1
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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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2
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Mackay HL, Stone HR, Ellis K, Ronson GE, Walker AK, Starowicz K, Garvin AJ, van Eijk P, Vaitsiankova A, Vijayendran S, Beesley JF, Petermann E, Brown EJ, Densham RM, Reed SH, Dobbs F, Saponaro M, Morris JR. USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574674. [PMID: 38260523 PMCID: PMC10802463 DOI: 10.1101/2024.01.10.574674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mammalian DNA replication employs several RecQ DNA helicases to orchestrate the faithful duplication of genetic information. Helicase function is often coupled to the activity of specific nucleases, but how helicase and nuclease activities are co-directed is unclear. Here we identify the inactive ubiquitin-specific protease, USP50, as a ubiquitin-binding and chromatin-associated protein required for ongoing replication, fork restart, telomere maintenance and cellular survival during replicative stress. USP50 supports WRN:FEN1 at stalled replication forks, suppresses MUS81-dependent fork collapse and restricts double-strand DNA breaks at GC-rich sequences. Surprisingly we find that cells depleted for USP50 and recovering from a replication block exhibit increased DNA2 and RECQL4 foci and that the defects in ongoing replication, poor fork restart and increased fork collapse seen in these cells are mediated by DNA2, RECQL4 and RECQL5. These data define a novel ubiquitin-dependent pathway that promotes the balance of helicase: nuclease use at ongoing and stalled replication forks.
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3
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Irony-Tur Sinai M, Kerem B. Insights into common fragile site instability: DNA replication challenges at DNA repeat sequences. Emerg Top Life Sci 2023; 7:277-287. [PMID: 37876349 PMCID: PMC10754330 DOI: 10.1042/etls20230023] [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: 08/02/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]
Abstract
Common fragile sites (CFS) are specific genomic regions prone to chromosomal instability under conditions of DNA replication stress. CFSs manifest as breaks, gaps, and constrictions on metaphase chromosomes under mild replication stress. These replication-sensitive CFS regions are preferentially unstable during cancer development, as reflected by their association with copy number variants (CNVs) frequently arise in most tumor types. Over the years, it became clear that a combination of different characteristics underlies the enhanced sensitivity of CFSs to replication stress. As of today, there is a strong evidence that the core fragility regions along CFSs overlap with actively transcribed large genes with delayed replication timing upon replication stress. Recently, the mechanistic basis for CFS instability was further extended to regions which span topologically associated domain (TAD) boundaries, generating a fragility signature composed of replication, transcription and genome organization. The presence of difficult-to-replicate AT-rich repeats was one of the early features suggested to characterize a subgroup of CFSs. These long stretches of AT-dinucleotide have the potential to fold into stable secondary structures which may impede replication fork progression, leaving the region under-replicated. Here, we focus on the molecular mechanisms underlying repeat instability at CFSs and on the proteins involved in the resolution of secondary structure impediments arising along repetitive sequence elements which are essential for the maintenance of genome stability.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
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4
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Mechetin GV, Zharkov DO. DNA Damage Response and Repair in Boron Neutron Capture Therapy. Genes (Basel) 2023; 14:127. [PMID: 36672868 PMCID: PMC9859301 DOI: 10.3390/genes14010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Boron neutron capture therapy (BNCT) is an approach to the radiotherapy of solid tumors that was first outlined in the 1930s but has attracted considerable attention recently with the advent of a new generation of neutron sources. In BNCT, tumor cells accumulate 10B atoms that react with epithermal neutrons, producing energetic α particles and 7Li atoms that damage the cell's genome. The damage inflicted by BNCT appears not to be easily repairable and is thus lethal for the cell; however, the molecular events underlying the action of BNCT remain largely unaddressed. In this review, the chemistry of DNA damage during BNCT is outlined, the major mechanisms of DNA break sensing and repair are summarized, and the specifics of the repair of BNCT-induced DNA lesions are discussed.
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Affiliation(s)
- Grigory V. Mechetin
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
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5
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Verma P, Kumari P, Negi S, Yadav G, Gaur V. Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism. Nucleic Acids Res 2022; 50:4630-4646. [PMID: 35412622 PMCID: PMC9071465 DOI: 10.1093/nar/gkac239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022] Open
Abstract
Holliday junction is the key homologous recombination intermediate, resolved by structure-selective endonucleases (SSEs). SLX1 is the most promiscuous SSE of the GIY-YIG nuclease superfamily. In fungi and animals, SLX1 nuclease activity relies on a non-enzymatic partner, SLX4, but no SLX1-SLX4 like complex has ever been characterized in plants. Plants exhibit specialized DNA repair and recombination machinery. Based on sequence similarity with the GIY-YIG nuclease domain of SLX1 proteins from fungi and animals, At-HIGLE was identified to be a possible SLX1 like nuclease from plants. Here, we elucidated the crystal structure of the At-HIGLE nuclease domain from Arabidopsis thaliana, establishing it as a member of the SLX1-lineage of the GIY-YIG superfamily with structural changes in DNA interacting regions. We show that At-HIGLE can process branched-DNA molecules without an SLX4 like protein. Unlike fungal SLX1, At-HIGLE exists as a catalytically active homodimer capable of generating two coordinated nicks during HJ resolution. Truncating the extended C-terminal region of At-HIGLE increases its catalytic activity, changes the nicking pattern, and monomerizes At-HIGLE. Overall, we elucidated the first structure of a plant SLX1-lineage protein, showed its HJ resolving activity independent of any regulatory protein, and identified an in-built novel regulatory mechanism engaging its C-terminal region.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Poonam Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shreya Negi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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6
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Whale AJ, King M, Hull RM, Krueger F, Houseley J. Stimulation of adaptive gene amplification by origin firing under replication fork constraint. Nucleic Acids Res 2022; 50:915-936. [PMID: 35018465 PMCID: PMC8789084 DOI: 10.1093/nar/gkab1257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
Adaptive mutations can cause drug resistance in cancers and pathogens, and increase the tolerance of agricultural pests and diseases to chemical treatment. When and how adaptive mutations form is often hard to discern, but we have shown that adaptive copy number amplification of the copper resistance gene CUP1 occurs in response to environmental copper due to CUP1 transcriptional activation. Here we dissect the mechanism by which CUP1 transcription in budding yeast stimulates copy number variation (CNV). We show that transcriptionally stimulated CNV requires TREX-2 and Mediator, such that cells lacking TREX-2 or Mediator respond normally to copper but cannot acquire increased resistance. Mediator and TREX-2 can cause replication stress by tethering transcribed loci to nuclear pores, a process known as gene gating, and transcription at the CUP1 locus causes a TREX-2-dependent accumulation of replication forks indicative of replication fork stalling. TREX-2-dependent CUP1 gene amplification occurs by a Rad52 and Rad51-mediated homologous recombination mechanism that is enhanced by histone H3K56 acetylation and repressed by Pol32 and Pif1. CUP1 amplification is also critically dependent on late-firing replication origins present in the CUP1 repeats, and mutations that remove or inactivate these origins strongly suppress the acquisition of copper resistance. We propose that replicative stress imposed by nuclear pore association causes replication bubbles from these origins to collapse soon after activation, leaving a tract of H3K56-acetylated chromatin that promotes secondary recombination events during elongation after replication fork re-start events. The capacity for inefficient replication origins to promote copy number variation renders certain genomic regions more fragile than others, and therefore more likely to undergo adaptive evolution through de novo gene amplification.
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Affiliation(s)
- Alex J Whale
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Michelle King
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Ryan M Hull
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Felix Krueger
- Babraham Bioinformatics, Babraham Institute, Cambridge, UK
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7
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Xu X, Wang M, Sun J, Yu Z, Li G, Yang N, Xu RM. Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex. Nucleic Acids Res 2021; 49:7740-7752. [PMID: 34181713 PMCID: PMC8287910 DOI: 10.1093/nar/gkab542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022] Open
Abstract
The SLX1–SLX4 structure-specific endonuclease complex is involved in processing diverse DNA damage intermediates, including resolution of Holliday junctions, collapse of stalled replication forks and removal of DNA flaps. The nuclease subunit SLX1 is inactive on its own, but become activated upon binding to SLX4 via its conserved C-terminal domain (CCD). Yet, how the SLX1–SLX4 complex recognizes specific DNA structure and chooses cleavage sites remains unknown. Here we show, through a combination of structural, biochemical and computational analyses, that the SAP domain of SLX4 is critical for efficient and accurate processing of 5′-flap DNA. It binds the minor groove of DNA about one turn away from the flap junction, and the 5′-flap is implicated in binding the core domain of SLX1. This binding mode accounts for specific recognition of 5′-flap DNA and specification of cleavage site by the SLX1–SLX4 complex.
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Affiliation(s)
- Xiang Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin 300353, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin 300353, China
| | - Zhenyu Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin 300353, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Thakur M, Mohan D, Singh AK, Agarwal A, Gopal B, Muniyappa K. Novel insights into ATP-Stimulated Cleavage of branched DNA and RNA Substrates through Structure-Guided Studies of the Holliday Junction Resolvase RuvX. J Mol Biol 2021; 433:167014. [PMID: 33933468 DOI: 10.1016/j.jmb.2021.167014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022]
Abstract
Much of our understanding of the homologous recombination (HR) machinery hinges on studies using Escherichia coli as a model organism. Interestingly enough, studies on the HR machinery in different bacterial species casts doubt on the universality of the E. coli paradigm. The human pathogen Mycobacterium tuberculosis encodes two Holliday junction (HJ)-resolvase paralogues, namely RuvC and RuvX; however, insights into their structural features and functional relevance is still limited. Here, we report on structure-guided functional studies of the M. tuberculosis RuvX HJ resolvase (MtRuvX). The crystalline MtRuvX is a dimer in the asymmetric unit, and each monomer has a RNAse H fold vis-à-vis RuvC-like nucleases. Interestingly, MtRuvX also contains some unique features, including the residues essential for ATP binding/coordination of Mg2+ ions. Indeed, MtRuvX exhibited an intrinsic, robust ATPase activity, which was further accentuated by DNA cofactors. Structure-guided substitutions of single residues at the ATP binding/Mg2+coordination sites while markedly attenuating the ATPase activity completely abrogated HJ cleavage, indicating an unanticipated relationship between ATP hydrolysis and DNA cleavage. However, the affinity of ATPase-deficient mutants for the HJ was not impaired. Contrary to RuvC, MtRuvX exhibits relaxed substrate specificity, cleaving a variety of branched DNA/RNA substrates. Notably, ATP hydrolysis plays a regulatory role, rendering MtRuvX from a canonical HJ resolvase to a DNA/RNA non-sequence specific endonuclease, indicating a link between HJ resolvase and nucleic acid metabolism. These findings provide novel insights into the structure and dual-functional activities of MtRuvX, and suggest that it may play an important role in DNA/RNA metabolism.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Disha Mohan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankur Kumar Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | | | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India.
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9
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DNA2 in Chromosome Stability and Cell Survival-Is It All about Replication Forks? Int J Mol Sci 2021; 22:ijms22083984. [PMID: 33924313 PMCID: PMC8069077 DOI: 10.3390/ijms22083984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 01/16/2023] Open
Abstract
The conserved nuclease-helicase DNA2 has been linked to mitochondrial myopathy, Seckel syndrome, and cancer. Across species, the protein is indispensable for cell proliferation. On the molecular level, DNA2 has been implicated in DNA double-strand break (DSB) repair, checkpoint activation, Okazaki fragment processing (OFP), and telomere homeostasis. More recently, a critical contribution of DNA2 to the replication stress response and recovery of stalled DNA replication forks (RFs) has emerged. Here, we review the available functional and phenotypic data and propose that the major cellular defects associated with DNA2 dysfunction, and the links that exist with human disease, can be rationalized through the fundamental importance of DNA2-dependent RF recovery to genome duplication. Being a crucial player at stalled RFs, DNA2 is a promising target for anti-cancer therapy aimed at eliminating cancer cells by replication-stress overload.
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10
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Fluorescence Microscopy for Analysis of Relocalization of Structure-Specific Endonucleases. Methods Mol Biol 2021; 2153:521-534. [PMID: 32840802 DOI: 10.1007/978-1-0716-0644-5_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The analysis of protein relocalization by fluorescence microscopy has been important for studying processes involved in genome integrity maintenance at the cellular level. Structure-specific endonucleases are required for genome stability, and work in budding yeast has revealed that these proteins accumulate and colocalize at discrete subnuclear foci following DNA damage. Here we describe protocols for fluorescence microscopy analysis of live budding-yeast cells containing fluorescent-tagged proteins that have been useful for the study of endonuclease relocalization during the cell cycle and under DNA-damaging conditions, all of which can be extended to the analysis of other proteins.
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11
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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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12
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Sharma N, Speed MC, Allen CP, Maranon DG, Williamson E, Singh S, Hromas R, Nickoloff JA. Distinct roles of structure-specific endonucleases EEPD1 and Metnase in replication stress responses. NAR Cancer 2020; 2:zcaa008. [PMID: 32743552 PMCID: PMC7380491 DOI: 10.1093/narcan/zcaa008] [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] [Received: 11/05/2019] [Revised: 05/20/2020] [Accepted: 05/31/2020] [Indexed: 12/16/2022] Open
Abstract
Accurate DNA replication and segregation are critical for maintaining genome integrity and suppressing cancer. Metnase and EEPD1 are DNA damage response (DDR) proteins frequently dysregulated in cancer and implicated in cancer etiology and tumor response to genotoxic chemo- and radiotherapy. Here, we examine the DDR in human cell lines with CRISPR/Cas9 knockout of Metnase or EEPD1. The knockout cell lines exhibit slightly slower growth rates, significant hypersensitivity to replication stress, increased genome instability and distinct alterations in DDR signaling. Metnase and EEPD1 are structure-specific nucleases. EEPD1 is recruited to and cleaves stalled forks to initiate fork restart by homologous recombination. Here, we demonstrate that Metnase is also recruited to stalled forks where it appears to dimethylate histone H3 lysine 36 (H3K36me2), raising the possibility that H3K36me2 promotes DDR factor recruitment or limits nucleosome eviction to protect forks from nucleolytic attack. We show that stalled forks are cleaved normally in the absence of Metnase, an important and novel result because a prior study indicated that Metnase nuclease is important for timely fork restart. A double knockout was as sensitive to etoposide as either single knockout, suggesting a degree of epistasis between Metnase and EEPD1. We propose that EEPD1 initiates fork restart by cleaving stalled forks, and that Metnase may promote fork restart by processing homologous recombination intermediates and/or inducing H3K36me2 to recruit DDR factors. By accelerating fork restart, Metnase and EEPD1 reduce the chance that stalled replication forks will adopt toxic or genome-destabilizing structures, preventing genome instability and cancer. Metnase and EEPD1 are overexpressed in some cancers and thus may also promote resistance to genotoxic therapeutics.
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Affiliation(s)
- Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
| | - Michael C Speed
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
| | - Christopher P Allen
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601Campus Delivery, Fort Collins, CO 80523-1601, USA
| | - David G Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
| | - Elizabeth Williamson
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas HealthScience Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Sudha Singh
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas HealthScience Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas HealthScience Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
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13
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Palma A, Pugliese GM, Murfuni I, Marabitti V, Malacaria E, Rinalducci S, Minoprio A, Sanchez M, Mazzei F, Zolla L, Franchitto A, Pichierri P. Phosphorylation by CK2 regulates MUS81/EME1 in mitosis and after replication stress. Nucleic Acids Res 2019; 46:5109-5124. [PMID: 29850896 PMCID: PMC6007509 DOI: 10.1093/nar/gky280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/04/2018] [Indexed: 12/21/2022] Open
Abstract
The MUS81 complex is crucial for preserving genome stability through the resolution of branched DNA intermediates in mitosis. However, untimely activation of the MUS81 complex in S-phase is dangerous. Little is known about the regulation of the human MUS81 complex and how deregulated activation affects chromosome integrity. Here, we show that the CK2 kinase phosphorylates MUS81 at Serine 87 in late-G2/mitosis, and upon mild replication stress. Phosphorylated MUS81 interacts with SLX4, and this association promotes the function of the MUS81 complex. In line with a role in mitosis, phosphorylation at Serine 87 is suppressed in S-phase and is mainly detected in the MUS81 molecules associated with EME1. Loss of CK2-dependent MUS81 phosphorylation contributes modestly to chromosome integrity, however, expression of the phosphomimic form induces DSBs accumulation in S-phase, because of unscheduled targeting of HJ-like DNA intermediates, and generates a wide chromosome instability phenotype. Collectively, our findings describe a novel regulatory mechanism controlling the MUS81 complex function in human cells. Furthermore, they indicate that, genome stability depends mainly on the ability of cells to counteract targeting of branched intermediates by the MUS81/EME1 complex in S-phase, rather than on a correct MUS81 function in mitosis.
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Affiliation(s)
- Anita Palma
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Giusj Monia Pugliese
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Ivana Murfuni
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Veronica Marabitti
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Sara Rinalducci
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Anna Minoprio
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Sanchez
- Core Facilities Center - Section of Cytometry, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Filomena Mazzei
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Lello Zolla
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
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14
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Falquet B, Rass U. Structure-Specific Endonucleases and the Resolution of Chromosome Underreplication. Genes (Basel) 2019; 10:E232. [PMID: 30893921 PMCID: PMC6470701 DOI: 10.3390/genes10030232] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Complete genome duplication in every cell cycle is fundamental for genome stability and cell survival. However, chromosome replication is frequently challenged by obstacles that impede DNA replication fork (RF) progression, which subsequently causes replication stress (RS). Cells have evolved pathways of RF protection and restart that mitigate the consequences of RS and promote the completion of DNA synthesis prior to mitotic chromosome segregation. If there is entry into mitosis with underreplicated chromosomes, this results in sister-chromatid entanglements, chromosome breakage and rearrangements and aneuploidy in daughter cells. Here, we focus on the resolution of persistent replication intermediates by the structure-specific endonucleases (SSEs) MUS81, SLX1-SLX4 and GEN1. Their actions and a recently discovered pathway of mitotic DNA repair synthesis have emerged as important facilitators of replication completion and sister chromatid detachment in mitosis. As RS is induced by oncogene activation and is a common feature of cancer cells, any advances in our understanding of the molecular mechanisms related to chromosome underreplication have important biomedical implications.
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Affiliation(s)
- Benoît Falquet
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
- Faculty of Natural Sciences, University of Basel, Petersplatz 10, CH-4003 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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15
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Kaushal S, Freudenreich CH. The role of fork stalling and DNA structures in causing chromosome fragility. Genes Chromosomes Cancer 2019; 58:270-283. [PMID: 30536896 DOI: 10.1002/gcc.22721] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative non-B form DNA structures, also called secondary structures, can form in certain DNA sequences under conditions that produce single-stranded DNA, such as during replication, transcription, and repair. Direct links between secondary structure formation, replication fork stalling, and genomic instability have been found for many repeated DNA sequences that cause disease when they expand. Common fragile sites (CFSs) are known to be AT-rich and break under replication stress, yet the molecular basis for their fragility is still being investigated. Over the past several years, new evidence has linked both the formation of secondary structures and transcription to fork stalling and fragility of CFSs. How these two events may synergize to cause fragility and the role of nuclease cleavage at secondary structures in rare and CFSs are discussed here. We also highlight evidence for a new hypothesis that secondary structures at CFSs not only initiate fragility but also inhibit healing, resulting in their characteristic appearance.
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Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts.,Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
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16
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Rass U. Freedom of movement. Nat Chem Biol 2019; 15:209-210. [PMID: 30664684 DOI: 10.1038/s41589-019-0224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ulrich Rass
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK.
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17
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Fanconi Anaemia-Like Mph1 Helicase Backs up Rad54 and Rad5 to Circumvent Replication Stress-Driven Chromosome Bridges. Genes (Basel) 2018; 9:genes9110558. [PMID: 30453647 PMCID: PMC6266064 DOI: 10.3390/genes9110558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023] Open
Abstract
Homologous recombination (HR) is a preferred mechanism to deal with DNA replication impairments. However, HR synapsis gives rise to joint molecules (JMs) between the nascent sister chromatids, challenging chromosome segregation in anaphase. Joint molecules are resolved by the actions of several structure-selective endonucleases (SSEs), helicases and topoisomerases. Previously, we showed that yeast double mutants for the Mus81-Mms4 and Yen1 SSEs lead to anaphase bridges (ABs) after replication stress. Here, we have studied the role of the Mph1 helicase in preventing these anaphase aberrations. Mph1, the yeast ortholog of Fanconi anaemia protein M (FANCM), is involved in the removal of the D-loop, the first JM to arise in canonical HR. Surprisingly, the absence of Mph1 alone did not increase ABs; rather, it blocked cells in G2. Interestingly, in the search for genetic interactions with functionally related helicases and translocases, we found additive effects on the G2 block and post-G2 aberrations between mph1Δ and knockout mutants for Srs2, Rad54 and Rad5. Based on these interactions, we suggest that Mph1 acts coordinately with these helicases in the non-canonical HR-driven fork regression mechanism to bypass stalled replication forks.
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18
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Watanabe T, Tanaka H, Horiuchi T. Complex repeat structure promotes hyper-amplification and amplicon evolution through rolling-circle replication. Nucleic Acids Res 2018; 46:5097-5108. [PMID: 29718479 PMCID: PMC6007334 DOI: 10.1093/nar/gky275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/04/2018] [Indexed: 11/30/2022] Open
Abstract
Inverted repeats (IRs) are abundant in genomes and frequently serve as substrates for chromosomal aberrations, including gene amplification. In the early stage of amplification, repeated cycles of chromosome breakage and rearrangement, called breakage-fusion-bridge (BFB), generate a large inverted structure, which evolves into highly-amplified, complex end products. However, it remains to be determined how IRs mediate chromosome rearrangements and promote subsequent hyper-amplification and amplicon evolutions. To dissect the complex processes, we constructed repetitive structures in a yeast chromosome and selected amplified cells using genetic markers with limited expression. The genomic architecture was associated with replication stress and produced extra-/intra-chromosomal amplification. Genetic analysis revealed structure-specific endonucleases, Mus81 and Rad27, and post-replication DNA repair protein, Rad18, suppress the amplification processes. Following BFB cycles, the intra-chromosomal products undergo intensive rearrangements, such as frequent inversions and deletions, indicative of rolling-circle replication. This study presents an integrated view linking BFB cycles to hyper-amplification driven by rolling-circle replication.
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Affiliation(s)
- Takaaki Watanabe
- Department of Molecular Life Science, Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan.,Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.,National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Takashi Horiuchi
- Department of Molecular Life Science, Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan.,National Institute for Basic Biology, Okazaki, Aichi, Japan
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19
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Saugar I, Jiménez-Martín A, Tercero JA. Subnuclear Relocalization of Structure-Specific Endonucleases in Response to DNA Damage. Cell Rep 2018; 20:1553-1562. [PMID: 28813668 DOI: 10.1016/j.celrep.2017.07.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/09/2017] [Accepted: 07/20/2017] [Indexed: 12/25/2022] Open
Abstract
Structure-specific endonucleases contribute to the maintenance of genome integrity by cleaving DNA intermediates that need to be resolved for faithful DNA repair, replication, or recombination. Despite advances in the understanding of their function and regulation, it is less clear how these proteins respond to genotoxic stress. Here, we show that the structure-specific endonuclease Mus81-Mms4/EME1 relocalizes to subnuclear foci following DNA damage and colocalizes with the endonucleases Rad1-Rad10 (XPF-ERCC1) and Slx1-Slx4. Recruitment takes place into a class of stress foci defined by Cmr1/WDR76, a protein involved in preserving genome stability, and depends on the E2-ubiquitin-conjugating enzyme Rad6 and the E3-ubiquitin ligase Bre1. Foci dynamics show that, in the presence of DNA intermediates that need resolution by Mus81-Mms4, Mus81 foci persist until this endonuclease is activated by Mms4 phosphorylation. Our data suggest that subnuclear relocalization is relevant for the function of Mus81-Mms4 and, probably, of the endonucleases that colocalize with it.
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Affiliation(s)
- Irene Saugar
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Cantoblanco, 28049 Madrid, Spain
| | | | - José Antonio Tercero
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Cantoblanco, 28049 Madrid, Spain.
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20
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Kojic M, Milisavljevic M, Holloman WK. Collaboration in the actions of Brh2 with resolving functions during DNA repair and replication stress in Ustilago maydis. DNA Repair (Amst) 2018; 63:47-55. [PMID: 29414053 DOI: 10.1016/j.dnarep.2018.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 11/17/2022]
Abstract
Cells maintain a small arsenal of resolving functions to process and eliminate complex DNA intermediates that result as a consequence of homologous recombination and distressed replication. Ordinarily the homologous recombination system serves as a high-fidelity mechanism to restore the integrity of a damaged genome, but in the absence of the appropriate resolving function it can turn DNA intermediates resulting from replication stress into pathological forms that are toxic to cells. Here we have investigated how the nucleases Mus81 and Gen1 and the helicase Blm contribute to survival after DNA damage or replication stress in Ustilago maydis cells with crippled yet homologous recombination-proficient forms of Brh2, the BRCA2 ortholog and primary Rad51 mediator. We found collaboration among the factors. Notable were three findings. First, the ability of Gen1 to rescue hydroxyurea sensitivity of dysfunctional Blm requires the absence of Mus81. Second, the response of mutants defective in Blm and Gen1 to hydroxyurea challenge is markedly similar suggesting cooperation of these factors in the same pathway. Third, the repair proficiency of Brh2 mutant variants deleted of its N-terminal DNA binding region requires not only Rad52 but also Gen1 and Mus81. We suggest these factors comprise a subpathway for channeling repair when Brh2 is compromised in its interplay with DNA.
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Affiliation(s)
- Milorad Kojic
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Mira Milisavljevic
- Laboratory for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Serbia
| | - William K Holloman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.
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21
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Hromas R, Kim HS, Sidhu G, Williamson E, Jaiswal A, Totterdale TA, Nole J, Lee SH, Nickoloff JA, Kong KY. The endonuclease EEPD1 mediates synthetic lethality in RAD52-depleted BRCA1 mutant breast cancer cells. Breast Cancer Res 2017; 19:122. [PMID: 29145865 PMCID: PMC5693420 DOI: 10.1186/s13058-017-0912-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/30/2017] [Indexed: 02/06/2023] Open
Abstract
Background Proper repair and restart of stressed replication forks requires intact homologous recombination (HR). HR at stressed replication forks can be initiated by the 5′ endonuclease EEPD1, which cleaves the stalled replication fork. Inherited or acquired defects in HR, such as mutations in breast cancer susceptibility protein-1 (BRCA1) or BRCA2, predispose to cancer, including breast and ovarian cancers. In order for these HR-deficient tumor cells to proliferate, they become addicted to a bypass replication fork repair pathway mediated by radiation repair protein 52 (RAD52). Depleting RAD52 can cause synthetic lethality in BRCA1/2 mutant cancers by an unknown molecular mechanism. Methods We hypothesized that cleavage of stressed replication forks by EEPD1 generates a fork repair intermediate that is toxic when HR-deficient cells cannot complete repair with the RAD52 bypass pathway. To test this hypothesis, we applied cell survival assays, immunofluorescence staining, DNA fiber and western blot analyses to look at the correlation between cell survival and genome integrity in control, EEPD1, RAD52 and EEPD1/RAD52 co-depletion BRCA1-deficient breast cancer cells. Results Our data show that depletion of EEPD1 suppresses synthetic lethality, genome instability, mitotic catastrophe, and hypersensitivity to stress of replication of RAD52-depleted, BRCA1 mutant breast cancer cells. Without HR and the RAD52-dependent backup pathway, the BRCA1 mutant cancer cells depleted of EEPD1 skew to the alternative non-homologous end-joining DNA repair pathway for survival. Conclusion This study indicates that the mechanism of synthetic lethality in RAD52-depleted BRCA1 mutant cancer cells depends on the endonuclease EEPD1. The data imply that EEPD1 cleavage of stressed replication forks may result in a toxic intermediate when replication fork repair cannot be completed. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0912-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert Hromas
- Department of Medicine and the Cancer Center, University of Florida Health, 1600 SW Archer Rd, Gainesville, FL, 32610, USA.
| | - Hyun-Suk Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Gurjit Sidhu
- Department of Medicine and the Cancer Center, University of Florida Health, 1600 SW Archer Rd, Gainesville, FL, 32610, USA
| | - Elizabeth Williamson
- Department of Medicine and the Cancer Center, University of Florida Health, 1600 SW Archer Rd, Gainesville, FL, 32610, USA
| | - Aruna Jaiswal
- Department of Medicine and the Cancer Center, University of Florida Health, 1600 SW Archer Rd, Gainesville, FL, 32610, USA
| | - Taylor A Totterdale
- Department of Medicine and the Cancer Center, University of Florida Health, 1600 SW Archer Rd, Gainesville, FL, 32610, USA
| | - Jocelyn Nole
- Department of Medicine and the Cancer Center, University of Florida Health, 1600 SW Archer Rd, Gainesville, FL, 32610, USA
| | - Suk-Hee Lee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kimi Y Kong
- Department of Medicine and the Cancer Center, University of Florida Health, 1600 SW Archer Rd, Gainesville, FL, 32610, USA.
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22
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Paths from DNA damage and signaling to genome rearrangements via homologous recombination. Mutat Res 2017; 806:64-74. [PMID: 28779875 DOI: 10.1016/j.mrfmmm.2017.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
Abstract
DNA damage is a constant threat to genome integrity. DNA repair and damage signaling networks play a central role maintaining genome stability, suppressing tumorigenesis, and determining tumor response to common cancer chemotherapeutic agents and radiotherapy. DNA double-strand breaks (DSBs) are critical lesions induced by ionizing radiation and when replication forks encounter damage. DSBs can result in mutations and large-scale genome rearrangements reflecting mis-repair by non-homologous end joining or homologous recombination. Ionizing radiation induces genetic change immediately, and it also triggers delayed events weeks or even years after exposure, long after the initial damage has been repaired or diluted through cell division. This review covers DNA damage signaling and repair pathways and cell fate following genotoxic insult, including immediate and delayed genome instability and cell survival/cell death pathways.
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23
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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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24
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Kan Y, Batada NN, Hendrickson EA. Human somatic cells deficient for RAD52 are impaired for viral integration and compromised for most aspects of homology-directed repair. DNA Repair (Amst) 2017; 55:64-75. [PMID: 28549257 DOI: 10.1016/j.dnarep.2017.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/25/2017] [Accepted: 04/27/2017] [Indexed: 01/28/2023]
Abstract
Homology-directed repair (HDR) maintains genomic integrity by eliminating lesions such as DNA double-strand breaks (DSBs), interstrand crosslinks (ICLs) and stalled replication forks and thus a deficiency in HDR is associated with genomic instability and cancer predisposition. The mechanism of HDR is best understood and most rigorously characterized in yeast. The inactivation of the fungal radiation sensitive 52 (RAD52) gene, which has both recombination mediator and single-strand annealing (SSA) activities in vitro, leads to severe HDR defects in vivo. Confusingly, however, the inactivation of murine and chicken RAD52 genes resulted in mouse and chicken cells, respectively, that were largely aphenotypic. To clarify this issue, we have generated RAD52 knockout human cell lines. Human RAD52-null cells retain a significant level of SSA activity demonstrating perforce that additional SSA-like activities must exist in human cells. Moreover, we confirmed that the SSA activity associated with RAD52 is involved in, but not absolutely required for, most HDR subpathways. Specifically, a deficiency in RAD52 impaired the repair of DNA DSBs and intriguingly decreased the random integration of recombinant adeno-associated virus (rAAV). Finally, an analysis of pan-cancer genome data from The Cancer Genome Atlas (TCGA) revealed an association between aberrant levels of RAD52 expression and poor overall survival in multiple cancers. In toto, our work demonstrates that RAD52 contributes to the maintenance of genome stability and tumor suppression in human cells.
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Affiliation(s)
- Yinan Kan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States
| | - Nizar N Batada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Eric A Hendrickson
- BMBB Department, University of Minnesota Medical School, 6-155 Jackson Hall, 321 Church St., SE., Minneapolis, MN 55455, United States.
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25
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Malacaria E, Franchitto A, Pichierri P. SLX4 Prevents GEN1-Dependent DSBs During DNA Replication Arrest Under Pathological Conditions in Human Cells. Sci Rep 2017; 7:44464. [PMID: 28290553 PMCID: PMC5349550 DOI: 10.1038/srep44464] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/08/2017] [Indexed: 01/06/2023] Open
Abstract
SLX4 is a versatile protein serving as docking for multiple structure-specific endonucleases during DNA repair, however, little is known about its function at demised replication forks. Using RNAi or FA-P cells complemented with SLX4 mutants that abrogate interaction with MUS81 or SLX1, we show that SLX4 cooperates with MUS81 to introduce DSBs after replication stress but also counteracts pathological targeting of demised forks by GEN1. Such unexpected function of SLX4 is unrelated to interaction with endonucleases, but concerns the physical presence of the protein. Strikingly, ectopic expression of the Holliday junction-binding protein RuvA inhibits DSBs in SLX4-deficient cells by preventing GEN1 chromatin-association, and rescues proliferation and genome integrity upon replication stress. Altogether, our results indicate that SLX4 is crucial to prevent accidental processing of Holliday junction-like intermediates at demised forks also suggesting that spontaneous genome instability in FA-P cells may derive, at least partially, from unscheduled action of GEN1 in S-phase.
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Affiliation(s)
- Eva Malacaria
- Section of Experimental and Computational Carcinogenesis, Department of Environment and Primary Prevention, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome Italy
| | - Annapaola Franchitto
- Section of Molecular Epidemiology, Department of Environment and Primary Prevention, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome Italy
| | - Pietro Pichierri
- Section of Experimental and Computational Carcinogenesis, Department of Environment and Primary Prevention, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome Italy
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26
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Chun C, Wu Y, Lee SH, Williamson EA, Reinert BL, Jaiswal AS, Nickoloff JA, Hromas RA. The homologous recombination component EEPD1 is required for genome stability in response to developmental stress of vertebrate embryogenesis. Cell Cycle 2017; 15:957-62. [PMID: 26900729 PMCID: PMC4889227 DOI: 10.1080/15384101.2016.1151585] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Stressed replication forks can be conservatively repaired and restarted using homologous recombination (HR), initiated by nuclease cleavage of branched structures at stalled forks. We previously reported that the 5' nuclease EEPD1 is recruited to stressed replication forks, where it plays critical early roles in HR initiation by promoting fork cleavage and end resection. HR repair of stressed replication forks prevents their repair by non-homologous end-joining (NHEJ), which would cause genome instability. Rapid cell division during vertebrate embryonic development generates enormous pressure to maintain replication speed and accuracy. To determine the role of EEPD1 in maintaining replication fork integrity and genome stability during rapid cell division in embryonic development, we assessed the role of EEPD1 during zebrafish embryogenesis. We show here that when EEPD1 is depleted, zebrafish embryos fail to develop normally and have a marked increase in death rate. Zebrafish embryos depleted of EEPD1 are far more sensitive to replication stress caused by nucleotide depletion. We hypothesized that the HR defect with EEPD1 depletion would shift repair of stressed replication forks to unopposed NHEJ, causing chromosome abnormalities. Consistent with this, EEPD1 depletion results in nuclear defects including anaphase bridges and micronuclei in stressed zebrafish embryos, similar to BRCA1 deficiency. These results demonstrate that the newly characterized HR protein EEPD1 maintains genome stability during embryonic replication stress. These data also imply that the rapid cell cycle transit seen during embryonic development produces replication stress that requires HR to resolve.
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Affiliation(s)
- Changzoon Chun
- a Division of Hematology/Oncology , Department of Medicine, University of Florida Health , Gainesville , FL , USA
| | - Yuehan Wu
- a Division of Hematology/Oncology , Department of Medicine, University of Florida Health , Gainesville , FL , USA
| | - Suk-Hee Lee
- b Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Elizabeth A Williamson
- a Division of Hematology/Oncology , Department of Medicine, University of Florida Health , Gainesville , FL , USA
| | - Brian L Reinert
- a Division of Hematology/Oncology , Department of Medicine, University of Florida Health , Gainesville , FL , USA
| | - Aruna Shanker Jaiswal
- a Division of Hematology/Oncology , Department of Medicine, University of Florida Health , Gainesville , FL , USA
| | - Jac A Nickoloff
- c Department of Environmental and Radiological Health Sciences , Colorado State University , Fort Collins , CO , USA
| | - Robert A Hromas
- a Division of Hematology/Oncology , Department of Medicine, University of Florida Health , Gainesville , FL , USA
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27
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Wyatt HDM, Laister RC, Martin SR, Arrowsmith CH, West SC. The SMX DNA Repair Tri-nuclease. Mol Cell 2017; 65:848-860.e11. [PMID: 28257701 PMCID: PMC5344696 DOI: 10.1016/j.molcel.2017.01.031] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/17/2017] [Accepted: 01/25/2017] [Indexed: 01/13/2023]
Abstract
The efficient removal of replication and recombination intermediates is essential for the maintenance of genome stability. Resolution of these potentially toxic structures requires the MUS81-EME1 endonuclease, which is activated at prometaphase by formation of the SMX tri-nuclease containing three DNA repair structure-selective endonucleases: SLX1-SLX4, MUS81-EME1, and XPF-ERCC1. Here we show that SMX tri-nuclease is more active than the three individual nucleases, efficiently cleaving replication forks and recombination intermediates. Within SMX, SLX4 co-ordinates the SLX1 and MUS81-EME1 nucleases for Holliday junction resolution, in a reaction stimulated by XPF-ERCC1. SMX formation activates MUS81-EME1 for replication fork and flap structure cleavage by relaxing substrate specificity. Activation involves MUS81's conserved N-terminal HhH domain, which mediates incision site selection and SLX4 binding. Cell cycle-dependent formation and activation of this tri-nuclease complex provides a unique mechanism by which cells ensure chromosome segregation and preserve genome integrity.
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Affiliation(s)
- Haley D M Wyatt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rob C Laister
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Wang C, Higgins JD, He Y, Lu P, Zhang D, Liang W. Resolvase OsGEN1 Mediates DNA Repair by Homologous Recombination. PLANT PHYSIOLOGY 2017; 173:1316-1329. [PMID: 28049740 PMCID: PMC5291025 DOI: 10.1104/pp.16.01726] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/29/2016] [Indexed: 05/18/2023]
Abstract
Yen1/GEN1 are canonical Holliday junction resolvases that belong to the RAD2/XPG family. In eukaryotes, such as budding yeast, mice, worms, and humans, Yen1/GEN1 work together with Mus81-Mms4/MUS81-EME1 and Slx1-Slx4/SLX1-SLX4 in DNA repair by homologous recombination to maintain genome stability. In plants, the biological function of Yen1/GEN1 remains largely unclear. In this study, we characterized the loss of function mutants of OsGEN1 and OsSEND1, a pair of paralogs of Yen1/GEN1 in rice (Oryza sativa). We first investigated the role of OsGEN1 during meiosis and found a reduction in chiasma frequency by ∼6% in osgen1 mutants, compared to the wild type, suggesting a possible involvement of OsGEN1 in the formation of crossovers. Postmeiosis, OsGEN1 foci were detected in wild-type microspore nuclei, but not in the osgen1 mutant concomitant with an increase in double-strand breaks. Persistent double-strand breaks led to programmed cell death of the male gametes and complete male sterility. In contrast, depletion of OsSEND1 had no effects on plant development and did not enhance osgen1 defects. Our results indicate that OsGEN1 is essential for homologous recombinational DNA repair at two stages of microsporogenesis in rice.
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Affiliation(s)
- Chong Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - James D Higgins
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Yi He
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Pingli Lu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.);
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.);
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
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Sekelsky J. DNA Repair in Drosophila: Mutagens, Models, and Missing Genes. Genetics 2017; 205:471-490. [PMID: 28154196 PMCID: PMC5289830 DOI: 10.1534/genetics.116.186759] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/18/2016] [Indexed: 12/22/2022] Open
Abstract
The numerous processes that damage DNA are counterbalanced by a complex network of repair pathways that, collectively, can mend diverse types of damage. Insights into these pathways have come from studies in many different organisms, including Drosophila melanogaster Indeed, the first ideas about chromosome and gene repair grew out of Drosophila research on the properties of mutations produced by ionizing radiation and mustard gas. Numerous methods have been developed to take advantage of Drosophila genetic tools to elucidate repair processes in whole animals, organs, tissues, and cells. These studies have led to the discovery of key DNA repair pathways, including synthesis-dependent strand annealing, and DNA polymerase theta-mediated end joining. Drosophila appear to utilize other major repair pathways as well, such as base excision repair, nucleotide excision repair, mismatch repair, and interstrand crosslink repair. In a surprising number of cases, however, DNA repair genes whose products play important roles in these pathways in other organisms are missing from the Drosophila genome, raising interesting questions for continued investigations.
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Affiliation(s)
- Jeff Sekelsky
- Department of Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, North Carolina 27599
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30
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Nikolova T, Roos WP, Krämer OH, Strik HM, Kaina B. Chloroethylating nitrosoureas in cancer therapy: DNA damage, repair and cell death signaling. Biochim Biophys Acta Rev Cancer 2017; 1868:29-39. [PMID: 28143714 DOI: 10.1016/j.bbcan.2017.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 01/20/2023]
Abstract
Chloroethylating nitrosoureas (CNU), such as lomustine, nimustine, semustine, carmustine and fotemustine are used for the treatment of malignant gliomas, brain metastases of different origin, melanomas and Hodgkin disease. They alkylate the DNA bases and give rise to the formation of monoadducts and subsequently interstrand crosslinks (ICL). ICL are critical cytotoxic DNA lesions that link the DNA strands covalently and block DNA replication and transcription. As a result, S phase progression is inhibited and cells are triggered to undergo apoptosis and necrosis, which both contribute to the effectiveness of CNU-based cancer therapy. However, tumor cells resist chemotherapy through the repair of CNU-induced DNA damage. The suicide enzyme O6-methylguanine-DNA methyltransferase (MGMT) removes the precursor DNA lesion O6-chloroethylguanine prior to its conversion into ICL. In cells lacking MGMT, the formed ICL evoke complex enzymatic networks to accomplish their removal. Here we discuss the mechanism of ICL repair as a survival strategy of healthy and cancer cells and DNA damage signaling as a mechanism contributing to CNU-induced cell death. We also discuss therapeutic implications and strategies based on sequential and simultaneous treatment with CNU and the methylating drug temozolomide.
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Affiliation(s)
- Teodora Nikolova
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany.
| | - Wynand P Roos
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
| | - Herwig M Strik
- Department of Neurology, University Medical Center, Baldinger Strasse, 35033 Marburg, Germany
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany.
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31
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Kim HS, Nickoloff JA, Wu Y, Williamson EA, Sidhu GS, Reinert BL, Jaiswal AS, Srinivasan G, Patel B, Kong K, Burma S, Lee SH, Hromas RA. Endonuclease EEPD1 Is a Gatekeeper for Repair of Stressed Replication Forks. J Biol Chem 2017; 292:2795-2804. [PMID: 28049724 PMCID: PMC5314175 DOI: 10.1074/jbc.m116.758235] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/29/2016] [Indexed: 01/21/2023] Open
Abstract
Replication is not as continuous as once thought, with DNA damage frequently stalling replication forks. Aberrant repair of stressed replication forks can result in cell death or genome instability and resulting transformation to malignancy. Stressed replication forks are most commonly repaired via homologous recombination (HR), which begins with 5′ end resection, mediated by exonuclease complexes, one of which contains Exo1. However, Exo1 requires free 5′-DNA ends upon which to act, and these are not commonly present in non-reversed stalled replication forks. To generate a free 5′ end, stalled replication forks must therefore be cleaved. Although several candidate endonucleases have been implicated in cleavage of stalled replication forks to permit end resection, the identity of such an endonuclease remains elusive. Here we show that the 5′-endonuclease EEPD1 cleaves replication forks at the junction between the lagging parental strand and the unreplicated DNA parental double strands. This cleavage creates the structure that Exo1 requires for 5′ end resection and HR initiation. We observed that EEPD1 and Exo1 interact constitutively, and Exo1 repairs stalled replication forks poorly without EEPD1. Thus, EEPD1 performs a gatekeeper function for replication fork repair by mediating the fork cleavage that permits initiation of HR-mediated repair and restart of stressed forks.
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Affiliation(s)
- Hyun-Suk Kim
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Jac A Nickoloff
- the Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Yuehan Wu
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Elizabeth A Williamson
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Gurjit Singh Sidhu
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Brian L Reinert
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Aruna S Jaiswal
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Gayathri Srinivasan
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Bhavita Patel
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Kimi Kong
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
| | - Sandeep Burma
- the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Suk-Hee Lee
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202,
| | - Robert A Hromas
- the Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida 32610, and
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32
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Kim HS, Williamson EA, Nickoloff JA, Hromas RA, Lee SH. Metnase Mediates Loading of Exonuclease 1 onto Single Strand Overhang DNA for End Resection at Stalled Replication Forks. J Biol Chem 2016; 292:1414-1425. [PMID: 27974460 DOI: 10.1074/jbc.m116.745646] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 12/13/2016] [Indexed: 11/06/2022] Open
Abstract
Stalling at DNA replication forks generates stretches of single-stranded (ss) DNA on both strands that are exposed to nucleolytic degradation, potentially compromising genome stability. One enzyme crucial for DNA replication fork repair and restart of stalled forks in human is Metnase (also known as SETMAR), a chimeric fusion protein consisting of a su(var)3-9, enhancer-of-zeste and trithorax (SET) histone methylase and transposase nuclease domain. We previously showed that Metnase possesses a unique fork cleavage activity necessary for its function in replication restart and that its SET domain is essential for recovery from hydroxyurea-induced DNA damage. However, its exact role in replication restart is unclear. In this study, we show that Metnase associates with exonuclease 1 (Exo1), a 5'-exonuclease crucial for 5'-end resection to mediate DNA processing at stalled forks. Metnase DNA cleavage activity was not required for Exo1 5'-exonuclease activity on the lagging strand daughter DNA, but its DNA binding activity mediated loading of Exo1 onto ssDNA overhangs. Metnase-induced enhancement of Exo1-mediated DNA strand resection required the presence of these overhangs but did not require Metnase's DNA cleavage activity. These results suggest that Metnase enhances Exo1-mediated exonuclease activity on the lagging strand DNA by facilitating Exo1 loading onto a single strand gap at the stalled replication fork.
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Affiliation(s)
- Hyun-Suk Kim
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Elizabeth A Williamson
- the Department of Medicine, University of Florida and Shands Health Care System, Gainesville, Florida 32610, and
| | - Jac A Nickoloff
- the Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Robert A Hromas
- the Department of Medicine, University of Florida and Shands Health Care System, Gainesville, Florida 32610, and
| | - Suk-Hee Lee
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202,
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33
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Replication intermediates that escape Dna2 activity are processed by Holliday junction resolvase Yen1. Nat Commun 2016; 7:13157. [PMID: 27779184 PMCID: PMC5093310 DOI: 10.1038/ncomms13157] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 09/08/2016] [Indexed: 12/29/2022] Open
Abstract
Cells have evolved mechanisms to protect, restart and repair perturbed replication forks, allowing full genome duplication, even under replication stress. Interrogating the interplay between nuclease-helicase Dna2 and Holliday junction (HJ) resolvase Yen1, we find the Dna2 helicase activity acts parallel to homologous recombination (HR) in promoting DNA replication and chromosome detachment at mitosis after replication fork stalling. Yen1, but not the HJ resolvases Slx1-Slx4 and Mus81-Mms4, safeguards chromosome segregation by removing replication intermediates that escape Dna2. Post-replicative DNA damage checkpoint activation in Dna2 helicase-defective cells causes terminal G2/M arrest by precluding Yen1-dependent repair, whose activation requires progression into anaphase. These findings explain the exquisite replication stress sensitivity of Dna2 helicase-defective cells, and identify a non-canonical role for Yen1 in the processing of replication intermediates that is distinct from HJ resolution. The involvement of Dna2 helicase activity in completing replication may have implications for DNA2-associated pathologies, including cancer and Seckel syndrome.
DNA replication stress drives genome instability and cancer. Here, Ölmezer and colleagues show that the helicase activity of multifunctional enzyme Dna2 suppresses dead-end replication structures that impair chromosome segregation if not removed by Holliday junction resolvase Yen1 in yeast.
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34
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Gasser S, Zhang WYL, Tan NYJ, Tripathi S, Suter MA, Chew ZH, Khatoo M, Ngeow J, Cheung FSG. Sensing of dangerous DNA. Mech Ageing Dev 2016; 165:33-46. [PMID: 27614000 DOI: 10.1016/j.mad.2016.09.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 12/19/2022]
Abstract
The presence of damaged and microbial DNA can pose a threat to the survival of organisms. Cells express various sensors that recognize specific aspects of such potentially dangerous DNA. Recognition of damaged or microbial DNA by sensors induces cellular processes that are important for DNA repair and inflammation. Here, we review recent evidence that the cellular response to DNA damage and microbial DNA are tightly intertwined. We also discuss insights into the parameters that enable DNA sensors to distinguish damaged and microbial DNA from DNA present in healthy cells.
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Affiliation(s)
- Stephan Gasser
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117597 Singapore.
| | - Wendy Y L Zhang
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore
| | - Nikki Yi Jie Tan
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore
| | - Shubhita Tripathi
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore
| | - Manuel A Suter
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore
| | - Zhi Huan Chew
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117597 Singapore
| | - Muznah Khatoo
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore
| | - Joanne Ngeow
- Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore; Divsion of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore; Oncology Academic Clinical Program, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore
| | - Florence S G Cheung
- Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore 117456, Singapore.
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35
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Cao X, Lu Y, Zhang X, Kovalovsky D. Zbtb1 Safeguards Genome Integrity and Prevents p53-Mediated Apoptosis in Proliferating Lymphoid Progenitors. THE JOURNAL OF IMMUNOLOGY 2016; 197:1199-211. [PMID: 27402700 DOI: 10.4049/jimmunol.1600013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/07/2016] [Indexed: 12/30/2022]
Abstract
Expression of the transcription factor Zbtb1 is required for normal lymphoid development. We report in the present study that Zbtb1 maintains genome integrity in immune progenitors, without which cells undergo increased DNA damage and p53-mediated apoptosis during replication and differentiation. Increased DNA damage in Zbtb1-mutant (ScanT) progenitors was due to increased sensitivity to replication stress, which was a consequence of inefficient activation of the S-phase checkpoint response. Increased p53-mediated apoptosis affected not only lymphoid but also myeloid development in competitive bone marrow chimeras, and prevention of apoptosis by transgenic Bcl2 expression and p53 deficiency rescued lymphoid as well as myeloid development from Zbtb1-mutant progenitors. Interestingly, however, protection from apoptosis rescued only the early stages of T cell development, and thymocytes remained arrested at the double-negative 3 developmental stage, indicating a strict requirement of Zbtb1 at later T cell developmental stages. Collectively, these results indicate that Zbtb1 prevents DNA damage in replicating immune progenitors, allowing the generation of B cells, T cells, and myeloid cells.
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Affiliation(s)
- Xin Cao
- College of Life Science and Engineering, Northwest University for Nationalities, Lanzhou 730030, China; and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ying Lu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Xianyu Zhang
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Damian Kovalovsky
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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36
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Cussiol JR, Dibitetto D, Pellicioli A, Smolka MB. Slx4 scaffolding in homologous recombination and checkpoint control: lessons from yeast. Chromosoma 2016; 126:45-58. [PMID: 27165041 DOI: 10.1007/s00412-016-0600-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 01/07/2023]
Abstract
Homologous recombination-mediated DNA repair is essential for maintaining genome integrity. It is a multi-step process that involves resection of DNA ends, strand invasion, DNA synthesis and/or DNA end ligation, and finally, the processing of recombination intermediates such as Holliday junctions or other joint molecules. Over the last 15 years, it has been established that the Slx4 protein plays key roles in the processing of recombination intermediates, functioning as a scaffold to coordinate the action of structure-specific endonucleases. Recent work in budding yeast has uncovered unexpected roles for Slx4 in the initial step of DNA-end resection and in the modulation of DNA damage checkpoint signaling. Here we review these latest findings and discuss the emerging role of yeast Slx4 as an important coordinator of DNA damage signaling responses and a regulator of multiple steps in homologous recombination-mediated repair.
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Affiliation(s)
- José R Cussiol
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Diego Dibitetto
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | | | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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37
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Holliday Junctions Are Associated with Transposable Element Sequences in the Human Genome. J Mol Biol 2016; 428:658-667. [PMID: 26780549 DOI: 10.1016/j.jmb.2016.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
Holliday junctions (HJs) constitute important intermediate structures for many cell functions such as DNA recombination and DNA repair. They derive from a 10-nt degenerate sequence, with a 3-nt core motif. In this study, we explored the human genome whether the HJ degenerate sequence associates with transposable elements (TEs) and mainly with those of the active and inactive ALU, LINE, SVA and HERV families. We identified six different forms of the HJ sequence motif, and we located the genomic coordinates of sequences containing both HJs and TEs. From 2982 total HJs, a significant number of 1319 TE-associated HJs were found, with a median distribution of 1 per 2.4 Mb. The HJs with higher GC content were observed more frequently at the genome. A high percentage of HJs were associated with all main TE families, with specificity for particular active or inactive elements: DNA elements and the retroelements ALUs, LINEs and HERVs up to 41.94%, 72.72%, 42.94% and 84.5%, respectively. Phylogenetic analysis revealed that HJs occur in both active and inactive TEs. Furthermore, the TE-associated HJs were almost exclusively found within a distance less than 1 Mb from human genes, while only 23 were not associated with any genes. This is the first report associating human HJs, with mobile elements. Our data pinpoint that particular HJ forms show preference for specific active retrotransposon families of ALUs and LINEs, suggesting that retrotransposon-incorporated HJs may relocate or replicate in the genome through retrotransposition, contributing to recombination, genome plasticity and DNA repair.
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38
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Nowotny M, Gaur V. Structure and mechanism of nucleases regulated by SLX4. Curr Opin Struct Biol 2016; 36:97-105. [PMID: 26827285 DOI: 10.1016/j.sbi.2016.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 01/08/2023]
Abstract
SLX4 is a multidomain platform that regulates various proteins that are involved in genome maintenance and stability. Among these proteins are three structure-selective nucleases (SSEs). XPF-ERCC1 and MUS81-EME1 are structurally similar and function as heterodimers of highly similar subunits, in which only one is active. Two independent modules are formed from subunits of the heterodimers - a dimer of nuclease and nuclease-like domains and a dimer of tandem helix-hairpin-helix HhH2 domains. Both modules are responsible for substrate recognition. The third SSE, SLX1, contains GIY-YIG and RING domains and is a promiscuous nuclease. Structural data imply that SLX1 exists in free form as an autoinhibited homodimer. Association with SLX4 platform disrupts the homodimer and activates SLX1. This review discusses the available structural and mechanistic information on SLX4-regulated SSEs.
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Affiliation(s)
- Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
| | - Vineet Gaur
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
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39
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Wu Y, Lee SH, Williamson EA, Reinert BL, Cho JH, Xia F, Jaiswal AS, Srinivasan G, Patel B, Brantley A, Zhou D, Shao L, Pathak R, Hauer-Jensen M, Singh S, Kong K, Wu X, Kim HS, Beissbarth T, Gaedcke J, Burma S, Nickoloff JA, Hromas RA. EEPD1 Rescues Stressed Replication Forks and Maintains Genome Stability by Promoting End Resection and Homologous Recombination Repair. PLoS Genet 2015; 11:e1005675. [PMID: 26684013 PMCID: PMC4684289 DOI: 10.1371/journal.pgen.1005675] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/26/2015] [Indexed: 12/13/2022] Open
Abstract
Replication fork stalling and collapse is a major source of genome instability leading to neoplastic transformation or cell death. Such stressed replication forks can be conservatively repaired and restarted using homologous recombination (HR) or non-conservatively repaired using micro-homology mediated end joining (MMEJ). HR repair of stressed forks is initiated by 5’ end resection near the fork junction, which permits 3’ single strand invasion of a homologous template for fork restart. This 5’ end resection also prevents classical non-homologous end-joining (cNHEJ), a competing pathway for DNA double-strand break (DSB) repair. Unopposed NHEJ can cause genome instability during replication stress by abnormally fusing free double strand ends that occur as unstable replication fork repair intermediates. We show here that the previously uncharacterized Exonuclease/Endonuclease/Phosphatase Domain-1 (EEPD1) protein is required for initiating repair and restart of stalled forks. EEPD1 is recruited to stalled forks, enhances 5’ DNA end resection, and promotes restart of stalled forks. Interestingly, EEPD1 directs DSB repair away from cNHEJ, and also away from MMEJ, which requires limited end resection for initiation. EEPD1 is also required for proper ATR and CHK1 phosphorylation, and formation of gamma-H2AX, RAD51 and phospho-RPA32 foci. Consistent with a direct role in stalled replication fork cleavage, EEPD1 is a 5’ overhang nuclease in an obligate complex with the end resection nuclease Exo1 and BLM. EEPD1 depletion causes nuclear and cytogenetic defects, which are made worse by replication stress. Depleting 53BP1, which slows cNHEJ, fully rescues the nuclear and cytogenetic abnormalities seen with EEPD1 depletion. These data demonstrate that genome stability during replication stress is maintained by EEPD1, which initiates HR and inhibits cNHEJ and MMEJ. The cell itself damages its own DNA throughout the cell cycle as a result of oxidative metabolism, and this damage creates barriers for replication fork progression. Thus, DNA replication is not a smooth and continuous process, but rather one of stalls and restarts. Therefore, proper replication fork restart is crucial to maintain the integrity of the cell’s genome, and preventing its own death or immortalization. To restart after stalling, the replication fork subverts a DNA repair pathway termed homologous recombination. Using any other pathway for fork repair will result in an unstable genome. How the homologous recombination repair pathway is initiated at the replication fork is not well defined. In this study we demonstrate the previously uncharacterized EEPD1 protein is a novel gatekeeper for the initiation of this fork repair pathway. EEPD1 promotes 5’ end resection, the initial step of homologous recombination, which also prevents alternative fork repair pathways that lead to unstable chromosomes. Thus, EEPD1 protects the integrity of the cell genome by promoting the safe homologous recombination fork repair pathway.
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Affiliation(s)
- Yuehan Wu
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Suk-Hee Lee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Elizabeth A. Williamson
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Brian L. Reinert
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Ju Hwan Cho
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Fen Xia
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Aruna Shanker Jaiswal
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Gayathri Srinivasan
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Bhavita Patel
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Alexis Brantley
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Daohong Zhou
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Lijian Shao
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Rupak Pathak
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Martin Hauer-Jensen
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Sudha Singh
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Kimi Kong
- Department of Craniofacial Regeneration, College of Dental Medicine, Columbia University, New York, New York, United States of America
| | - Xaiohua Wu
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California, United States of America
| | - Hyun-Suk Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Timothy Beissbarth
- Department of Medical Statistics, and General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jochen Gaedcke
- Department of Medical Statistics, and General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Sandeep Burma
- Department of Radiation Oncology, University of Texas Southwestern, Dallas, Texas, United States of America
| | - Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail: (JAN); (RAH)
| | - Robert A. Hromas
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
- * E-mail: (JAN); (RAH)
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40
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Shao X, He Y, Ji M, Chen X, Qi J, Shi W, Hao T, Ju S. Quantitative analysis of cell-free DNA in ovarian cancer. Oncol Lett 2015; 10:3478-3482. [PMID: 26788153 PMCID: PMC4665352 DOI: 10.3892/ol.2015.3771] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 08/17/2015] [Indexed: 12/23/2022] Open
Abstract
The aim of the present study was to investigate the association between cell-free DNA (cf-DNA) levels and clinicopathological characteristics of patients with ovarian cancer using a branched DNA (bDNA) technique, and to determine the value of quantitative cf-DNA detection in assisting with the diagnosis of ovarian cancer. Serum specimens were collected from 36 patients with ovarian cancer on days 1, 3 and 7 following surgery, and additional serum samples were also collected from 22 benign ovarian tumor cases, and 19 healthy, non-cancerous ovaries. bDNA techniques were used to detect serum cf-DNA concentrations. All data were analyzed using SPSS version 18.0. The cf-DNA levels were significantly increased in the ovarian cancer group compared with those of the benign ovarian tumor group and healthy ovarian group (P<0.01). Furthermore, cf-DNA levels were significantly increased in stage III and IV ovarian cancer compared with those of stages I and II (P<0.01). In addition, cf-DNA levels were significantly increased on the first day post-surgery (P<0.01), and subsequently demonstrated a gradual decrease. In the ovarian cancer group, the area under the receiver operating characteristic curve of cf-DNA and the sensitivity were 0.917 and 88.9%, respectively, which was higher than those of cancer antigen 125 (0.724, 75%) and human epididymis protein 4 (0.743, 80.6%). There was a correlation between the levels of serum cf-DNA and the occurrence and development of ovarian cancer in the patients evaluated. bDNA techniques possessed higher sensitivity and specificity than other methods for the detection of serum cf-DNA in patients exhibiting ovarian cancer, and bDNA techniques are more useful for detecting cf-DNA than other factors. Thus, the present study demonstrated the potential value for the use of bDNA as an adjuvant diagnostic method for ovarian cancer.
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Affiliation(s)
- Xuefeng Shao
- Department of Clinical Laboratory, Maternity and Child Healthcare Hospital of Nantong, Nantong, Jiangsu 226018, P.R. China
| | - Yan He
- Department of Gynecology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830000, P.R. China
| | - Min Ji
- Department of Internal Medicine, Maternity and Child Healthcare Hospital of Nantong, Nantong, Jiangsu 226018, P.R. China
| | - Xiaofang Chen
- Department of Gynecology, Maternity and Child Healthcare Hospital of Nantong, Nantong, Jiangsu 226018, P.R. China
| | - Jing Qi
- Department of Laboratory of Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226018, P.R. China
| | - Wei Shi
- Department of Laboratory of Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226018, P.R. China
| | - Tianbo Hao
- Department of Laboratory of Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226018, P.R. China
| | - Shaoqing Ju
- Department of Laboratory of Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226018, P.R. China
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41
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Blanco MG, Matos J. Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1. Front Genet 2015; 6:253. [PMID: 26284109 PMCID: PMC4519697 DOI: 10.3389/fgene.2015.00253] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/13/2015] [Indexed: 12/21/2022] Open
Abstract
Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs) act upon recombining joint molecules (JMs) to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs – MUS81 and Yen1/GEN1– uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM-processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions.
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Affiliation(s)
- Miguel G Blanco
- Department of Biochemistry and Molecular Biology, Center for Research in Molecular Medicine and Chronic Diseases, University of Santiago de Compostela , Santiago de Compostela, Spain
| | - Joao Matos
- Institute of Biochemistry, Swiss Federal Institute of Technology in Zürich , Zürich, Switzerland
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42
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Neelsen KJ, Lopes M. Replication fork reversal in eukaryotes: from dead end to dynamic response. Nat Rev Mol Cell Biol 2015; 16:207-20. [PMID: 25714681 DOI: 10.1038/nrm3935] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The remodelling of replication forks into four-way junctions following replication perturbation, known as fork reversal, was hypothesized to promote DNA damage tolerance and repair during replication. Albeit conceptually attractive, for a long time fork reversal in vivo was found only in prokaryotes and specific yeast mutants, calling its evolutionary conservation and physiological relevance into question. Based on the recent visualization of replication forks in metazoans, fork reversal has emerged as a global, reversible and regulated process, with intriguing implications for replication completion, chromosome integrity and the DNA damage response. The study of the putative in vivo roles of recently identified eukaryotic factors in fork remodelling promises to shed new light on mechanisms of genome maintenance and to provide novel attractive targets for cancer therapy.
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Affiliation(s)
- Kai J Neelsen
- 1] Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. [2] The Novo Nordisk Foundation Center for Protein Research, 2200 Copenhagen, Denmark
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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43
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Mus81-Mms4 and Yen1 resolve a novel anaphase bridge formed by noncanonical Holliday junctions. Nat Commun 2014; 5:5652. [PMID: 25466415 DOI: 10.1038/ncomms6652] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 10/24/2014] [Indexed: 02/07/2023] Open
Abstract
Downregulation of separase, condensin, Smc5/6, topoisomerase II and Cdc14 in Saccharomyces cerevisiae yields anaphase bridges formed by unresolved sister chromatids (SCBs). Here we report that the overlapping actions of the structure-selective endonucleases (SSEs) Mus81-Mms4/EME1 and Yen1/GEN1, but not Slx1-Slx4, are also essential to prevent the formation of spontaneous SCBs that depend on the homologous recombination pathway. We further show that the frequency of SCBs is boosted after mild replication stress and that they contain joint molecules enriched in non-canonical forms of the Holliday junction (HJ), including nicked-HJ (nHJ). We show that SCBs are mostly reversible upon activation of either Mus81-Mms4 or Yen1 in late anaphase, which is concomitant with the disappearance of non-canonical HJs and restoration of viable progeny. On the basis of these findings, we propose a model where unresolved recombination intermediates are a source of mitotic SCBs, and Mus81-Mms4 and Yen1 play a central role in their resolution in vivo.
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44
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Abstract
The links between recombination and replication have been appreciated for decades and it is now generally accepted that these two fundamental aspects of DNA metabolism are inseparable: Homologous recombination is essential for completion of DNA replication and vice versa. This review focuses on the roles that recombination enzymes play in underpinning genome duplication, aiding replication fork movement in the face of the many replisome barriers that challenge genome stability. These links have many conserved features across all domains of life, reflecting the conserved nature of the substrate for these reactions, DNA.
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Affiliation(s)
- Aisha H Syeda
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Peter McGlynn
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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45
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Sarbajna S, West SC. Holliday junction processing enzymes as guardians of genome stability. Trends Biochem Sci 2014; 39:409-19. [PMID: 25131815 DOI: 10.1016/j.tibs.2014.07.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 12/14/2022]
Abstract
Holliday junctions (HJs) are four-stranded DNA intermediates that arise during the recombinational repair of DNA double-strand breaks (DSBs). Their timely removal is crucial for faithful chromosome segregation and genome stability. In mammalian cells, HJs are processed by the BTR (BLM-topoisomerase IIIα-RMI1-RMI2) complex, the SLX-MUS (SLX1-SLX4-MUS81-EME1) complex, and the GEN1 resolvase. Recent studies have linked the deficiency of one or more of these enzymes to perturbed DNA replication, impaired crosslink repair, chromosomal instability, and defective mitoses, coupled with the transmission of widespread DNA damage and high levels of mortality. We review these key advances and how they have cemented the status of HJ-processing enzymes as guardians of genome integrity and viability in mammalian cells.
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Affiliation(s)
- Shriparna Sarbajna
- London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Hertfordshire, EN6 3LD, UK
| | - Stephen C West
- London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Hertfordshire, EN6 3LD, UK.
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46
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García-Luis J, Clemente-Blanco A, Aragón L, Machín F. Cdc14 targets the Holliday junction resolvase Yen1 to the nucleus in early anaphase. Cell Cycle 2014; 13:1392-9. [PMID: 24626187 DOI: 10.4161/cc.28370] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The only canonical Holliday junction (HJ) resolvase identified in eukaryotes thus far is Yen1/GEN1. Nevertheless, Yen1/GEN1 appears to have a minor role in HJ resolution, and, instead, other structure-specific endonucleases (SSE) that recognize branched DNA play the leading roles, Mus81-Mms4/EME1 being the most important in budding yeast. Interestingly, cells tightly regulate the activity of each HJ resolvase during the yeast cell cycle. Thus, Mus81-Mms4 is activated in G 2/M, while Yen1 gets activated shortly afterwards. Nevertheless, cytological studies have shown that Yen1 is sequestered out of the nucleus when cyclin-dependent kinase activity is high, i.e., all of the cell cycle but G 1. We here show that the mitotic master phosphatase Cdc14 targets Yen1 to the nucleus in early anaphase through the FEAR network. We will further show that this FEAR-mediated Cdc14-driven event is sufficient to back-up Mus81-Mms4 in removing branched DNA structures, which are especially found in the long chromosome arms upon replication stress. Finally, we found that MEN-driven Cdc14 re-activation in late anaphase is essential to keep Yen1 in the nucleus until the next G 1. Our results highlight the essential role that early-activated Cdc14, i.e., through the FEAR network, has in removing all kind of non-proteinaceous linkages that preclude faithful sister chromatid segregation in anaphase. In addition, our results support the general idea of Yen1 acting as a last resource endonuclease to deal with any remaining HJ that might compromise genetic stability during chromosome segregation.
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Affiliation(s)
- Jonay García-Luis
- Genomic Instability & Cancer Group; Unidad de Investigación; Hospital Universitario Nuestra Señora de Candelaria; Santa Cruz de Tenerife, Spain
| | | | - Luis Aragón
- Cell Cycle Group; MRC Clinical Sciences Centre; Imperial College London; London, UK
| | - Félix Machín
- Genomic Instability & Cancer Group; Unidad de Investigación; Hospital Universitario Nuestra Señora de Candelaria; Santa Cruz de Tenerife, Spain
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