1
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Sridalla K, Woodhouse MV, Hu J, Scheer J, Ferlez B, Crickard JB. The translocation activity of Rad54 reduces crossover outcomes during homologous recombination. Nucleic Acids Res 2024:gkae474. [PMID: 38828785 DOI: 10.1093/nar/gkae474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that requires the selection of an appropriate DNA sequence to facilitate repair. Selection occurs during a homology search that must be executed rapidly and with high fidelity. Failure to efficiently perform the homology search can result in complex intermediates that generate genomic rearrangements, a hallmark of human cancers. Rad54 is an ATP dependent DNA motor protein that functions during the homology search by regulating the recombinase Rad51. How this regulation reduces genomic exchanges is currently unknown. To better understand how Rad54 can reduce these outcomes, we evaluated several amino acid mutations in Rad54 that were identified in the COSMIC database. COSMIC is a collection of amino acid mutations identified in human cancers. These substitutions led to reduced Rad54 function and the discovery of a conserved motif in Rad54. Through genetic, biochemical and single-molecule approaches, we show that disruption of this motif leads to failure in stabilizing early strand invasion intermediates, causing increased crossovers between homologous chromosomes. Our study also suggests that the translocation rate of Rad54 is a determinant in balancing genetic exchange. The latch domain's conservation implies an interaction likely fundamental to eukaryotic biology.
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Affiliation(s)
- Krishay Sridalla
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Mitchell V Woodhouse
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jingyi Hu
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jessica Scheer
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bryan Ferlez
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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2
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Graham E, Esashi F. DNA strand breaks at centromeres: Friend or foe? Semin Cell Dev Biol 2024; 156:141-151. [PMID: 37872040 DOI: 10.1016/j.semcdb.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Centromeres are large structural regions in the genomic DNA, which are essential for accurately transmitting a complete set of chromosomes to daughter cells during cell division. In humans, centromeres consist of highly repetitive α-satellite DNA sequences and unique epigenetic components, forming large proteinaceous structures required for chromosome segregation. Despite their biological importance, there is a growing body of evidence for centromere breakage across the cell cycle, including periods of quiescence. In this review, we provide an up-to-date examination of the distinct centromere environments at different stages of the cell cycle, highlighting their plausible contribution to centromere breakage. Additionally, we explore the implications of these breaks on centromere function, both in terms of negative consequences and potential positive effects.
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Affiliation(s)
- Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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3
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Di Tommaso E, Giunta S. Dynamic interplay between human alpha-satellite DNA structure and centromere functions. Semin Cell Dev Biol 2024; 156:130-140. [PMID: 37926668 DOI: 10.1016/j.semcdb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.
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Affiliation(s)
- Elena Di Tommaso
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy.
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4
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Marcon F, Giunta S, Bignami M. Emerging roles of DNA repair factors in the stability of centromeres. Semin Cell Dev Biol 2024; 156:121-129. [PMID: 37852903 DOI: 10.1016/j.semcdb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Satellite DNA sequences are an integral part of centromeres, regions critical for faithful segregation of chromosomes during cell division. Because of their complex repetitive structure, satellite DNA may act as a barrier to DNA replication and other DNA based transactions ultimately resulting in chromosome breakage. Over the past two decades, several DNA repair proteins have been shown to bind and function at centromeres. While the importance of these repair factors is highlighted by various structural and numerical chromosome aberrations resulting from their inactivation, their roles in helping to maintain genome stability by solving the intrinsic difficulties of satellite DNA replication or promoting their repair are just starting to emerge. In this review, we summarize the current knowledge on the role of DNA repair and DNA damage response proteins in maintaining the structure and function of centromeres in different contexts. We also report the recent connection between the roles of specific DNA repair factors at these genomic loci with age-related increase of chromosomal instability under physiological and pathological conditions.
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Affiliation(s)
- Francesca Marcon
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, 00185, Italy
| | - Margherita Bignami
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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5
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Xu R, Pan Z, Nakagawa T. Gross Chromosomal Rearrangement at Centromeres. Biomolecules 2023; 14:28. [PMID: 38254628 PMCID: PMC10813616 DOI: 10.3390/biom14010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Centromeres play essential roles in the faithful segregation of chromosomes. CENP-A, the centromere-specific histone H3 variant, and heterochromatin characterized by di- or tri-methylation of histone H3 9th lysine (H3K9) are the hallmarks of centromere chromatin. Contrary to the epigenetic marks, DNA sequences underlying the centromere region of chromosomes are not well conserved through evolution. However, centromeres consist of repetitive sequences in many eukaryotes, including animals, plants, and a subset of fungi, including fission yeast. Advances in long-read sequencing techniques have uncovered the complete sequence of human centromeres containing more than thousands of alpha satellite repeats and other types of repetitive sequences. Not only tandem but also inverted repeats are present at a centromere. DNA recombination between centromere repeats can result in gross chromosomal rearrangement (GCR), such as translocation and isochromosome formation. CENP-A chromatin and heterochromatin suppress the centromeric GCR. The key player of homologous recombination, Rad51, safeguards centromere integrity through conservative noncrossover recombination between centromere repeats. In contrast to Rad51-dependent recombination, Rad52-mediated single-strand annealing (SSA) and microhomology-mediated end-joining (MMEJ) lead to centromeric GCR. This review summarizes recent findings on the role of centromere and recombination proteins in maintaining centromere integrity and discusses how GCR occurs at centromeres.
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Affiliation(s)
- Ran Xu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Ziyi Pan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
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6
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Mongia P, Toyofuku N, Pan Z, Xu R, Kinoshita Y, Oki K, Takahashi H, Ogura Y, Hayashi T, Nakagawa T. Fission yeast Srr1 and Skb1 promote isochromosome formation at the centromere. Commun Biol 2023; 6:551. [PMID: 37237082 DOI: 10.1038/s42003-023-04925-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Rad51 maintains genome integrity, whereas Rad52 causes non-canonical homologous recombination leading to gross chromosomal rearrangements (GCRs). Here we find that fission yeast Srr1/Ber1 and Skb1/PRMT5 promote GCRs at centromeres. Genetic and physical analyses show that srr1 and skb1 mutations reduce isochromosome formation mediated by centromere inverted repeats. srr1 increases DNA damage sensitivity in rad51 cells but does not abolish checkpoint response, suggesting that Srr1 promotes Rad51-independent DNA repair. srr1 and rad52 additively, while skb1 and rad52 epistatically reduce GCRs. Unlike srr1 or rad52, skb1 does not increase damage sensitivity. Skb1 regulates cell morphology and cell cycle with Slf1 and Pom1, respectively, but neither Slf1 nor Pom1 causes GCRs. Mutating conserved residues in the arginine methyltransferase domain of Skb1 greatly reduces GCRs. These results suggest that, through arginine methylation, Skb1 forms aberrant DNA structures leading to Rad52-dependent GCRs. This study has uncovered roles for Srr1 and Skb1 in GCRs at centromeres.
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Affiliation(s)
- Piyusha Mongia
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Naoko Toyofuku
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ziyi Pan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ran Xu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yakumo Kinoshita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Keitaro Oki
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
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7
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Saayman X, Graham E, Nathan WJ, Nussenzweig A, Esashi F. Centromeres as universal hotspots of DNA breakage, driving RAD51-mediated recombination during quiescence. Mol Cell 2023; 83:523-538.e7. [PMID: 36702125 PMCID: PMC10009740 DOI: 10.1016/j.molcel.2023.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 10/07/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023]
Abstract
Centromeres are essential for chromosome segregation in most animals and plants yet are among the most rapidly evolving genome elements. The mechanisms underlying this paradoxical phenomenon remain enigmatic. Here, we report that human centromeres innately harbor a striking enrichment of DNA breaks within functionally active centromere regions. Establishing a single-cell imaging strategy that enables comparative assessment of DNA breaks at repetitive regions, we show that centromeric DNA breaks are induced not only during active cellular proliferation but also de novo during quiescence. Markedly, centromere DNA breaks in quiescent cells are resolved enzymatically by the evolutionarily conserved RAD51 recombinase, which in turn safeguards the specification of functional centromeres. This study highlights the innate fragility of centromeres, which may have been co-opted over time to reinforce centromere specification while driving rapid evolution. The findings also provide insights into how fragile centromeres are likely to contribute to human disease.
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Affiliation(s)
- Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - William J Nathan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892-4254, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892-4254, USA
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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8
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Kramarz K, Dziadkowiec D. Rrp1, Rrp2 and Uls1 - Yeast SWI2/SNF2 DNA dependent translocases in genome stability maintenance. DNA Repair (Amst) 2022; 116:103356. [PMID: 35716431 DOI: 10.1016/j.dnarep.2022.103356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/12/2022] [Accepted: 06/08/2022] [Indexed: 11/03/2022]
Abstract
Multiple eukaryotic SWI2/SNF2 DNA translocases safeguard genome integrity, mostly by remodelling nucleosomes, but also by fine-tuning mechanisms of DNA repair, such as homologous recombination. Among this large family there is a unique class of Rad5/16-like enzymes, including Saccharomyces cerevisiae Uls1 and its Schizosaccharomyces pombe orthologues Rrp1 and Rrp2, that have both translocase and E3 ubiquitin ligase activities, and are often directed towards their substrates by SUMOylation. Here we summarize recent advances in understanding how different activities of these yeast proteins jointly contribute to their important roles in replication stress response particularly at centromeres and telomeres. This extends the possible range of functions performed by this class of SNF2 enzymes in human cells involving both their translocase and ubiquitin ligase activities and related to SUMOylation pathways within the nucleus.
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Affiliation(s)
- Karol Kramarz
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wrocław, Poland.
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9
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Disbennett WM, Hawk TM, Rollins PD, Nelakurti DD, Lucas BE, McPherson MT, Hylton HM, Petreaca RC. Genetic interaction of the histone chaperone hip1 + with double strand break repair genes in Schizosaccharomyces pombe. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000545. [PMID: 35622511 PMCID: PMC9005195 DOI: 10.17912/micropub.biology.000545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/06/2022]
Abstract
Schizosaccharomyces pombe hip1 + (human HIRA) is a histone chaperone and transcription factor involved in establishment of the centromeric chromatin and chromosome segregation, regulation of histone transcription, and cellular response to stress. We carried out a double mutant genetic screen of Δhip1 and mutations in double strand break repair pathway. We find that hip1 + functions after the MRN complex which initiates resection of blunt double strand break ends but before recruitment of the DNA damage repair machinery. Further, deletion of hip1 + partially suppresses sensitivity to DNA damaging agents of mutations in genes involved in Break Induced Replication (BIR), one mechanism of rescue of stalled or collapses replication forks ( rad51 + , cdc27 + ). Δhip1 also suppresses mutations in two checkpoint genes ( cds1 + , rad3 + ) on hydroxyurea a drug that stalls replication forks. Our results show that hip1 + forms complex interactions with the DNA double strand break repair genes and may be involved in facilitating communication between damage sensors and downstream factors.
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Affiliation(s)
| | - Tila M. Hawk
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - P. Daniel Rollins
- Molecular Genetics Undergraduate Program, The Ohio State University, Columbus, OH
| | - Devi D Nelakurti
- Biomedical Science Undergraduate Program, The Ohio State University Medical School, Columbus, OH
| | - Bailey E Lucas
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | - Hannah M Hylton
- Biology Undergraduate Program, The Ohio State University, Marion, OH
| | - Ruben C Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH
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10
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Muraszko J, Kramarz K, Argunhan B, Ito K, Baranowska G, Kurokawa Y, Murayama Y, Tsubouchi H, Lambert S, Iwasaki H, Dziadkowiec D. Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast. Nucleic Acids Res 2021; 49:6832-6848. [PMID: 34157114 PMCID: PMC8266636 DOI: 10.1093/nar/gkab511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/20/2022] Open
Abstract
Rad51 is the key protein in homologous recombination that plays important roles during DNA replication and repair. Auxiliary factors regulate Rad51 activity to facilitate productive recombination, and prevent inappropriate, untimely or excessive events, which could lead to genome instability. Previous genetic analyses identified a function for Rrp1 (a member of the Rad5/16-like group of SWI2/SNF2 translocases) in modulating Rad51 function, shared with the Rad51 mediator Swi5-Sfr1 and the Srs2 anti-recombinase. Here, we show that Rrp1 overproduction alleviates the toxicity associated with excessive Rad51 levels in a manner dependent on Rrp1 ATPase domain. Purified Rrp1 binds to DNA and has a DNA-dependent ATPase activity. Importantly, Rrp1 directly interacts with Rad51 and removes it from double-stranded DNA, confirming that Rrp1 is a translocase capable of modulating Rad51 function. Rrp1 affects Rad51 binding at centromeres. Additionally, we demonstrate in vivo and in vitro that Rrp1 possesses E3 ubiquitin ligase activity with Rad51 as a substrate, suggesting that Rrp1 regulates Rad51 in a multi-tiered fashion.
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Affiliation(s)
| | - Karol Kramarz
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Bilge Argunhan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Kentaro Ito
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | | | - Yumiko Kurokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Yasuto Murayama
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hideo Tsubouchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Hiroshi Iwasaki
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
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11
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Su J, Xu R, Mongia P, Toyofuku N, Nakagawa T. Fission yeast Rad8/HLTF facilitates Rad52-dependent chromosomal rearrangements through PCNA lysine 107 ubiquitination. PLoS Genet 2021; 17:e1009671. [PMID: 34292936 PMCID: PMC8297803 DOI: 10.1371/journal.pgen.1009671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/18/2021] [Indexed: 11/19/2022] Open
Abstract
Gross chromosomal rearrangements (GCRs), including translocation, deletion, and inversion, can cause cell death and genetic diseases such as cancer in multicellular organisms. Rad51, a DNA strand exchange protein, suppresses GCRs by repairing spontaneous DNA damage through a conservative way of homologous recombination, gene conversion. On the other hand, Rad52 that catalyzes single-strand annealing (SSA) causes GCRs using homologous sequences. However, the detailed mechanism of Rad52-dependent GCRs remains unclear. Here, we provide genetic evidence that fission yeast Rad8/HLTF facilitates Rad52-dependent GCRs through the ubiquitination of lysine 107 (K107) of PCNA, a DNA sliding clamp. In rad51Δ cells, loss of Rad8 eliminated 75% of the isochromosomes resulting from centromere inverted repeat recombination, showing that Rad8 is essential for the formation of the majority of isochromosomes in rad51Δ cells. Rad8 HIRAN and RING finger mutations reduced GCRs, suggesting that Rad8 facilitates GCRs through 3’ DNA-end binding and ubiquitin ligase activity. Mms2 and Ubc4 but not Ubc13 ubiquitin-conjugating enzymes were required for GCRs. Consistent with this, mutating PCNA K107 rather than the well-studied PCNA K164 reduced GCRs. Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs, as PCNA K107R, rad8, and rad52 mutations epistatically reduced GCRs. In contrast to GCRs, PCNA K107R did not significantly change gene conversion rates, suggesting a specific role of PCNA K107 ubiquitination in GCRs. PCNA K107R enhanced temperature-sensitive growth defects of DNA ligase I cdc17-K42 mutant, implying that PCNA K107 ubiquitination occurs when Okazaki fragment maturation fails. Remarkably, K107 is located at the interface between PCNA subunits, and an interface mutation D150E bypassed the requirement of PCNA K107 and Rad8 ubiquitin ligase for GCRs. These data suggest that Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs by changing the PCNA clamp structure. Gross chromosomal rearrangements (GCRs), including translocation, can alter gene dosage and activity, resulting in genetic diseases such as cancer. However, GCRs can occur by some enzymes, including Rad52 recombinase, and result in chromosomal evolution. Therefore, GCRs are not only pathological but also physiological phenomena from an evolutionary point of view. However, the detailed mechanism of GCRs remains unclear. Here, using fission yeast, we show that the homolog of human HLTF, Rad8 causes GCRs through noncanonical ubiquitination of proliferating cellular nuclear antigen (PCNA) at a lysine 107 (K107). Rad51, a DNA strand exchange protein, suppresses the formation of isochromosomes whose arms mirror each another and chromosomal truncation. We found that, like Rad52, Rad8 is required for isochromosome formation but not chromosomal truncation in rad51Δ cells, showing a specific role of Rad8 in homology-mediated GCRs. Mutations in Rad8 ubiquitin E3 ligase RING finger domain, Mms2-Ubc4 ubiquitin-conjugating enzymes, and PCNA K107 reduced GCRs in rad51Δ cells, suggesting that Rad8-Mms2-Ubc4-dependent PCNA K107 ubiquitination facilitates GCRs. PCNA trimers form a DNA sliding clamp. The K107 residue is located at the PCNA-PCNA interface, and an interface mutation D150E restored GCRs in PCNA K107R mutant cells. This study provides genetic evidence that Rad8-dependent PCNA K107 ubiquitination facilitates GCRs by changing the PCNA clamp structure.
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Affiliation(s)
- Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Ran Xu
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Piyusha Mongia
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Naoko Toyofuku
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
- * E-mail:
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12
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Li T, Petreaca RC, Forsburg SL. Schizosaccharomyces pombe KAT5 contributes to resection and repair of a DNA double-strand break. Genetics 2021; 218:6173406. [PMID: 33723569 DOI: 10.1093/genetics/iyab042] [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: 02/02/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
Chromatin remodeling is essential for effective repair of a DNA double-strand break (DSB). KAT5 (Schizosaccharomyces pombe Mst1, human TIP60) is a MYST family histone acetyltransferase conserved from yeast to humans that coordinates various DNA damage response activities at a DNA DSB, including histone remodeling and activation of the DNA damage checkpoint. In S. pombe, mutations in mst1+ causes sensitivity to DNA damaging drugs. Here we show that Mst1 is recruited to DSBs. Mutation of mst1+ disrupts recruitment of repair proteins and delays resection. These defects are partially rescued by deletion of pku70, which has been previously shown to antagonize repair by homologous recombination (HR). These phenotypes of mst1 are similar to pht1-4KR, a nonacetylatable form of histone variant H2A.Z, which has been proposed to affect resection. Our data suggest that Mst1 functions to direct repair of DSBs toward HR pathways by modulating resection at the DSB.
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Affiliation(s)
- Tingting Li
- Program of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Ruben C Petreaca
- Program of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
- Department of Molecular Genetics, Ohio State University, Marion, OH 43302, USA
| | - Susan L Forsburg
- Program of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
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13
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Shah SS, Hartono S, Piazza A, Som V, Wright W, Chédin F, Heyer WD. Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and limits D-loop length. eLife 2020; 9:59112. [PMID: 33185188 PMCID: PMC7695457 DOI: 10.7554/elife.59112] [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: 05/20/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023] Open
Abstract
Displacement loops (D-loops) are critical intermediates formed during homologous recombination. Rdh54 (a.k.a. Tid1), a Rad54 paralog in Saccharomyces cerevisiae, is well-known for its role with Dmc1 recombinase during meiotic recombination. Yet contrary to Dmc1, Rdh54/Tid1 is also present in somatic cells where its function is less understood. While Rdh54/Tid1 enhances the Rad51 DNA strand invasion activity in vitro, it is unclear how it interplays with Rad54. Here, we show that Rdh54/Tid1 inhibits D-loop formation by Rad51 and Rad54 in an ATPase-independent manner. Using a novel D-loop Mapping Assay, we further demonstrate that Rdh54/Tid1 uniquely restricts the length of Rad51-Rad54-mediated D-loops. The alterations in D-loop properties appear to be important for cell survival and mating-type switch in haploid yeast. We propose that Rdh54/Tid1 and Rad54 compete for potential binding sites within the Rad51 filament, where Rdh54/Tid1 acts as a physical roadblock to Rad54 translocation, limiting D-loop formation and D-loop length.
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Affiliation(s)
- Shanaya Shital Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Stella Hartono
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Aurèle Piazza
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,CR CNRS UMR5239, Team Genome Mechanics, Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon 46, Lyon, France
| | - Vanessa Som
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - William Wright
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,Mammoth Biosciences, South San Francisco, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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14
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Damasceno JD, Reis-Cunha J, Crouch K, Beraldi D, Lapsley C, Tosi LRO, Bartholomeu D, McCulloch R. Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication. PLoS Genet 2020; 16:e1008828. [PMID: 32609721 PMCID: PMC7360064 DOI: 10.1371/journal.pgen.1008828] [Citation(s) in RCA: 14] [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: 11/15/2019] [Revised: 07/14/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Homologous recombination (HR) has an intimate relationship with genome replication, both during repair of DNA lesions that might prevent DNA synthesis and in tackling stalls to the replication fork. Recent studies led us to ask if HR might have a more central role in replicating the genome of Leishmania, a eukaryotic parasite. Conflicting evidence has emerged regarding whether or not HR genes are essential, and genome-wide mapping has provided evidence for an unorthodox organisation of DNA replication initiation sites, termed origins. To answer this question, we have employed a combined CRISPR/Cas9 and DiCre approach to rapidly generate and assess the effect of conditional ablation of RAD51 and three RAD51-related proteins in Leishmania major. Using this approach, we demonstrate that loss of any of these HR factors is not immediately lethal but in each case growth slows with time and leads to DNA damage and accumulation of cells with aberrant DNA content. Despite these similarities, we show that only loss of RAD51 or RAD51-3 impairs DNA synthesis and causes elevated levels of genome-wide mutation. Furthermore, we show that these two HR factors act in distinct ways, since ablation of RAD51, but not RAD51-3, has a profound effect on DNA replication, causing loss of initiation at the major origins and increased DNA synthesis at subtelomeres. Our work clarifies questions regarding the importance of HR to survival of Leishmania and reveals an unanticipated, central role for RAD51 in the programme of genome replication in a microbial eukaryote.
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Affiliation(s)
- Jeziel D. Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
- * E-mail: (JDD); (RM)
| | - João Reis-Cunha
- Laboratório de Imunologia e Genômica de Parasitos, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Kathryn Crouch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
| | - Dario Beraldi
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
| | - Luiz R. O. Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo; Ribeirão Preto, SP, Brazil
| | - Daniella Bartholomeu
- Laboratório de Imunologia e Genômica de Parasitos, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, United Kingdom
- * E-mail: (JDD); (RM)
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15
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Onaka AT, Su J, Katahira Y, Tang C, Zafar F, Aoki K, Kagawa W, Niki H, Iwasaki H, Nakagawa T. DNA replication machinery prevents Rad52-dependent single-strand annealing that leads to gross chromosomal rearrangements at centromeres. Commun Biol 2020; 3:202. [PMID: 32355220 PMCID: PMC7193609 DOI: 10.1038/s42003-020-0934-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/09/2020] [Indexed: 12/27/2022] Open
Abstract
Homologous recombination between repetitive sequences can lead to gross chromosomal rearrangements (GCRs). At fission yeast centromeres, Rad51-dependent conservative recombination predominantly occurs between inverted repeats, thereby suppressing formation of isochromosomes whose arms are mirror images. However, it is unclear how GCRs occur in the absence of Rad51 and how GCRs are prevented at centromeres. Here, we show that homology-mediated GCRs occur through Rad52-dependent single-strand annealing (SSA). The rad52-R45K mutation, which impairs SSA activity of Rad52 protein, dramatically reduces isochromosome formation in rad51 deletion cells. A ring-like complex Msh2-Msh3 and a structure-specific endonuclease Mus81 function in the Rad52-dependent GCR pathway. Remarkably, mutations in replication fork components, including DNA polymerase α and Swi1/Tof1/Timeless, change the balance between Rad51-dependent recombination and Rad52-dependent SSA at centromeres, increasing Rad52-dependent SSA that forms isochromosomes. Our results uncover a role of DNA replication machinery in the recombination pathway choice that prevents Rad52-dependent GCRs at centromeres.
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Affiliation(s)
- Atsushi T Onaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Chitose Laboratory Corporation, 2-13-3 Nogawa-honcho, Miyamae-ku, Kawasaki, Kanagawa, 216-0041, Japan
| | - Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasuhiro Katahira
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Department of Immunoregulation, Institute of Medical Science, Tokyo Medical University, 6-1-1 Shinjuku-ku, Tokyo, 160-8402, Japan
| | - Crystal Tang
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Faria Zafar
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Keita Aoki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Wataru Kagawa
- Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hiroshi Iwasaki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
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16
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Gutbrod MJ, Martienssen RA. Conserved chromosomal functions of RNA interference. Nat Rev Genet 2020; 21:311-331. [PMID: 32051563 DOI: 10.1038/s41576-019-0203-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi), a cellular process through which small RNAs target and regulate complementary RNA transcripts, has well-characterized roles in post-transcriptional gene regulation and transposon repression. Recent studies have revealed additional conserved roles for RNAi proteins, such as Argonaute and Dicer, in chromosome function. By guiding chromatin modification, RNAi components promote chromosome segregation during both mitosis and meiosis and regulate chromosomal and genomic dosage response. Small RNAs and the RNAi machinery also participate in the resolution of DNA damage. Interestingly, many of these lesser-studied functions seem to be more strongly conserved across eukaryotes than are well-characterized functions such as the processing of microRNAs. These findings have implications for the evolution of RNAi since the last eukaryotic common ancestor, and they provide a more complete view of the functions of RNAi.
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Affiliation(s)
- Michael J Gutbrod
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert A Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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17
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Barg-Wojas A, Muraszko J, Kramarz K, Schirmeisen K, Baranowska G, Carr AM, Dziadkowiec D. Schizosaccharomyces pombe DNA translocases Rrp1 and Rrp2 have distinct roles at centromeres and telomeres that ensure genome stability. J Cell Sci 2020; 133:jcs230193. [PMID: 31932509 DOI: 10.1242/jcs.230193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
The regulation of telomere and centromere structure and function is essential for maintaining genome integrity. Schizosaccharomyces pombe Rrp1 and Rrp2 are orthologues of Saccharomyces cerevisiae Uls1, a SWI2/SNF2 DNA translocase and SUMO-targeted ubiquitin ligase. Here, we show that Rrp1 or Rrp2 overproduction leads to chromosome instability and growth defects, a reduction in global histone levels and mislocalisation of centromere-specific histone Cnp1. These phenotypes depend on putative DNA translocase activities of Rrp1 and Rrp2, suggesting that Rrp1 and Rrp2 may be involved in modulating nucleosome dynamics. Furthermore, we confirm that Rrp2, but not Rrp1, acts at telomeres, reflecting a previously described interaction between Rrp2 and Top2. In conclusion, we identify roles for Rrp1 and Rrp2 in maintaining centromere function by modulating histone dynamics, contributing to the preservation of genome stability during vegetative cell growth.
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Affiliation(s)
- Anna Barg-Wojas
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Jakub Muraszko
- Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Karol Kramarz
- Institut Curie, Centre National de la Recherche Scientifique, F-91405, Orsay, France
| | | | | | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
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18
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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19
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Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:genes11010079. [PMID: 31936815 PMCID: PMC7016768 DOI: 10.3390/genes11010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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20
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Lucas BE, McPherson MT, Hawk TM, Wilson LN, Kroh JM, Hickman KG, Fitzgerald SR, Disbennett WM, Rollins PD, Hylton HM, Baseer MA, Montgomery PN, Wu JQ, Petreaca RC. An Assay to Study Intra-Chromosomal Deletions in Yeast. Methods Protoc 2019; 2:mps2030074. [PMID: 31454903 PMCID: PMC6789737 DOI: 10.3390/mps2030074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/30/2023] Open
Abstract
An accurate DNA damage response pathway is critical for the repair of DNA double-strand breaks. Repair may occur by homologous recombination, of which many different sub-pathways have been identified. Some recombination pathways are conservative, meaning that the chromosome sequences are preserved, and others are non-conservative, leading to some alteration of the DNA sequence. We describe an in vivo genetic assay to study non-conservative intra-chromosomal deletions at regions of non-tandem direct repeats in Schizosaccharomyces pombe. This assay can be used to study both spontaneous breaks arising during DNA replication and induced double-strand breaks created with the S. cerevisiae homothallic endonuclease (HO). The preliminary genetic validation of this assay shows that spontaneous breaks require rad52+ but not rad51+, while induced breaks require both genes, in agreement with previous studies. This assay will be useful in the field of DNA damage repair for studying mechanisms of intra-chromosomal deletions.
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Affiliation(s)
- Bailey E Lucas
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Matthew T McPherson
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Tila M Hawk
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Lexia N Wilson
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Jacob M Kroh
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Kyle G Hickman
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Sean R Fitzgerald
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | | | - P Daniel Rollins
- Molecular Genetics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Hannah M Hylton
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Mohammed A Baseer
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Paige N Montgomery
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
| | - Jian-Qiu Wu
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Ruben C Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA.
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21
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Toma M, Skorski T, Sliwinski T. DNA Double Strand Break Repair - Related Synthetic Lethality. Curr Med Chem 2019; 26:1446-1482. [PMID: 29421999 DOI: 10.2174/0929867325666180201114306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022]
Abstract
Cancer is a heterogeneous disease with a high degree of diversity between and within tumors. Our limited knowledge of their biology results in ineffective treatment. However, personalized approach may represent a milestone in the field of anticancer therapy. It can increase specificity of treatment against tumor initiating cancer stem cells (CSCs) and cancer progenitor cells (CPCs) with minimal effect on normal cells and tissues. Cancerous cells carry multiple genetic and epigenetic aberrations which may disrupt pathways essential for cell survival. Discovery of synthetic lethality has led a new hope of creating effective and personalized antitumor treatment. Synthetic lethality occurs when simultaneous inactivation of two genes or their products causes cell death whereas individual inactivation of either gene is not lethal. The effectiveness of numerous anti-tumor therapies depends on induction of DNA damage therefore tumor cells expressing abnormalities in genes whose products are crucial for DNA repair pathways are promising targets for synthetic lethality. Here, we discuss mechanistic aspects of synthetic lethality in the context of deficiencies in DNA double strand break repair pathways. In addition, we review clinical trials utilizing synthetic lethality interactions and discuss the mechanisms of resistance.
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Affiliation(s)
- Monika Toma
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Tomasz Skorski
- Department of Microbiology and Immunology, 3400 North Broad Street, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, United States
| | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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22
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Bhattacharjee S, Roche B, Martienssen RA. RNA-induced initiation of transcriptional silencing (RITS) complex structure and function. RNA Biol 2019; 16:1133-1146. [PMID: 31213126 DOI: 10.1080/15476286.2019.1621624] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Heterochromatic regions of the genome are epigenetically regulated to maintain a heritable '"silent state"'. In fission yeast and other organisms, epigenetic silencing is guided by nascent transcripts, which are targeted by the RNA interference pathway. The key effector complex of the RNA interference pathway consists of small interfering RNA molecules (siRNAs) associated with Argonaute, assembled into the RNA-induced transcriptional silencing (RITS) complex. This review focuses on our current understanding of how RITS promotes heterochromatin formation, and in particular on the role of Argonaute-containing complexes in many other functions such as quelling, release of RNA polymerases, cellular quiescence and genome defense.
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Affiliation(s)
- Sonali Bhattacharjee
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Benjamin Roche
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Robert A Martienssen
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
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23
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Nakagawa T, Okita AK. Transcriptional silencing of centromere repeats by heterochromatin safeguards chromosome integrity. Curr Genet 2019; 65:1089-1098. [PMID: 30997531 DOI: 10.1007/s00294-019-00975-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/11/2019] [Accepted: 04/13/2019] [Indexed: 12/25/2022]
Abstract
The centromere region of chromosomes consists of repetitive DNA sequences, and is, therefore, one of the fragile sites of chromosomes in many eukaryotes. In the core region, the histone H3 variant CENP-A forms centromere-specific nucleosomes that are required for kinetochore formation. In the pericentromeric region, histone H3 is methylated at lysine 9 (H3K9) and heterochromatin is formed. The transcription of pericentromeric repeats by RNA polymerase II is strictly repressed by heterochromatin. However, the role of the transcriptional silencing of the pericentromeric repeats remains largely unclear. Here, we focus on the chromosomal rearrangements that occur at the repetitive centromeres, and highlight our recent studies showing that transcriptional silencing by heterochromatin suppresses gross chromosomal rearrangements (GCRs) at centromeres in fission yeast. Inactivation of the Clr4 methyltransferase, which is essential for the H3K9 methylation, increased GCRs with breakpoints located in centromeric repeats. However, mutations in RNA polymerase II or the transcription factor Tfs1/TFIIS, which promotes restart of RNA polymerase II following its backtracking, reduced the GCRs that occur in the absence of Clr4, demonstrating that heterochromatin suppresses GCRs by repressing the Tfs1-dependent transcription. We also discuss how the transcriptional restart gives rise to chromosomal rearrangements at centromeres.
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Affiliation(s)
- Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
| | - Akiko K Okita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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24
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Okita AK, Zafar F, Su J, Weerasekara D, Kajitani T, Takahashi TS, Kimura H, Murakami Y, Masukata H, Nakagawa T. Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription. Commun Biol 2019; 2:17. [PMID: 30652128 PMCID: PMC6329695 DOI: 10.1038/s42003-018-0251-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Heterochromatin, characterized by histone H3 lysine 9 (H3K9) methylation, assembles on repetitive regions including centromeres. Although centromeric heterochromatin is important for correct segregation of chromosomes, its exact role in maintaining centromere integrity remains elusive. Here, we found in fission yeast that heterochromatin suppresses gross chromosomal rearrangements (GCRs) at centromeres. Mutations in Clr4/Suv39 methyltransferase increased the formation of isochromosomes, whose breakpoints were located in centromere repeats. H3K9A and H3K9R mutations also increased GCRs, suggesting that Clr4 suppresses centromeric GCRs via H3K9 methylation. HP1 homologs Swi6 and Chp2 and the RNAi component Chp1 were the chromodomain proteins essential for full suppression of GCRs. Remarkably, mutations in RNA polymerase II (RNAPII) or Tfs1/TFIIS, the transcription factor that facilitates restart of RNAPII after backtracking, specifically bypassed the requirement of Clr4 for suppressing GCRs. These results demonstrate that heterochromatin suppresses GCRs by repressing Tfs1-dependent transcription of centromere repeats.
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Affiliation(s)
- Akiko K. Okita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
| | - Faria Zafar
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
| | - Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
| | - Dayalini Weerasekara
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
| | - Takuya Kajitani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810 Japan
- Present Address: Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853 USA
| | - Tatsuro S. Takahashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
- Present Address: Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8503 Japan
| | - Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810 Japan
| | - Hisao Masukata
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
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Hu X, Wu X, Liu H, Cheng Z, Zhao Z, Xiang C, Feng X, Takeda S, Qing Y. Genistein-induced DNA damage is repaired by nonhomologous end joining and homologous recombination in TK6 cells. J Cell Physiol 2018; 234:2683-2692. [PMID: 30070703 DOI: 10.1002/jcp.27082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/28/2018] [Indexed: 02/05/2023]
Abstract
Genistein (GES), a phytoestrogen, has potential chemopreventive and chemotherapeutic effects on cancer. The anticancer mechanism of GES may be related with topoisomerase II associated DNA double-strand breaks (DSBs). However, the precise molecular mechanism remains elusive. Here, we performed genetic analyses using human lymphoblastoid TK6 cell lines to investigate whether non-homologous DNA end joining (NHEJ) and homologous recombination (HR), the two major repair pathways of DSBs, were involved in repairing GES-induced DNA damage. Our results showed that GES induced DSBs in TK6 cells. Cells lacking Ligase4, an NHEJ enzyme, are hypersensitive to GES. Furthermore, the sensitivity of Ligase4-/- cells was associated with enhanced DNA damage when comparing the accumulation of γ-H2AX foci and number of chromosomal aberrations (CAs) with WT cells. In addition, cells lacking Rad54, a HR enzyme, also presented hypersensitivity and increased DNA damages in response to GES. Meanwhile, Treatment of GES-lacking enhanced the accumulation of Rad51, an HR factor, in TK6 cells, especially in Ligase4-/- . These results provided direct evidence that GES induced DSBs in TK6 cells and clarified that both NHEJ and HR were involved in the repair of GES-induced DNA damage, suggesting that GES in combination with inhibition of NHEJ or HR would provide a potential anticancer strategy.
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Affiliation(s)
- Xiaoqing Hu
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohua Wu
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Hao Liu
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Ziyuan Cheng
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Zilu Zhao
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Cuifang Xiang
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoyu Feng
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yong Qing
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
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Zafar F, Okita AK, Onaka AT, Su J, Katahira Y, Nakayama JI, Takahashi TS, Masukata H, Nakagawa T. Regulation of mitotic recombination between DNA repeats in centromeres. Nucleic Acids Res 2017; 45:11222-11235. [PMID: 28977643 PMCID: PMC5737691 DOI: 10.1093/nar/gkx763] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/17/2017] [Indexed: 12/18/2022] Open
Abstract
Centromeres that are essential for faithful segregation of chromosomes consist of unique DNA repeats in many eukaryotes. Although recombination is under-represented around centromeres during meiosis, little is known about recombination between centromere repeats in mitotic cells. Here, we compared spontaneous recombination that occurs between ade6B/ade6X inverted repeats integrated at centromere 1 (cen1) or at a non-centromeric ura4 locus in fission yeast. Remarkably, distinct mechanisms of homologous recombination (HR) were observed in centromere and non-centromere regions. Rad51-dependent HR that requires Rad51, Rad54 and Rad52 was predominant in the centromere, whereas Rad51-independent HR that requires Rad52 also occurred in the arm region. Crossovers between inverted repeats (i.e. inversions) were under-represented in the centromere as compared to the arm region. While heterochromatin was dispensable, Mhf1/CENP–S, Mhf2/CENP–X histone-fold proteins and Fml1/FANCM helicase were required to suppress crossovers. Furthermore, Mhf1 and Fml1 were found to prevent gross chromosomal rearrangements mediated by centromere repeats. These data uncovered the regulation of mitotic recombination between DNA repeats in centromeres and its physiological role in maintaining genome integrity.
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Affiliation(s)
- Faria Zafar
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akiko K Okita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Atsushi T Onaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiro Katahira
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 44-8585, Japan
| | - Tatsuro S Takahashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hisao Masukata
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Forsburg SL, Shen KF. Centromere Stability: The Replication Connection. Genes (Basel) 2017; 8:genes8010037. [PMID: 28106789 PMCID: PMC5295031 DOI: 10.3390/genes8010037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 11/16/2022] Open
Abstract
The fission yeast centromere, which is similar to metazoan centromeres, contains highly repetitive pericentromere sequences that are assembled into heterochromatin. This is required for the recruitment of cohesin and proper chromosome segregation. Surprisingly, the pericentromere replicates early in the S phase. Loss of heterochromatin causes this domain to become very sensitive to replication fork defects, leading to gross chromosome rearrangements. This review examines the interplay between components of DNA replication, heterochromatin assembly, and cohesin dynamics that ensures maintenance of genome stability and proper chromosome segregation.
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Affiliation(s)
- Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA.
| | - Kuo-Fang Shen
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA.
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