1
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Oehler J, Morrow CA, Whitby MC. Gene duplication and deletion caused by over-replication at a fork barrier. Nat Commun 2023; 14:7730. [PMID: 38007544 PMCID: PMC10676400 DOI: 10.1038/s41467-023-43494-7] [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: 07/17/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023] Open
Abstract
Replication fork stalling can provoke fork reversal to form a four-way DNA junction. This remodelling of the replication fork can facilitate repair, aid bypass of DNA lesions, and enable replication restart, but may also pose a risk of over-replication during fork convergence. We show that replication fork stalling at a site-specific barrier in fission yeast can induce gene duplication-deletion rearrangements that are independent of replication restart-associated template switching and Rad51-dependent multi-invasion. Instead, they resemble targeted gene replacements (TGRs), requiring the DNA annealing activity of Rad52, the 3'-flap nuclease Rad16-Swi10, and mismatch repair protein Msh2. We propose that excess DNA, generated during the merging of a canonical fork with a reversed fork, can be liberated by a nuclease and integrated at an ectopic site via a TGR-like mechanism. This highlights how over-replication at replication termination sites can threaten genome stability in eukaryotes.
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Affiliation(s)
- Judith Oehler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Carl A Morrow
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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2
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SUMO-Based Regulation of Nuclear Positioning to Spatially Regulate Homologous Recombination Activities at Replication Stress Sites. Genes (Basel) 2021; 12:genes12122010. [PMID: 34946958 PMCID: PMC8701742 DOI: 10.3390/genes12122010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
DNA lesions have properties that allow them to escape their nuclear compartment to achieve DNA repair in another one. Recent studies uncovered that the replication fork, when its progression is impaired, exhibits increased mobility when changing nuclear positioning and anchors to nuclear pore complexes, where specific types of homologous recombination pathways take place. In yeast models, increasing evidence points out that nuclear positioning is regulated by small ubiquitin-like modifier (SUMO) metabolism, which is pivotal to maintaining genome integrity at sites of replication stress. Here, we review how SUMO-based pathways are instrumental to spatially segregate the subsequent steps of homologous recombination during replication fork restart. In particular, we discussed how routing towards nuclear pore complex anchorage allows distinct homologous recombination pathways to take place at halted replication forks.
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3
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Muraszko J, Kramarz K, Argunhan B, Ito K, Baranowska G, Kurokawa Y, Murayama Y, Tsubouchi H, Lambert S, Iwasaki H, Dziadkowiec D. Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast. Nucleic Acids Res 2021; 49:6832-6848. [PMID: 34157114 PMCID: PMC8266636 DOI: 10.1093/nar/gkab511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/20/2022] Open
Abstract
Rad51 is the key protein in homologous recombination that plays important roles during DNA replication and repair. Auxiliary factors regulate Rad51 activity to facilitate productive recombination, and prevent inappropriate, untimely or excessive events, which could lead to genome instability. Previous genetic analyses identified a function for Rrp1 (a member of the Rad5/16-like group of SWI2/SNF2 translocases) in modulating Rad51 function, shared with the Rad51 mediator Swi5-Sfr1 and the Srs2 anti-recombinase. Here, we show that Rrp1 overproduction alleviates the toxicity associated with excessive Rad51 levels in a manner dependent on Rrp1 ATPase domain. Purified Rrp1 binds to DNA and has a DNA-dependent ATPase activity. Importantly, Rrp1 directly interacts with Rad51 and removes it from double-stranded DNA, confirming that Rrp1 is a translocase capable of modulating Rad51 function. Rrp1 affects Rad51 binding at centromeres. Additionally, we demonstrate in vivo and in vitro that Rrp1 possesses E3 ubiquitin ligase activity with Rad51 as a substrate, suggesting that Rrp1 regulates Rad51 in a multi-tiered fashion.
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Affiliation(s)
| | - Karol Kramarz
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Bilge Argunhan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Kentaro Ito
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | | | - Yumiko Kurokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Yasuto Murayama
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hideo Tsubouchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Hiroshi Iwasaki
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
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4
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Williams RM, Zhang X. Roles of ATM and ATR in DNA double strand breaks and replication stress. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 161:27-38. [DOI: 10.1016/j.pbiomolbio.2020.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
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5
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Tian T, Bu M, Chen X, Ding L, Yang Y, Han J, Feng XH, Xu P, Liu T, Ying S, Lei Y, Li Q, Huang J. The ZATT-TOP2A-PICH Axis Drives Extensive Replication Fork Reversal to Promote Genome Stability. Mol Cell 2020; 81:198-211.e6. [PMID: 33296677 DOI: 10.1016/j.molcel.2020.11.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/03/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022]
Abstract
Replication fork reversal is a global response to replication stress in mammalian cells, but precisely how it occurs remains poorly understood. Here, we show that, upon replication stress, DNA topoisomerase IIalpha (TOP2A) is recruited to stalled forks in a manner dependent on the SNF2-family DNA translocases HLTF, ZRANB3, and SMARCAL1. This is accompanied by an increase in TOP2A SUMOylation mediated by the SUMO E3 ligase ZATT and followed by recruitment of a SUMO-targeted DNA translocase, PICH. Disruption of the ZATT-TOP2A-PICH axis results in accumulation of partially reversed forks and enhanced genome instability. These results suggest that fork reversal occurs via a sequential two-step process. First, HLTF, ZRANB3, and SMARCAL1 initiate limited fork reversal, creating superhelical strain in the newly replicated sister chromatids. Second, TOP2A drives extensive fork reversal by resolving the resulting topological barriers and via its role in recruiting PICH to stalled forks.
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Affiliation(s)
- Tian Tian
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Min Bu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xu Chen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Linli Ding
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jinhua Han
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Pinglong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ting Liu
- Department of Cell Biology and Department of General Surgery of Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Songmin Ying
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yang Lei
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qing Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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6
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The nuclear pore primes recombination-dependent DNA synthesis at arrested forks by promoting SUMO removal. Nat Commun 2020; 11:5643. [PMID: 33159083 PMCID: PMC7648084 DOI: 10.1038/s41467-020-19516-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022] Open
Abstract
Nuclear Pore complexes (NPCs) act as docking sites to anchor particular DNA lesions facilitating DNA repair by elusive mechanisms. Using replication fork barriers in fission yeast, we report that relocation of arrested forks to NPCs occurred after Rad51 loading and its enzymatic activity. The E3 SUMO ligase Pli1 acts at arrested forks to safeguard integrity of nascent strands and generates poly-SUMOylation which promote relocation to NPCs but impede the resumption of DNA synthesis by homologous recombination (HR). Anchorage to NPCs allows SUMO removal by the SENP SUMO protease Ulp1 and the proteasome, promoting timely resumption of DNA synthesis. Preventing Pli1-mediated SUMO chains was sufficient to bypass the need for anchorage to NPCs and the inhibitory effect of poly-SUMOylation on HR-mediated DNA synthesis. Our work establishes a novel spatial control of Recombination-Dependent Replication (RDR) at a unique sequence that is distinct from mechanisms engaged at collapsed-forks and breaks within repeated sequences. In yeast, collapsed forks shift to the nuclear periphery to associate with two distinct perinuclear anchorage sites such as the nuclear pore complex. Here, the authors reveal the mechanisms engaged at nuclear pore complex facilitating fork integrity and restart via SUMO regulation.
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7
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Appanah R, Jones D, Falquet B, Rass U. Limiting homologous recombination at stalled replication forks is essential for cell viability: DNA2 to the rescue. Curr Genet 2020; 66:1085-1092. [PMID: 32909097 PMCID: PMC7599155 DOI: 10.1007/s00294-020-01106-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022]
Abstract
The disease-associated nuclease–helicase DNA2 has been implicated in DNA end-resection during DNA double-strand break repair, Okazaki fragment processing, and the recovery of stalled DNA replication forks (RFs). Its role in Okazaki fragment processing has been proposed to explain why DNA2 is indispensable for cell survival across organisms. Unexpectedly, we found that DNA2 has an essential role in suppressing homologous recombination (HR)-dependent replication restart at stalled RFs. In the absence of DNA2-mediated RF recovery, excessive HR-restart of stalled RFs results in toxic levels of abortive recombination intermediates that lead to DNA damage-checkpoint activation and terminal cell-cycle arrest. While HR proteins protect and restart stalled RFs to promote faithful genome replication, these findings show how HR-dependent replication restart is actively constrained by DNA2 to ensure cell survival. These new insights disambiguate the effects of DNA2 dysfunction on cell survival, and provide a framework to rationalize the association of DNA2 with cancer and the primordial dwarfism disorder Seckel syndrome based on its role in RF recovery.
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Affiliation(s)
- Rowin Appanah
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - David Jones
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Benoît Falquet
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, 4056, Basel, Switzerland
| | - Ulrich Rass
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
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8
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Pardo B, Moriel‐Carretero M, Vicat T, Aguilera A, Pasero P. Homologous recombination and Mus81 promote replication completion in response to replication fork blockage. EMBO Rep 2020; 21:e49367. [PMID: 32419301 PMCID: PMC7332989 DOI: 10.15252/embr.201949367] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Impediments to DNA replication threaten genome stability. The homologous recombination (HR) pathway has been involved in the restart of blocked replication forks. Here, we used a method to increase yeast cell permeability in order to study at the molecular level the fate of replication forks blocked by DNA topoisomerase I poisoning by camptothecin (CPT). Our results indicate that Rad52 and Rad51 HR factors are required to complete DNA replication in response to CPT. Recombination events occurring during S phase do not generally lead to the restart of DNA synthesis but rather protect blocked forks until they merge with convergent forks. This fusion generates structures requiring their resolution by the Mus81 endonuclease in G2 /M. At the global genome level, the multiplicity of replication origins in eukaryotic genomes and the fork protection mechanism provided by HR appear therefore to be essential to complete DNA replication in response to fork blockage.
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Affiliation(s)
- Benjamin Pardo
- Institut de Génétique HumaineUniversité de Montpellier‐CNRSMontpellierFrance
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
| | - María Moriel‐Carretero
- Institut de Génétique HumaineUniversité de Montpellier‐CNRSMontpellierFrance
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
- Present address:
Centre de Recherche en Biologie cellulaire de MontpellierUniversité de Montpellier‐CNRSMontpellierFrance
| | - Thibaud Vicat
- Institut de Génétique HumaineUniversité de Montpellier‐CNRSMontpellierFrance
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevilleSpain
| | - Philippe Pasero
- Institut de Génétique HumaineUniversité de Montpellier‐CNRSMontpellierFrance
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9
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Boeckemeier L, Kraehenbuehl R, Keszthelyi A, Gasasira MU, Vernon EG, Beardmore R, Vågbø CB, Chaplin D, Gollins S, Krokan HE, Lambert SAE, Paizs B, Hartsuiker E. Mre11 exonuclease activity removes the chain-terminating nucleoside analog gemcitabine from the nascent strand during DNA replication. SCIENCE ADVANCES 2020; 6:eaaz4126. [PMID: 32523988 PMCID: PMC7259961 DOI: 10.1126/sciadv.aaz4126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
The Mre11 nuclease is involved in early responses to DNA damage, often mediated by its role in DNA end processing. MRE11 mutations and aberrant expression are associated with carcinogenesis and cancer treatment outcomes. While, in recent years, progress has been made in understanding the role of Mre11 nuclease activities in DNA double-strand break repair, their role during replication has remained elusive. The nucleoside analog gemcitabine, widely used in cancer therapy, acts as a replication chain terminator; for a cell to survive treatment, gemcitabine needs to be removed from replicating DNA. Activities responsible for this removal have, so far, not been identified. We show that Mre11 3' to 5' exonuclease activity removes gemcitabine from nascent DNA during replication. This contributes to replication progression and gemcitabine resistance. We thus uncovered a replication-supporting role for Mre11 exonuclease activity, which is distinct from its previously reported detrimental role in uncontrolled resection in recombination-deficient cells.
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Affiliation(s)
- L. Boeckemeier
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - R. Kraehenbuehl
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - A. Keszthelyi
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - M. U. Gasasira
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - E. G. Vernon
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - R. Beardmore
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - C. B. Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - D. Chaplin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - S. Gollins
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - H. E. Krokan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - S. A. E. Lambert
- Institut Curie, Paris-Saclay University, UMR3348, F-91450 Orsay, France
| | - B. Paizs
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - E. Hartsuiker
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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10
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He D, Li T, Sheng M, Yang B. Exonuclease 1 (Exo1) Participates in Mammalian Non-Homologous End Joining and Contributes to Drug Resistance in Ovarian Cancer. Med Sci Monit 2020; 26:e918751. [PMID: 32167078 PMCID: PMC7092659 DOI: 10.12659/msm.918751] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Exonuclease 1 (Exo1) participates in a variety of DNA damage repair, including mismatch repair, nucleotide excision repair, and homologous recombination. Genetic study in yeast indicates a role of Exo1 in non-homologous end joining (NHEJ), acting as a regulator for accuracy repairing DNA. This study aimed to investigate the effects of human Exo1 in NHEJ and drug resistance in ovarian cells. Material/Methods Ectopic expression of Exo1 was carried out using pcDNA3.1-EXO1 plasmid in SKOV3 cells. GST-tagged human Exo1 was purified using pTXB1-gst-EXO1 and the his-tagged-Ku was collected using pET15b.his.Ku. Exo1 and Ku70 proteins expressed in bacteria were harvested and purified. DNA-protein binding was examined using affinity capture assay. The cells were treated using drugs for 72 hours. Then, the viabilities of cells were evaluated with sulforhodamine B cell viability analysis. The protein expression was evaluated using western blot assay. Results As expected, human cells that deficient of Exo1 were sensitive to ionizing radiation and DNA damaging drugs (cisplatin and doxorubicin). Cisplatin resistant ovarian cancer cell line and Exo1 deficient cell lines were successfully generated. Exo1 interacts with NHEJ required factor Ku70 and affects NHEJ efficiency. We observed that Exo1 expression level was upregulated in drug resistant cell line and knockdown of Exo1 in drug resistant cells sensitized cells to cisplatin and doxorubicin. Conclusions Exo1 participated in mammalian non-homologous end joining and contributed to drug resistance in ovarian cancer.
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Affiliation(s)
- Dongyun He
- Department of Gynaecology and Obstetrics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Tao Li
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Minjia Sheng
- Department of Gynaecology and Obstetrics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Ben Yang
- Department of Ophthalmology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
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11
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Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:genes11010079. [PMID: 31936815 PMCID: PMC7016768 DOI: 10.3390/genes11010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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12
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Ait-Saada A, Khorosjutina O, Chen J, Kramarz K, Maksimov V, Svensson JP, Lambert S, Ekwall K. Chromatin remodeler Fft3 plays a dual role at blocked DNA replication forks. Life Sci Alliance 2019; 2:e201900433. [PMID: 31575705 PMCID: PMC6771652 DOI: 10.26508/lsa.201900433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 01/26/2023] Open
Abstract
Here, we investigate the function of fission yeast Fun30/Smarcad1 family of SNF2 ATPase-dependent chromatin remodeling enzymes in DNA damage repair. There are three Fun30 homologues in fission yeast, Fft1, Fft2, and Fft3. We find that only Fft3 has a function in DNA repair and it is needed for single-strand annealing of an induced double-strand break. Furthermore, we use an inducible replication fork barrier system to show that Fft3 has two distinct roles at blocked DNA replication forks. First, Fft3 is needed for the resection of nascent strands, and second, it is required to restart the blocked forks. The latter function is independent of its ATPase activity.
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Affiliation(s)
- Anissia Ait-Saada
- Institut Curie, Paris-Saclay University, Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 3348, F-91405, Orsay, France
| | - Olga Khorosjutina
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jiang Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karol Kramarz
- Institut Curie, Paris-Saclay University, Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 3348, F-91405, Orsay, France
| | - Vladimir Maksimov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sarah Lambert
- Institut Curie, Paris-Saclay University, Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 3348, F-91405, Orsay, France
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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13
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Saatchi F, Kirchmaier AL. Tolerance of DNA Replication Stress Is Promoted by Fumarate Through Modulation of Histone Demethylation and Enhancement of Replicative Intermediate Processing in Saccharomyces cerevisiae. Genetics 2019; 212:631-654. [PMID: 31123043 PMCID: PMC6614904 DOI: 10.1534/genetics.119.302238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Fumarase is a well-characterized TCA cycle enzyme that catalyzes the reversible conversion of fumarate to malate. In mammals, fumarase acts as a tumor suppressor, and loss-of-function mutations in the FH gene in hereditary leiomyomatosis and renal cell cancer result in the accumulation of intracellular fumarate-an inhibitor of α-ketoglutarate-dependent dioxygenases. Fumarase promotes DNA repair by nonhomologous end joining in mammalian cells through interaction with the histone variant H2A.Z, and inhibition of KDM2B, a H3 K36-specific histone demethylase. Here, we report that Saccharomyces cerevisiae fumarase, Fum1p, acts as a response factor during DNA replication stress, and fumarate enhances survival of yeast lacking Htz1p (H2A.Z in mammals). We observed that exposure to DNA replication stress led to upregulation as well as nuclear enrichment of Fum1p, and raising levels of fumarate in cells via deletion of FUM1 or addition of exogenous fumarate suppressed the sensitivity to DNA replication stress of htz1Δ mutants. This suppression was independent of modulating nucleotide pool levels. Rather, our results are consistent with fumarate conferring resistance to DNA replication stress in htz1Δ mutants by inhibiting the H3 K4-specific histone demethylase Jhd2p, and increasing H3 K4 methylation. Although the timing of checkpoint activation and deactivation remained largely unaffected by fumarate, sensors and mediators of the DNA replication checkpoint were required for fumarate-dependent resistance to replication stress in the htz1Δ mutants. Together, our findings imply metabolic enzymes and metabolites aid in processing replicative intermediates by affecting chromatin modification states, thereby promoting genome integrity.
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Affiliation(s)
- Faeze Saatchi
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907
| | - Ann L Kirchmaier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907
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14
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Jalan M, Oehler J, Morrow CA, Osman F, Whitby MC. Factors affecting template switch recombination associated with restarted DNA replication. eLife 2019; 8:41697. [PMID: 30667359 PMCID: PMC6358216 DOI: 10.7554/elife.41697] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination helps ensure the timely completion of genome duplication by restarting collapsed replication forks. However, this beneficial function is not without risk as replication restarted by homologous recombination is prone to template switching (TS) that can generate deleterious genome rearrangements associated with diseases such as cancer. Previously we established an assay for studying TS in Schizosaccharomyces pombe (Nguyen et al., 2015). Here, we show that TS is detected up to 75 kb downstream of a collapsed replication fork and can be triggered by head-on collision between the restarted fork and RNA Polymerase III transcription. The Pif1 DNA helicase, Pfh1, promotes efficient restart and also suppresses TS. A further three conserved helicases (Fbh1, Rqh1 and Srs2) strongly suppress TS, but there is no change in TS frequency in cells lacking Fml1 or Mus81. We discuss how these factors likely influence TS.
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Affiliation(s)
- Manisha Jalan
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Judith Oehler
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Carl A Morrow
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Fekret Osman
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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15
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Bonetti D, Colombo CV, Clerici M, Longhese MP. Processing of DNA Ends in the Maintenance of Genome Stability. Front Genet 2018; 9:390. [PMID: 30258457 PMCID: PMC6143663 DOI: 10.3389/fgene.2018.00390] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/29/2018] [Indexed: 12/17/2022] Open
Abstract
DNA double-strand breaks (DSBs) are particularly hazardous lesions as their inappropriate repair can result in chromosome rearrangements, an important driving force of tumorigenesis. DSBs can be repaired by end joining mechanisms or by homologous recombination (HR). HR requires the action of several nucleases that preferentially remove the 5′-terminated strands at both DSB ends in a process called DNA end resection. The same nucleases are also involved in the processing of replication fork structures. Much of our understanding of these pathways has come from studies in the model organism Saccharomyces cerevisiae. Here, we review the current knowledge of the mechanism of resection at DNA DSBs and replication forks.
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Affiliation(s)
- Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | | | - Michela Clerici
- 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
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16
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Abstract
Flaws in the DNA replication process have emerged as a leading driver of genome instability in human diseases. Alteration to replication fork progression is a defining feature of replication stress and the consequent failure to maintain fork integrity and complete genome duplication within a single round of S-phase compromises genetic integrity. This includes increased mutation rates, small and large scale genomic rearrangement and deleterious consequences for the subsequent mitosis that result in the transmission of additional DNA damage to the daughter cells. Therefore, preserving fork integrity and replication competence is an important aspect of how cells respond to replication stress and avoid genetic change. Homologous recombination is a pivotal pathway in the maintenance of genome integrity in the face of replication stress. Here we review our recent understanding of the mechanisms by which homologous recombination acts to protect, restart and repair replication forks. We discuss the dynamics of these genetically distinct functions and their contribution to faithful mitoticsegregation.
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17
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Pasero P, Vindigni A. Nucleases Acting at Stalled Forks: How to Reboot the Replication Program with a Few Shortcuts. Annu Rev Genet 2018; 51:477-499. [PMID: 29178820 DOI: 10.1146/annurev-genet-120116-024745] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In a lifetime, a human being synthesizes approximately 2×1016 meters of DNA, a distance that corresponds to 130,000 times the distance between the Earth and the Sun. This daunting task is executed by thousands of replication forks, which progress along the chromosomes and frequently stall when they encounter DNA lesions, unusual DNA structures, RNA polymerases, or tightly-bound protein complexes. To complete DNA synthesis before the onset of mitosis, eukaryotic cells have evolved complex mechanisms to process and restart arrested forks through the coordinated action of multiple nucleases, topoisomerases, and helicases. In this review, we discuss recent advances in understanding the role and regulation of nucleases acting at stalled forks with a focus on the nucleolytic degradation of nascent DNA, a process commonly referred to as fork resection. We also discuss the effects of deregulated fork resection on genomic instability and on the unscheduled activation of the interferon response under replication stress conditions.
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Affiliation(s)
- Philippe Pasero
- Institute of Human Genetics, CNRS UMR9002, University of Montpellier, 34396 Montpellier, France;
| | - Alessandro Vindigni
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA;
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18
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García-Rodríguez N, Morawska M, Wong RP, Daigaku Y, Ulrich HD. Spatial separation between replisome- and template-induced replication stress signaling. EMBO J 2018; 37:embj.201798369. [PMID: 29581097 PMCID: PMC5920239 DOI: 10.15252/embj.201798369] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/29/2018] [Accepted: 02/26/2018] [Indexed: 11/09/2022] Open
Abstract
Polymerase‐blocking DNA lesions are thought to elicit a checkpoint response via accumulation of single‐stranded DNA at stalled replication forks. However, as an alternative to persistent fork stalling, re‐priming downstream of lesions can give rise to daughter‐strand gaps behind replication forks. We show here that the processing of such structures by an exonuclease, Exo1, is required for timely checkpoint activation, which in turn prevents further gap erosion in S phase. This Rad9‐dependent mechanism of damage signaling is distinct from the Mrc1‐dependent, fork‐associated response to replication stress induced by conditions such as nucleotide depletion or replisome‐inherent problems, but reminiscent of replication‐independent checkpoint activation by single‐stranded DNA. Our results indicate that while replisome stalling triggers a checkpoint response directly at the stalled replication fork, the response to replication stress elicited by polymerase‐blocking lesions mainly emanates from Exo1‐processed, postreplicative daughter‐strand gaps, thus offering a mechanistic explanation for the dichotomy between replisome‐ versus template‐induced checkpoint signaling.
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Affiliation(s)
| | - Magdalena Morawska
- Institute of Molecular Biology (IMB), Mainz, Germany.,Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane South Mimms, UK
| | - Ronald P Wong
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Yasukazu Daigaku
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane South Mimms, UK
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19
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Eastman A. Improving anticancer drug development begins with cell culture: misinformation perpetrated by the misuse of cytotoxicity assays. Oncotarget 2018; 8:8854-8866. [PMID: 27750219 PMCID: PMC5352448 DOI: 10.18632/oncotarget.12673] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/12/2016] [Indexed: 11/25/2022] Open
Abstract
The high failure rate of anticancer drug discovery and development has consumed billions of dollars annually. While many explanations have been provided, I believe that misinformation arising from inappropriate cell-based screens has been completely over-looked. Most cell culture experiments are irrelevant to how drugs are subsequently administered to patients. Usually, drug development focuses on growth inhibition rather than cell killing. Drugs are selected based on continuous incubation of cells, then frequently administered to the patient as a bolus. Target identification and validation is often performed by gene suppression that inevitably mimics continuous target inhibition. Drug concentrations in vitro frequently far exceed in vivo concentrations. Studies of drug synergy are performed at sub-optimal concentrations. And the focus on a limited number of cell lines can misrepresent the potential efficacy in a patient population. The intent of this review is to encourage more appropriate experimental design and data interpretation, and to improve drug development in the area of cell-based assays. Application of these principles should greatly enhance the successful translation of novel drugs to the patient.
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Affiliation(s)
- Alan Eastman
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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20
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Villa M, Bonetti D, Carraro M, Longhese MP. Rad9/53BP1 protects stalled replication forks from degradation in Mec1/ATR-defective cells. EMBO Rep 2018; 19:351-367. [PMID: 29301856 PMCID: PMC5797966 DOI: 10.15252/embr.201744910] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/16/2022] Open
Abstract
Nucleolytic processing by nucleases can be a relevant mechanism to allow repair/restart of stalled replication forks. However, nuclease action needs to be controlled to prevent overprocessing of damaged replication forks that can be detrimental to genome stability. The checkpoint protein Rad9/53BP1 is known to limit nucleolytic degradation (resection) of DNA double-strand breaks (DSBs) in both yeast and mammals. Here, we show that loss of the inhibition that Rad9 exerts on resection exacerbates the sensitivity to replication stress of Mec1/ATR-defective yeast cells by exposing stalled replication forks to Dna2-dependent degradation. This Rad9 protective function is independent of checkpoint activation and relies mainly on Rad9-Dpb11 interaction. We propose that Rad9/53BP1 supports cell viability by protecting stalled replication forks from extensive resection when the intra-S checkpoint is not fully functional.
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Affiliation(s)
- Matteo Villa
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Massimo Carraro
- 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
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21
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Teixeira-Silva A, Ait Saada A, Hardy J, Iraqui I, Nocente MC, Fréon K, Lambert SAE. The end-joining factor Ku acts in the end-resection of double strand break-free arrested replication forks. Nat Commun 2017; 8:1982. [PMID: 29215009 PMCID: PMC5719404 DOI: 10.1038/s41467-017-02144-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/08/2017] [Indexed: 01/13/2023] Open
Abstract
Replication requires homologous recombination (HR) to stabilize and restart terminally arrested forks. HR-mediated fork processing requires single stranded DNA (ssDNA) gaps and not necessarily double strand breaks. We used genetic and molecular assays to investigate fork-resection and restart at dysfunctional, unbroken forks in Schizosaccharomyces pombe. Here, we report that fork-resection is a two-step process regulated by the non-homologous end joining factor Ku. An initial resection mediated by MRN-Ctp1 removes Ku from terminally arrested forks, generating ~110 bp sized gaps obligatory for subsequent Exo1-mediated long-range resection and replication restart. The mere lack of Ku impacts the processing of arrested forks, leading to an extensive resection, a reduced recruitment of RPA and Rad51 and a slower fork-restart process. We propose that terminally arrested forks undergo fork reversal, providing a single DNA end for Ku binding. We uncover a role for Ku in regulating end-resection of unbroken forks and in fine-tuning HR-mediated replication restart.
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Affiliation(s)
- Ana Teixeira-Silva
- Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, F-91405, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, Orsay, F-91405, France
| | - Anissia Ait Saada
- Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, F-91405, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, Orsay, F-91405, France
| | - Julien Hardy
- Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, F-91405, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, Orsay, F-91405, France
| | - Ismail Iraqui
- Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, F-91405, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, Orsay, F-91405, France
| | - Marina Charlotte Nocente
- Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, F-91405, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, Orsay, F-91405, France
| | - Karine Fréon
- Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, F-91405, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, Orsay, F-91405, France
| | - Sarah A E Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348, Orsay, F-91405, France. .,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, Orsay, F-91405, France.
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22
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Nguyen JHG, Viterbo D, Anand RP, Verra L, Sloan L, Richard GF, Freudenreich CH. Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats. Nucleic Acids Res 2017; 45:4519-4531. [PMID: 28175398 PMCID: PMC5416882 DOI: 10.1093/nar/gkx088] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/31/2017] [Indexed: 12/25/2022] Open
Abstract
Trinucleotide repeats are a source of genome instability, causing replication fork stalling, chromosome fragility, and impaired repair. Specialized helicases play an important role in unwinding DNA structures to maintain genome stability. The Srs2 helicase unwinds DNA hairpins, facilitates replication, and prevents repeat instability and fragility. However, since Srs2 is a multifunctional protein with helicase activity and the ability to displace Rad51 recombinase, it was unclear which functions were required for its various protective roles. Here, using SRS2 separation-of-function alleles, we show that in the absence of Srs2 recruitment to PCNA or in helicase-deficient mutants, breakage at a CAG/CTG repeat increases. We conclude that Srs2 interaction with PCNA allows the helicase activity to unwind fork-blocking CAG/CTG hairpin structures to prevent breaks. Independently of PCNA binding, Srs2 also displaces Rad51 from nascent strands to prevent recombination-dependent repeat expansions and contractions. By 2D gel electrophoresis, we detect two different kinds of structured intermediates or joint molecules (JMs). Some JMs are Rad51-independent and exhibit properties of reversed forks, including being processed by the Exo1 nuclease. In addition, in a helicase-deficient mutant, Rad51-dependent JMs are detected, probably corresponding to recombination between sisters. These results clarify the many roles of Srs2 in facilitating replication through fork-blocking hairpin lesions.
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Affiliation(s)
| | - David Viterbo
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
| | - Ranjith P Anand
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Lauren Verra
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Laura Sloan
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Guy-Franck Richard
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
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23
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Ait Saada A, Teixeira-Silva A, Iraqui I, Costes A, Hardy J, Paoletti G, Fréon K, Lambert SAE. Unprotected Replication Forks Are Converted into Mitotic Sister Chromatid Bridges. Mol Cell 2017; 66:398-410.e4. [PMID: 28475874 DOI: 10.1016/j.molcel.2017.04.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/08/2017] [Accepted: 04/03/2017] [Indexed: 01/23/2023]
Abstract
Replication stress and mitotic abnormalities are key features of cancer cells. Temporarily paused forks are stabilized by the intra-S phase checkpoint and protected by the association of Rad51, which prevents Mre11-dependent resection. However, if a fork becomes dysfunctional and cannot resume, this terminally arrested fork is rescued by a converging fork to avoid unreplicated parental DNA during mitosis. Alternatively, dysfunctional forks are restarted by homologous recombination. Using fission yeast, we report that Rad52 and the DNA binding activity of Rad51, but not its strand-exchange activity, act to protect terminally arrested forks from unrestrained Exo1-nucleolytic activity. In the absence of recombination proteins, large ssDNA gaps, up to 3 kb long, occur behind terminally arrested forks, preventing efficient fork merging and leading to mitotic sister chromatid bridging. Thus, Rad52 and Rad51 prevent temporarily and terminally arrested forks from degrading and, despite the availability of converging forks, converting to anaphase bridges causing aneuploidy and cell death.
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Affiliation(s)
- Anissia Ait Saada
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Ana Teixeira-Silva
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Ismail Iraqui
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Audrey Costes
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Julien Hardy
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Giulia Paoletti
- Institut Curie, PSL Research University, CNRS, UMR144, F-75248 Paris, France
| | - Karine Fréon
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France
| | - Sarah A E Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France; Labeled Team Fondation pour la Recherche Médicale, UMR3348, F-91405 Orsay, France.
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24
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Stalled replication forks generate a distinct mutational signature in yeast. Proc Natl Acad Sci U S A 2017; 114:9665-9670. [PMID: 28827358 DOI: 10.1073/pnas.1706640114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proliferating cells acquire genome alterations during the act of DNA replication. This leads to mutation accumulation and somatic cell mosaicism in multicellular organisms, and is also implicated as an underlying cause of aging and tumorigenesis. The molecular mechanisms of DNA replication-associated genome rearrangements are poorly understood, largely due to methodological difficulties in analyzing specific replication forks in vivo. To provide an insight into this process, we analyzed the mutagenic consequences of replication fork stalling at a single, site-specific replication barrier (the Escherichia coli Tus/Ter complex) engineered into the yeast genome. We demonstrate that transient stalling at this barrier induces a distinct pattern of genome rearrangements in the newly replicated region behind the stalled fork, which primarily consist of localized losses and duplications of DNA sequences. These genetic alterations arise through the aberrant repair of a single-stranded DNA gap, in a process that is dependent on Exo1- and Shu1-dependent homologous recombination repair (HRR). Furthermore, aberrant processing of HRR intermediates, and elevated HRR-associated mutagenesis, is detectable in a yeast model of the human cancer predisposition disorder, Bloom's syndrome. Our data reveal a mechanism by which cellular responses to stalled replication forks can actively generate genomic alterations and genetic diversity in normal proliferating cells.
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25
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Morrow CA, Nguyen MO, Fower A, Wong IN, Osman F, Bryer C, Whitby MC. Inter-Fork Strand Annealing causes genomic deletions during the termination of DNA replication. eLife 2017; 6. [PMID: 28586299 PMCID: PMC5461108 DOI: 10.7554/elife.25490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/22/2017] [Indexed: 11/29/2022] Open
Abstract
Problems that arise during DNA replication can drive genomic alterations that are instrumental in the development of cancers and many human genetic disorders. Replication fork barriers are a commonly encountered problem, which can cause fork collapse and act as hotspots for replication termination. Collapsed forks can be rescued by homologous recombination, which restarts replication. However, replication restart is relatively slow and, therefore, replication termination may frequently occur by an active fork converging on a collapsed fork. We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. Based on our findings, we propose that IFSA is a potential threat to genomic stability in eukaryotes. DOI:http://dx.doi.org/10.7554/eLife.25490.001
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Affiliation(s)
- Carl A Morrow
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Michael O Nguyen
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Andrew Fower
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Io Nam Wong
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Fekret Osman
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Claire Bryer
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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26
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The RecQ DNA helicase Rqh1 constrains Exonuclease 1-dependent recombination at stalled replication forks. Sci Rep 2016; 6:22837. [PMID: 26957021 PMCID: PMC4783781 DOI: 10.1038/srep22837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 01/28/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) involves resection of the break to expose a 3' single-stranded DNA tail. In budding yeast, resection occurs in two steps: initial short-range resection, performed by Mre11-Rad50-Xrs2 and Sae2; and long-range resection catalysed by either Exo1 or Sgs1-Dna2. Here we use genetic assays to investigate the importance of Exo1 and the Sgs1 homologue Rqh1 for DNA repair and promotion of direct repeat recombination in the fission yeast Schizosaccharomyces pombe. We find that Exo1 and Rqh1 function in alternative redundant pathways for promoting survival following replication fork breakage. Exo1 promotes replication fork barrier-induced direct repeat recombination but intriguingly limits recombination induced by fork breakage. Direct repeat recombination induced by ultraviolet light depends on either Exo1 or Rqh1. Finally, we show that Rqh1 plays a major role in limiting Exo1-dependent direct repeat recombination induced by replication fork stalling but only a minor role in constraining recombination induced by fork breakage. The implications of our findings are discussed in the context of the benefits that long-range resection may bring to processing perturbed replication forks.
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27
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Lorenz A. New cassettes for single-step drug resistance and prototrophic marker switching in fission yeast. Yeast 2015; 32:703-10. [PMID: 26305038 DOI: 10.1002/yea.3097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/10/2015] [Accepted: 08/10/2015] [Indexed: 11/05/2022] Open
Abstract
Construction of multiply mutated strains for genetic interaction analysis and of strains carrying different epitope tags at multiple open reading frames for testing protein localization, abundance and protein-protein interactions is hampered by the availability of a sufficient number of different selectable markers. Moreover, strains with single gene deletions or tags often already exist in strain collections; for historical reasons these will mostly carry the ura4(+) gene or the G418-resistance kanMX as marker. Because it is rather cumbersome to produce multiply deleted or tagged strains using the same marker, or to completely reconstruct a particular strain with a different marker, single-step exchange protocols of markers are a time-saving alternative. In recent years, dominant drug resistance markers (DDRMs) against clonNAT, hygromycin B and bleomycin have been adapted and successfully used in Schizosaccharomyces pombe. The corresponding DDRM cassettes, natMX, hphMX and bleMX, carry the TEF promotor and terminator sequences from Ashbya gossypii as kanMX; this provides flanking homologies to enable single-step marker swapping by homologous gene targeting. To expand this very useful toolset for single-step marker exchange, I constructed MX cassettes containing the nutritional markers arg3(+), his3(+), leu1(+) and ura4(+). Furthermore, a set of constructs was created to enable single-step exchange of ura4(+) to kanMX6, natMX4 and hphMX4. The functionality of the cassettes is demonstrated by successful single-step marker swapping at several loci. These constructs allow straightforward and rapid remarking of existing ura4(+) - and MX-deleted and -tagged strains.
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28
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Su XA, Dion V, Gasser SM, Freudenreich CH. Regulation of recombination at yeast nuclear pores controls repair and triplet repeat stability. Genes Dev 2015; 29:1006-17. [PMID: 25940904 PMCID: PMC4441049 DOI: 10.1101/gad.256404.114] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/10/2015] [Indexed: 12/16/2022]
Abstract
Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, Su et al. find that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery and that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process. Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, we found that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery. This positioning is transient, occurs in late S phase, requires replication, and is associated with decreased subnuclear mobility of the locus. In contrast to persistent double-stranded breaks, expanded CAG repeats at the nuclear envelope associate with pores but not with the inner nuclear membrane protein Mps3. Relocation requires Nup84 and the Slx5/8 SUMO-dependent ubiquitin ligase but not Rad51, Mec1, or Tel1. Importantly, the presence of the Nup84 pore subcomplex and Slx5/8 suppresses CAG repeat fragility and instability. Repeat instability in nup84, slx5, or slx8 mutant cells arises through aberrant homologous recombination and is distinct from instability arising from the loss of ligase 4-dependent end-joining. Genetic and physical analysis of Rad52 sumoylation and binding at the CAG tract suggests that Slx5/8 targets sumoylated Rad52 for degradation at the pore to facilitate recovery from acute replication stress by promoting replication fork restart. We thereby confirmed that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process.
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Affiliation(s)
- Xiaofeng A Su
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Vincent Dion
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA; Program in Genetics, Tufts University, Medford, Massachusetts 02155, USA;
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29
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Checkpoints are blind to replication restart and recombination intermediates that result in gross chromosomal rearrangements. Nat Commun 2015; 6:6357. [PMID: 25721418 PMCID: PMC4351560 DOI: 10.1038/ncomms7357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 01/23/2015] [Indexed: 01/23/2023] Open
Abstract
Replication fork inactivation can be overcome by homologous recombination, but this can cause gross chromosomal rearrangements that subsequently missegregate at mitosis, driving further chromosome instability. It is unclear when the chromosome rearrangements are generated and whether individual replication problems or the resulting recombination intermediates delay the cell cycle. Here we have investigated checkpoint activation during HR-dependent replication restart using a site-specific replication fork-arrest system. Analysis during a single cell cycle shows that HR-dependent replication intermediates arise in S phase, shortly after replication arrest, and are resolved into acentric and dicentric chromosomes in G2. Despite this, cells progress into mitosis without delay. Neither the DNA damage nor the intra-S phase checkpoints are activated in the first cell cycle, demonstrating that these checkpoints are blind to replication and recombination intermediates as well as to rearranged chromosomes. The dicentrics form anaphase bridges that subsequently break, inducing checkpoint activation in the second cell cycle. Homologous recombination can overcome replication fork inactivation, but this can cause gross chromosomal rearrangements. Here, the authors show that DNA damage and intra-S phase checkpoints are blind to chromosome rearrangement in the first cell cycle, and are only induced in the second cell cycle.
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30
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Kondratova A, Watanabe T, Marotta M, Cannon M, Segall AM, Serre D, Tanaka H. Replication fork integrity and intra-S phase checkpoint suppress gene amplification. Nucleic Acids Res 2015; 43:2678-90. [PMID: 25672394 PMCID: PMC4357702 DOI: 10.1093/nar/gkv084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gene amplification is a phenotype-causing form of chromosome instability and is initiated by DNA double-strand breaks (DSBs). Cells with mutant p53 lose G1/S checkpoint and are permissive to gene amplification. In this study we show that mammalian cells become proficient for spontaneous gene amplification when the function of the DSB repair protein complex MRN (Mre11/Rad50/Nbs1) is impaired. Cells with impaired MRN complex experienced severe replication stress and gained substrates for gene amplification during replication, as evidenced by the increase of replication-associated single-stranded breaks that were converted to DSBs most likely through replication fork reversal. Impaired MRN complex directly compromised ATM/ATR-mediated checkpoints and allowed cells to progress through cell cycle in the presence of DSBs. Such compromised intra-S phase checkpoints promoted gene amplification independently from mutant p53. Finally, cells adapted to endogenous replication stress by globally suppressing genes for DNA replication and cell cycle progression. Our results indicate that the MRN complex suppresses gene amplification by stabilizing replication forks and by securing DNA damage response to replication-associated DSBs.
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Affiliation(s)
- Anna Kondratova
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Takaaki Watanabe
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Michael Marotta
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Matthew Cannon
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Anca M Segall
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Hisashi Tanaka
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
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31
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Mohebi S, Lambert SAE, Carr AM. Analyzing the Response to Dysfunction Replication Forks Using the RTS1 Barrier System in Fission Yeast. Methods Mol Biol 2015; 1300:239-59. [PMID: 25916716 DOI: 10.1007/978-1-4939-2596-4_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
The study of how eukaryotic cells overcome problems associated with dysfunctional DNA replication forks is assisted by experimental systems that allow site-specific replication fork arrest. Here we provide protocols for the use of the fission yeast RTS1 replication fork barrier. The RTS1 barrier is a directional, or polar, replication fork barrier that evolved to ensure directional replication of the fission yeast mating-type locus. We have moved the 859 bp RTS1 sequence to another locus in the genome and demonstrated that it arrests replication forks in a dysfunctional confirmation and that replication is restarted within ~20 min by the action of homologous recombination. We describe here the barrier constructs currently available, the methods by which we regulate the activity of the barrier, how to synchronize cells for analysis of replication intermediates by 2D gel electrophoresis, and the use of a replication slippage assay to measure fork fidelity.
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Affiliation(s)
- Saed Mohebi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, John Maynard Smith Building, Falmer, Brighton, BN1 9RQ, UK
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32
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Ngo GHP, Balakrishnan L, Dubarry M, Campbell JL, Lydall D. The 9-1-1 checkpoint clamp stimulates DNA resection by Dna2-Sgs1 and Exo1. Nucleic Acids Res 2014; 42:10516-28. [PMID: 25122752 PMCID: PMC4176354 DOI: 10.1093/nar/gku746] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) at DNA ends is an important regulator of the DNA damage response. Resection, the generation of ssDNA, affects DNA damage checkpoint activation, DNA repair pathway choice, ssDNA-associated mutation and replication fork stability. In eukaryotes, extensive DNA resection requires the nuclease Exo1 and nuclease/helicase pair: Dna2 and Sgs1BLM. How Exo1 and Dna2-Sgs1BLM coordinate during resection remains poorly understood. The DNA damage checkpoint clamp (the 9-1-1 complex) has been reported to play an important role in stimulating resection but the exact mechanism remains unclear. Here we show that the human 9-1-1 complex enhances the cleavage of DNA by both DNA2 and EXO1 in vitro, showing that the resection-stimulatory role of the 9-1-1 complex is direct. We also show that in Saccharomyces cerevisiae, the 9-1-1 complex promotes both Dna2-Sgs1 and Exo1-dependent resection in response to uncapped telomeres. Our results suggest that the 9-1-1 complex facilitates resection by recruiting both Dna2-Sgs1 and Exo1 to sites of resection. This activity of the 9-1-1 complex in supporting resection is strongly inhibited by the checkpoint adaptor Rad953BP1. Our results provide important mechanistic insights into how DNA resection is regulated by checkpoint proteins and have implications for genome stability in eukaryotes.
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Affiliation(s)
- Greg H P Ngo
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Marion Dubarry
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Judith L Campbell
- Divisions of Biology and Chemistry, Caltech, Braun Laboratories, Pasadena, CA 91125, USA
| | - David Lydall
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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