cells from HS patients had an increased number of proliferating progenitor cells and lost quiescent stem cells. Remarkably, we also showed that the progression of replication forks was altered in ORSCs from hair follicles of HS patients, leading to activation of the ATR/CHK1 pathway. These alterations were associated with an increased number of micronuclei and with the presence of cytoplasmic ssDNA, leading to the activation of the IFI16/STING pathway and the production of type I IFNs. This mechanistic analysis of the etiology of HS in the HFSC compartment establishes a formal link between genetic predisposition and skin inflammation observed in HS.
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Affiliation(s)
- Cindy Orvain
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France
| | - Yea-Lih Lin
- Equipe Labellisée Ligue contre le Cancer, Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier France
| | - Francette Jean-Louis
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France
| | - Hakim Hocini
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France
| | - Barbara Hersant
- Service de chirurgie plastique et reconstructive.,Groupe Hospitalier Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP), Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France
| | - Yamina Bennasser
- Equipe Labellisée Ligue contre le Cancer, Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier France
| | - Nicolas Ortonne
- Groupe Hospitalier Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP), Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France.,Service d'anatomopathologie
| | - Claire Hotz
- Service de chirurgie plastique et reconstructive.,Groupe Hospitalier Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP), Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France.,Service de Dermatologie
| | - Pierre Wolkenstein
- Service de chirurgie plastique et reconstructive.,Groupe Hospitalier Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP), Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France.,Service de Dermatologie
| | - Michele Boniotto
- INSERM U955, Equipe 16, Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France
| | - Pascaline Tisserand
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France
| | - Cécile Lefebvre
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France
| | - Jean-Daniel Lelièvre
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France.,Groupe Hospitalier Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP), Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France.,Service d'Immunologie Clinique, and
| | - Monsef Benkirane
- Equipe Labellisée Ligue contre le Cancer, Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier France
| | - Philippe Pasero
- Equipe Labellisée Ligue contre le Cancer, Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier France
| | - Yves Lévy
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France.,Groupe Hospitalier Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP), Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France.,Service d'Immunologie Clinique, and
| | - Sophie Hüe
- INSERM U955, Equipe 16, Créteil, France.,Vaccine Research Institute (VRI), Université Paris Est Créteil, Faculté de Médecine, Créteil, France.,Groupe Hospitalier Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP), Créteil, France.,Faculté de Médecine, Université Paris-Est Créteil (UPEC), Créteil, France.,Service d'Immunologie Biologique, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
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34
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Tirman S, Cybulla E, Quinet A, Meroni A, Vindigni A. PRIMPOL ready, set, reprime! Crit Rev Biochem Mol Biol 2021; 56:17-30. [PMID: 33179522 PMCID: PMC7906090 DOI: 10.1080/10409238.2020.1841089] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
DNA replication forks are constantly challenged by DNA lesions induced by endogenous and exogenous sources. DNA damage tolerance mechanisms ensure that DNA replication continues with minimal effects on replication fork elongation either by using specialized DNA polymerases, which have the ability to replicate through the damaged template, or by skipping the damaged DNA, leaving it to be repaired after replication. These mechanisms are evolutionarily conserved in bacteria, yeast, and higher eukaryotes, and are paramount to ensure timely and faithful duplication of the genome. The Primase and DNA-directed Polymerase (PRIMPOL) is a recently discovered enzyme that possesses both primase and polymerase activities. PRIMPOL is emerging as a key player in DNA damage tolerance, particularly in vertebrate and human cells. Here, we review our current understanding of the function of PRIMPOL in DNA damage tolerance by focusing on the structural aspects that define its dual enzymatic activity, as well as on the mechanisms that control its chromatin recruitment and expression levels. We also focus on the latest findings on the mitochondrial and nuclear functions of PRIMPOL and on the impact of loss of these functions on genome stability and cell survival. Defining the function of PRIMPOL in DNA damage tolerance is becoming increasingly important in the context of human disease. In particular, we discuss recent evidence pointing at the PRIMPOL pathway as a novel molecular target to improve cancer cell response to DNA-damaging chemotherapy and as a predictive parameter to stratify patients in personalized cancer therapy.
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Affiliation(s)
- Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Alice Meroni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
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Jenkins T, Northall SJ, Ptchelkine D, Lever R, Cubbon A, Betts H, Taresco V, Cooper CDO, McHugh PJ, Soultanas P, Bolt EL. The HelQ human DNA repair helicase utilizes a PWI-like domain for DNA loading through interaction with RPA, triggering DNA unwinding by the HelQ helicase core. NAR Cancer 2021; 3:zcaa043. [PMID: 34316696 PMCID: PMC8210318 DOI: 10.1093/narcan/zcaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/30/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Genome instability is a characteristic enabling factor for carcinogenesis. HelQ helicase is a component of human DNA maintenance systems that prevent or reverse genome instability arising during DNA replication. Here, we provide details of the molecular mechanisms that underpin HelQ function-its recruitment onto ssDNA through interaction with replication protein A (RPA), and subsequent translocation of HelQ along ssDNA. We describe for the first time a functional role for the non-catalytic N-terminal region of HelQ, by identifying and characterizing its PWI-like domain. We present evidence that this domain of HelQ mediates interaction with RPA that orchestrates loading of the helicase domains onto ssDNA. Once HelQ is loaded onto the ssDNA, ATP-Mg2+ binding in the catalytic site activates the helicase core and triggers translocation along ssDNA as a dimer. Furthermore, we identify HelQ-ssDNA interactions that are critical for the translocation mechanism. Our data are novel and detailed insights into the mechanisms of HelQ function relevant for understanding how human cells avoid genome instability provoking cancers, and also how cells can gain resistance to treatments that rely on DNA crosslinking agents.
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Affiliation(s)
- Tabitha Jenkins
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Sarah J Northall
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | | | - Rebecca Lever
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Andrew Cubbon
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
| | - Hannah Betts
- School of Chemistry, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Vincenzo Taresco
- School of Pharmacy, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Christopher D O Cooper
- Department of Biological and Geographical Sciences, School of Applied Sciences, The University of Huddersfield, HD1 3DH, Huddersfield, UK
| | - Peter J McHugh
- MRC Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, OX3 9DS, Oxford, UK
| | - Panos Soultanas
- School of Chemistry, The University of Nottingham, NG7 2RD, Nottingham, UK
| | - Edward L Bolt
- School of Life Sciences, The University of Nottingham, NG7 2UH, Nottingham, UK
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36
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Rinaldi C, Pizzul P, Longhese MP, Bonetti D. Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability. Front Cell Dev Biol 2021; 8:618157. [PMID: 33505970 PMCID: PMC7829580 DOI: 10.3389/fcell.2020.618157] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
DNA transcription and replication are two essential physiological processes that can turn into a threat for genome integrity when they compete for the same DNA substrate. During transcription, the nascent RNA strongly binds the template DNA strand, leading to the formation of a peculiar RNA-DNA hybrid structure that displaces the non-template single-stranded DNA. This three-stranded nucleic acid transition is called R-loop. Although a programed formation of R-loops plays important physiological functions, these structures can turn into sources of DNA damage and genome instability when their homeostasis is altered. Indeed, both R-loop level and distribution in the genome are tightly controlled, and the list of factors involved in these regulatory mechanisms is continuously growing. Over the last years, our knowledge of R-loop homeostasis regulation (formation, stabilization, and resolution) has definitely increased. However, how R-loops affect genome stability and how the cellular response to their unscheduled formation is orchestrated are still not fully understood. In this review, we will report and discuss recent findings about these questions and we will focus on the role of ATM- and Rad3-related (ATR) and Ataxia-telangiectasia-mutated (ATM) kinases in the activation of an R-loop-dependent DNA damage response.
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Affiliation(s)
- Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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37
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Chansel-Da Cruz M, Hohl M, Ceppi I, Kermasson L, Maggiorella L, Modesti M, de Villartay JP, Ileri T, Cejka P, Petrini JHJ, Revy P. A Disease-Causing Single Amino Acid Deletion in the Coiled-Coil Domain of RAD50 Impairs MRE11 Complex Functions in Yeast and Humans. Cell Rep 2020; 33:108559. [PMID: 33378670 PMCID: PMC7788285 DOI: 10.1016/j.celrep.2020.108559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/30/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
The MRE11-RAD50-NBS1 complex plays a central role in response to DNA double-strand breaks. Here, we identify a patient with bone marrow failure and developmental defects caused by biallelic RAD50 mutations. One of the mutations creates a null allele, whereas the other (RAD50E1035Δ) leads to the loss of a single residue in the heptad repeats within the RAD50 coiled-coil domain. This mutation represents a human RAD50 separation-of-function mutation that impairs DNA repair, DNA replication, and DNA end resection without affecting ATM-dependent DNA damage response. Purified recombinant proteins indicate that RAD50E1035Δ impairs MRE11 nuclease activity. The corresponding mutation in Saccharomyces cerevisiae causes severe thermosensitive defects in both DNA repair and Tel1ATM-dependent signaling. These findings demonstrate that a minor heptad break in the RAD50 coiled coil suffices to impede MRE11 complex functions in human and yeast. Furthermore, these results emphasize the importance of the RAD50 coiled coil to regulate MRE11-dependent DNA end resection in humans.
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Affiliation(s)
- Marie Chansel-Da Cruz
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France; Genomic Vision, R&D Innovation Department, Bagneux, France
| | - Marcel Hohl
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Laëtitia Kermasson
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | | | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Jean-Pierre de Villartay
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Talia Ileri
- Ankara University School of Medicine, Pediatric Hematology and Oncology, Ankara, Turkey
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - John H J Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France.
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38
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Panagopoulos A, Altmeyer M. The Hammer and the Dance of Cell Cycle Control. Trends Biochem Sci 2020; 46:301-314. [PMID: 33279370 DOI: 10.1016/j.tibs.2020.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/22/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
Cell cycle checkpoints secure ordered progression from one cell cycle phase to the next. They are important to signal cell stress and DNA lesions and to stop cell cycle progression when severe problems occur. Recent work suggests, however, that the cell cycle control machinery responds in more subtle and sophisticated ways when cells are faced with naturally occurring challenges, such as replication impediments associated with endogenous replication stress. Instead of following a stop and go approach, cells use fine-tuned deceleration and brake release mechanisms under the control of ataxia telangiectasia and Rad3-related protein kinase (ATR) and checkpoint kinase 1 (CHK1) to more flexibly adapt their cell cycle program to changing conditions. We highlight emerging examples of such intrinsic cell cycle checkpoint regulation and discuss their physiological and clinical relevance.
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Affiliation(s)
- Andreas Panagopoulos
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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39
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Stroik S, Kurtz K, Lin K, Karachenets S, Myers CL, Bielinsky AK, Hendrickson EA. EXO1 resection at G-quadruplex structures facilitates resolution and replication. Nucleic Acids Res 2020; 48:4960-4975. [PMID: 32232411 PMCID: PMC7229832 DOI: 10.1093/nar/gkaa199] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/08/2020] [Accepted: 03/16/2020] [Indexed: 01/25/2023] Open
Abstract
G-quadruplexes represent unique roadblocks to DNA replication, which tends to stall at these secondary structures. Although G-quadruplexes can be found throughout the genome, telomeres, due to their G-richness, are particularly predisposed to forming these structures and thus represent difficult-to-replicate regions. Here, we demonstrate that exonuclease 1 (EXO1) plays a key role in the resolution of, and replication through, telomeric G-quadruplexes. When replication forks encounter G-quadruplexes, EXO1 resects the nascent DNA proximal to these structures to facilitate fork progression and faithful replication. In the absence of EXO1, forks accumulate at stabilized G-quadruplexes and ultimately collapse. These collapsed forks are preferentially repaired via error-prone end joining as depletion of EXO1 diverts repair away from error-free homology-dependent repair. Such aberrant repair leads to increased genomic instability, which is exacerbated at chromosome termini in the form of dysfunction and telomere loss.
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Affiliation(s)
- Susanna Stroik
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel, Hill, NC 27514, USA
| | - Kevin Kurtz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kevin Lin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Sergey Karachenets
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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40
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Benedict B, van Bueren MA, van Gemert FP, Lieftink C, Guerrero Llobet S, van Vugt MA, Beijersbergen RL, Te Riele H. The RECQL helicase prevents replication fork collapse during replication stress. Life Sci Alliance 2020; 3:3/10/e202000668. [PMID: 32820027 PMCID: PMC7441523 DOI: 10.26508/lsa.202000668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/24/2022] Open
Abstract
Most tumors lack the G1/S phase checkpoint and are insensitive to antigrowth signals. Loss of G1/S control can severely perturb DNA replication as revealed by slow replication fork progression and frequent replication fork stalling. Cancer cells may thus rely on specific pathways that mitigate the deleterious consequences of replication stress. To identify vulnerabilities of cells suffering from replication stress, we performed an shRNA-based genetic screen. We report that the RECQL helicase is specifically essential in replication stress conditions and protects stalled replication forks against MRE11-dependent double strand break (DSB) formation. In line with these findings, knockdown of RECQL in different cancer cells increased the level of DNA DSBs. Thus, RECQL plays a critical role in sustaining DNA synthesis under conditions of replication stress and as such may represent a target for cancer therapy.
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Affiliation(s)
- Bente Benedict
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marit Ae van Bueren
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frank Pa van Gemert
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sergi Guerrero Llobet
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcel Atm van Vugt
- Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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41
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Joseph SA, Taglialatela A, Leuzzi G, Huang JW, Cuella-Martin R, Ciccia A. Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease. DNA Repair (Amst) 2020; 95:102943. [PMID: 32971328 DOI: 10.1016/j.dnarep.2020.102943] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Over the course of DNA replication, DNA lesions, transcriptional intermediates and protein-DNA complexes can impair the progression of replication forks, thus resulting in replication stress. Failure to maintain replication fork integrity in response to replication stress leads to genomic instability and predisposes to the development of cancer and other genetic disorders. Multiple DNA damage and repair pathways have evolved to allow completion of DNA replication following replication stress, thus preserving genomic integrity. One of the processes commonly induced in response to replication stress is fork reversal, which consists in the remodeling of stalled replication forks into four-way DNA junctions. In normal conditions, fork reversal slows down replication fork progression to ensure accurate repair of DNA lesions and facilitates replication fork restart once the DNA lesions have been removed. However, in certain pathological situations, such as the deficiency of DNA repair factors that protect regressed forks from nuclease-mediated degradation, fork reversal can cause genomic instability. In this review, we describe the complex molecular mechanisms regulating fork reversal, with a focus on the role of the SNF2-family fork remodelers SMARCAL1, ZRANB3 and HLTF, and highlight the implications of fork reversal for tumorigenesis and cancer therapy.
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Affiliation(s)
- Sarah A Joseph
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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42
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Promonet A, Padioleau I, Liu Y, Sanz L, Biernacka A, Schmitz AL, Skrzypczak M, Sarrazin A, Mettling C, Rowicka M, Ginalski K, Chedin F, Chen CL, Lin YL, Pasero P. Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites. Nat Commun 2020; 11:3940. [PMID: 32769985 PMCID: PMC7414224 DOI: 10.1038/s41467-020-17858-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
R-loops have both positive and negative impacts on chromosome functions. To identify toxic R-loops in the human genome, here, we map RNA:DNA hybrids, replication stress markers and DNA double-strand breaks (DSBs) in cells depleted for Topoisomerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation. RNA:DNA hybrids are found at both promoters (TSS) and terminators (TTS) of highly expressed genes. In contrast, the phosphorylation of RPA by ATR is only detected at TTS, which are preferentially replicated in a head-on orientation relative to the direction of transcription. In Top1-depleted cells, DSBs also accumulate at TTS, leading to persistent checkpoint activation, spreading of γ-H2AX on chromatin and global replication fork slowdown. These data indicate that fork pausing at the TTS of highly expressed genes containing R-loops prevents head-on conflicts between replication and transcription and maintains genome integrity in a Top1-dependent manner.
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Affiliation(s)
- Alexy Promonet
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Ismaël Padioleau
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
- Institut Gustave Roussy, Villejuif, France
| | - Yaqun Liu
- Institut Curie, PSL Research University, CNRS, UMR3244, Sorbonne Université, Paris, France
| | - Lionel Sanz
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - Anna Biernacka
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Anne-Lyne Schmitz
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Amélie Sarrazin
- BioCampus Montpellier, CNRS et Université de Montpellier, Montpellier, France
| | - Clément Mettling
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Montpellier, France
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Frédéric Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS, UMR3244, Sorbonne Université, Paris, France.
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France.
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43
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Telomere replication-When the going gets tough. DNA Repair (Amst) 2020; 94:102875. [PMID: 32650286 DOI: 10.1016/j.dnarep.2020.102875] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 12/28/2022]
Abstract
Telomeres consist of repetitive tracts of DNA that shield a chromosome's contents from erosion and replicative attrition. However, telomeres are also late-replicating regions of the genome in which a myriad of replicative obstructions reside. The obstacles contained within telomeres, as well as their genomic location, drive replicative stalling and subsequent fork collapse in these regions. Consequently, large scale deletions, under-replicated DNA, translocations, and fusion events arise following telomere replication failure. Further, under-replicated DNA and telomere fusions that are permitted to enter mitosis will produce mitotic DNA bridges - known drivers of genetic loss and chromothripsis. Thus, aberrant telomere replication promotes genomic instability, which, in turn leads either to cellular death, senescence or oncogenic transformation. The importance of these issues for organismal well-being necessitates a need for resolute telomere maintenance. Here, we describe recent advances in identifying and understanding the molecular mechanisms that are in place in human cells to escort the replisome through the telomere's unwieldy structures and repetitive sequences. Finally, we review the pathways that combat the deleterious outcomes that occur when telomeric replication forks do collapse.
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Bai G, Kermi C, Stoy H, Schiltz CJ, Bacal J, Zaino AM, Hadden MK, Eichman BF, Lopes M, Cimprich KA. HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis. Mol Cell 2020; 78:1237-1251.e7. [PMID: 32442397 PMCID: PMC7305998 DOI: 10.1016/j.molcel.2020.04.031] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023]
Abstract
DNA replication stress can stall replication forks, leading to genome instability. DNA damage tolerance pathways assist fork progression, promoting replication fork reversal, translesion DNA synthesis (TLS), and repriming. In the absence of the fork remodeler HLTF, forks fail to slow following replication stress, but underlying mechanisms and cellular consequences remain elusive. Here, we demonstrate that HLTF-deficient cells fail to undergo fork reversal in vivo and rely on the primase-polymerase PRIMPOL for repriming, unrestrained replication, and S phase progression upon limiting nucleotide levels. By contrast, in an HLTF-HIRAN mutant, unrestrained replication relies on the TLS protein REV1. Importantly, HLTF-deficient cells also exhibit reduced double-strand break (DSB) formation and increased survival upon replication stress. Our findings suggest that HLTF promotes fork remodeling, preventing other mechanisms of replication stress tolerance in cancer cells. This remarkable plasticity of the replication fork may determine the outcome of replication stress in terms of genome integrity, tumorigenesis, and response to chemotherapy.
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Affiliation(s)
- Gongshi Bai
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Chames Kermi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Carl J Schiltz
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Julien Bacal
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Angela M Zaino
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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45
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Saccharomyces cerevisiae Mus81-Mms4 prevents accelerated senescence in telomerase-deficient cells. PLoS Genet 2020; 16:e1008816. [PMID: 32469862 PMCID: PMC7286520 DOI: 10.1371/journal.pgen.1008816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/10/2020] [Accepted: 04/30/2020] [Indexed: 01/31/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) in human cells is a conserved process that is often activated in telomerase-deficient human cancers. This process exploits components of the recombination machinery to extend telomere ends, thus allowing for increased proliferative potential. Human MUS81 (Mus81 in Saccharomyces cerevisiae) is the catalytic subunit of structure-selective endonucleases involved in recombination and has been implicated in the ALT mechanism. However, it is unclear whether MUS81 activity at the telomere is specific to ALT cells or if it is required for more general aspects of telomere stability. In this study, we use S. cerevisiae to evaluate the contribution of the conserved Mus81-Mms4 endonuclease in telomerase-deficient yeast cells that maintain their telomeres by mechanisms akin to human ALT. Similar to human cells, we find that yeast Mus81 readily localizes to telomeres and its activity is important for viability after initial loss of telomerase. Interestingly, our analysis reveals that yeast Mus81 is not required for the survival of cells undergoing recombination-mediated telomere lengthening, i.e. for ALT itself. Rather we infer from genetic analysis that Mus81-Mms4 facilitates telomere replication during times of telomere instability. Furthermore, combining mus81 mutants with mutants of a yeast telomere replication factor, Rrm3, reveals that the two proteins function in parallel to promote normal growth during times of telomere stress. Combined with previous reports, our data can be interpreted in a consistent model in which both yeast and human MUS81-dependent nucleases participate in the recovery of stalled replication forks within telomeric DNA. Furthermore, this process becomes crucial under conditions of additional replication stress, such as telomere replication in telomerase-deficient cells. Cancer cell divisions require active chromosome lengthening through extension of their highly repetitive ends, called telomeres. This process is accomplished through two main mechanisms: the activity of an RNA-protein complex, telomerase, or through a telomerase-independent process termed alternative lengthening of telomeres (ALT). Human MUS81, the catalytic subunit of a set of structure-selective endonucleases, was found to be essential in human cells undergoing ALT and proposed to be directly involved in telomere lengthening. Using telomerase-deficient Saccharomyces cerevisiae cells as a model for ALT, we tested the hypothesis that Mus81-Mms4, the budding yeast homolog of human MUS81-dependent nucleases, is essential for telomere lengthening as proposed for human cells. Using genetic and molecular assays we confirm that Mus81-Mms4 is involved in telomere metabolism in yeast. However, to our surprise, we find that Mus81-Mms4 is not directly involved in recombination-based mechanisms of telomere lengthening. Rather it appears that Mus81-Mms4 is involved in resolving replication stress at telomeres, which is augmented in cells undergoing telomere instability. This model is consistent with observations in mammalian cells and suggest that cells undergoing telomere shortening experience replication stress at telomeres.
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Tisi R, Vertemara J, Zampella G, Longhese MP. Functional and structural insights into the MRX/MRN complex, a key player in recognition and repair of DNA double-strand breaks. Comput Struct Biotechnol J 2020; 18:1137-1152. [PMID: 32489527 PMCID: PMC7260605 DOI: 10.1016/j.csbj.2020.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 01/20/2023] Open
Abstract
Chromosomal DNA double-strand breaks (DSBs) are potentially lethal DNA lesions that pose a significant threat to genome stability and therefore need to be repaired to preserve genome integrity. Eukaryotic cells possess two main mechanisms for repairing DSBs: non-homologous end-joining (NHEJ) and homologous recombination (HR). HR requires that the 5' terminated strands at both DNA ends are nucleolytically degraded by a concerted action of nucleases in a process termed DNA-end resection. This degradation leads to the formation of 3'-ended single-stranded DNA (ssDNA) ends that are essential to use homologous DNA sequences for repair. The evolutionarily conserved Mre11-Rad50-Xrs2/NBS1 complex (MRX/MRN) has enzymatic and structural activities to initiate DSB resection and to maintain the DSB ends tethered to each other for their repair. Furthermore, it is required to recruit and activate the protein kinase Tel1/ATM, which plays a key role in DSB signaling. All these functions depend on ATP-regulated DNA binding and nucleolytic activities of the complex. Several structures have been obtained in recent years for Mre11 and Rad50 subunits from archaea, and a few from the bacterial and eukaryotic orthologs. Nevertheless, the mechanism of activation of this protein complex is yet to be fully elucidated. In this review, we focused on recent biophysical and structural insights on the MRX complex and their interplay.
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Affiliation(s)
- Renata Tisi
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
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Tarsounas M, Sung P. The antitumorigenic roles of BRCA1-BARD1 in DNA repair and replication. Nat Rev Mol Cell Biol 2020; 21:284-299. [PMID: 32094664 PMCID: PMC7204409 DOI: 10.1038/s41580-020-0218-z] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 11/09/2022]
Abstract
The tumour suppressor breast cancer type 1 susceptibility protein (BRCA1) promotes DNA double-strand break (DSB) repair by homologous recombination and protects DNA replication forks from attrition. BRCA1 partners with BRCA1-associated RING domain protein 1 (BARD1) and other tumour suppressor proteins to mediate the initial nucleolytic resection of DNA lesions and the recruitment and regulation of the recombinase RAD51. The discovery of the opposing functions of BRCA1 and the p53-binding protein 1 (53BP1)-associated complex in DNA resection sheds light on how BRCA1 influences the choice of homologous recombination over non-homologous end joining and potentially other mutagenic pathways of DSB repair. Understanding the functional crosstalk between BRCA1-BARD1 and its cofactors and antagonists will illuminate the molecular basis of cancers that arise from a deficiency or misregulation of chromosome damage repair and replication fork maintenance. Such knowledge will also be valuable for understanding acquired tumour resistance to poly(ADP-ribose) polymerase (PARP) inhibitors and other therapeutics and for the development of new treatments. In this Review, we discuss recent advances in elucidating the mechanisms by which BRCA1-BARD1 functions in DNA repair, replication fork maintenance and tumour suppression, and its therapeutic relevance.
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Affiliation(s)
- Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA.
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Ragu S, Matos-Rodrigues G, Lopez BS. Replication Stress, DNA Damage, Inflammatory Cytokines and Innate Immune Response. Genes (Basel) 2020; 11:E409. [PMID: 32283785 PMCID: PMC7230342 DOI: 10.3390/genes11040409] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/21/2022] Open
Abstract
Complete and accurate DNA replication is essential to genome stability maintenance during cellular division. However, cells are routinely challenged by endogenous as well as exogenous agents that threaten DNA stability. DNA breaks and the activation of the DNA damage response (DDR) arising from endogenous replication stress have been observed at pre- or early stages of oncogenesis and senescence. Proper detection and signalling of DNA damage are essential for the autonomous cellular response in which the DDR regulates cell cycle progression and controls the repair machinery. In addition to this autonomous cellular response, replicative stress changes the cellular microenvironment, activating the innate immune response that enables the organism to protect itself against the proliferation of damaged cells. Thereby, the recent descriptions of the mechanisms of the pro-inflammatory response activation after replication stress, DNA damage and DDR defects constitute important conceptual novelties. Here, we review the links of replication, DNA damage and DDR defects to innate immunity activation by pro-inflammatory paracrine effects, highlighting the implications for human syndromes and immunotherapies.
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Affiliation(s)
| | | | - Bernard S. Lopez
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, 24 rue du Faubourg St Jacques, 75014 Paris, France; (S.R.); (G.M.-R.)
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Abstract
Programmed fork pausing is a complex process allowing cells to arrest replication forks at specific loci in a polar manner. Studies in budding yeast and other model organisms indicate that such replication fork barriers do not act as roadblocks passively impeding fork progression but rather elicit complex interactions between fork and barrier components. In this issue of Genes & Development, Shyian and colleagues (pp. 87-98) show that in budding yeast, the fork protection complex Tof1-Csm3 interacts physically with DNA topoisomerase I (Top1) at replication forks through the C-terminal domain of Tof1. Fork pausing at the ribosomal DNA (rDNA) replication fork barrier (RFB) is impaired in the absence of Top1 or in a tof1 mutant that does not bind Top1, but the function of Top1 can be partially compensated for by Top2. Together, these data indicate that topoisomerases play an unexpected role in the regulation of programmed fork pausing in Saccharomyces cerevisiae.
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Affiliation(s)
- Mélanie V Larcher
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier 34396, France
| | - Philippe Pasero
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier 34396, France
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Abstract
Effective maintenance and stability of our genomes is essential for normal cell division, tissue homeostasis, and cellular and organismal fitness. The processes of chromosome replication and segregation require continual surveillance to insure fidelity. Accurate and efficient repair of DNA damage preserves genome integrity, which if lost can lead to multiple diseases, including cancer. Poly(ADP-ribose) a dynamic and reversible posttranslational modification and the enzymes that catalyze it (PARP1, PARP2, tankyrase 1, and tankyrase 2) function to maintain genome stability through diverse mechanisms. Here we review the role of these enzymes and the modification in genome repair, replication, and resolution in human cells.
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Affiliation(s)
- Kameron Azarm
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
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