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Carreira R, Lama-Diaz T, Crugeiras M, Aguado F, Sebesta M, Krejci L, Blanco M. Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors. Nucleic Acids Res 2024; 52:7012-7030. [PMID: 38832625 PMCID: PMC11229367 DOI: 10.1093/nar/gkae453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination involves the formation of branched DNA molecules that may interfere with chromosome segregation. To resolve these persistent joint molecules, cells rely on the activation of structure-selective endonucleases (SSEs) during the late stages of the cell cycle. However, the premature activation of SSEs compromises genome integrity, due to untimely processing of replication and/or recombination intermediates. Here, we used a biochemical approach to show that the budding yeast SSEs Mus81 and Yen1 possess the ability to cleave the central recombination intermediate known as the displacement loop or D-loop. Moreover, we demonstrate that, consistently with previous genetic data, the simultaneous action of Mus81 and Yen1, followed by ligation, is sufficient to recreate the formation of a half-crossover precursor in vitro. Our results provide not only mechanistic explanation for the formation of a half-crossover, but also highlight the critical importance for precise regulation of these SSEs to prevent chromosomal rearrangements.
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Affiliation(s)
- Raquel Carreira
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Maria Crugeiras
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - F Javier Aguado
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Marek Sebesta
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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2
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Gu Y, Yang Y, Kou C, Peng Y, Yang W, Zhang J, Jin H, Han X, Wang Y, Shen X. Classical and novel properties of Holliday junction resolvase SynRuvC from Synechocystis sp. PCC6803. Front Microbiol 2024; 15:1362880. [PMID: 38699476 PMCID: PMC11063404 DOI: 10.3389/fmicb.2024.1362880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/29/2024] [Indexed: 05/05/2024] Open
Abstract
Cyanobacteria, which have a photoautotrophic lifestyle, are threatened by ultraviolet solar rays and the reactive oxygen species generated during photosynthesis. They can adapt to environmental conditions primarily because of their DNA damage response and repair mechanisms, notably an efficient homologous recombination repair system. However, research on double-strand break (DSB) repair pathways, including the Holliday junction (HJ) resolution process, in Synechocystis sp. PCC6803 is limited. Here, we report that SynRuvC from cyanobacteria Synechocystis sp. PCC6803 has classical HJ resolution activity. We investigated the structural specificity, sequence preference, and biochemical properties of SynRuvC. SynRuvC strongly preferred Mn2+ as a cofactor, and its cleavage site predominantly resides within the 5'-TG↓(G/A)-3' sequence. Interestingly, novel flap endonuclease and replication fork intermediate cleavage activities of SynRuvC were also determined, which distinguish it from other reported RuvCs. To explore the effect of SynRuvC on cell viability, we constructed a knockdown mutant and an overexpression strain of Synechocystis sp. PCC6803 (synruvCKD and synruvCOE) and assessed their survival under a variety of conditions. Knockdown of synruvC increased the sensitivity of cells to MMS, HU, and H2O2. The findings suggest that a novel RuvC family HJ resolvase SynRuvC is important in a variety of DNA repair processes and stress resistance in Synechocystis sp. PCC6803.
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Affiliation(s)
- Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yantao Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunhua Kou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ying Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenguang Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayu Zhang
- Suzhou XinBio Co., Ltd., Suzhou, Jiangsu, China
| | - Han Jin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoru Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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3
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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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4
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Lian Q, Maestroni L, Gaudin M, Llorente B, Mercier R. Meiotic recombination is confirmed to be unusually high in the fission yeast Schizosaccharomyces pombe. iScience 2023; 26:107614. [PMID: 37664590 PMCID: PMC10474467 DOI: 10.1016/j.isci.2023.107614] [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: 12/16/2022] [Revised: 03/20/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
In most eukaryotes, meiotic crossovers (COs) are limited to 1-3 per chromosome, and are prevented from occurring close to one another by CO interference. The fission yeast Schizosaccharomyces pombe, an exception to these general rules, was reported to have the highest CO number per chromosome and no or weak interference. However, global CO frequency was indirectly estimated, calling for confirmation. Here, we used an innovative strategy to determine COs genome-wide in S. pombe. We confirmed weak CO interference, acting at physical distances compatible with the patterning of recombination precursors. We revealed a slight co-variation in CO number between chromosomes, suggesting that a limiting pro-CO factor varies between meiocytes. CO number per chromosome varies proportionally with chromosome size, with the three chromosomes having, on average, 15.9, 12.5, and 7.0 COs, respectively. This reinforces S. pombe's status as the eukaryote with the highest CO number per chromosome described to date.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Maxime Gaudin
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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5
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Fan S, Wang Y, Jiang H, Jiang X, Zhou J, Jiao Y, Ye J, Xu Z, Wang Y, Xie X, Zhang H, Li Y, Liu W, Zhang X, Ma H, Shi B, Zhang Y, Zubair M, Shah W, Xu Z, Xu B, Shi Q. A novel recombination protein C12ORF40/REDIC1 is required for meiotic crossover formation. Cell Discov 2023; 9:88. [PMID: 37612290 PMCID: PMC10447524 DOI: 10.1038/s41421-023-00577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 08/25/2023] Open
Abstract
During meiosis, at least one crossover must occur per homologous chromosome pair to ensure normal progression of meiotic division and accurate chromosome segregation. However, the mechanism of crossover formation is not fully understood. Here, we report a novel recombination protein, C12ORF40/REDIC1, essential for meiotic crossover formation in mammals. A homozygous frameshift mutation in C12orf40 (c.232_233insTT, p.Met78Ilefs*2) was identified in two infertile men with meiotic arrest. Spread mouse spermatocyte fluorescence immunostaining showed that REDIC1 forms discrete foci between the paired regions of homologous chromosomes depending on strand invasion and colocalizes with MSH4 and later with MLH1 at the crossover sites. Redic1 knock-in (KI) mice homozygous for mutation c.232_233insTT are infertile in both sexes due to insufficient crossovers and consequent meiotic arrest, which is also observed in our patients. The foci of MSH4 and TEX11, markers of recombination intermediates, are significantly reduced numerically in the spermatocytes of Redic1 KI mice. More importantly, our biochemical results show that the N-terminus of REDIC1 binds branched DNAs present in recombination intermediates, while the identified mutation impairs this interaction. Thus, our findings reveal a crucial role for C12ORF40/REDIC1 in meiotic crossover formation by stabilizing the recombination intermediates, providing prospective molecular targets for the clinical diagnosis and therapy of infertility.
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Affiliation(s)
- Suixing Fan
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuewen Wang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Hanwei Jiang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaohua Jiang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianteng Zhou
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuying Jiao
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Jingwei Ye
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Zishuo Xu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Yue Wang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Xuefeng Xie
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Huan Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Yang Li
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei Liu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiangjun Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Hui Ma
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Baolu Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuanwei Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Muhammad Zubair
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Wasim Shah
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhipeng Xu
- Institute of Andrology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China.
| | - Bo Xu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China.
| | - Qinghua Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, Anhui, China.
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6
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Tsui V, Lyu R, Novakovic S, Stringer JM, Dunleavy JE, Granger E, Semple T, Leichter A, Martelotto LG, Merriner DJ, Liu R, McNeill L, Zerafa N, Hoffmann ER, O’Bryan MK, Hutt K, Deans AJ, Heierhorst J, McCarthy DJ, Crismani W. Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals. CELL GENOMICS 2023; 3:100349. [PMID: 37601968 PMCID: PMC10435384 DOI: 10.1016/j.xgen.2023.100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/30/2023] [Accepted: 06/02/2023] [Indexed: 08/22/2023]
Abstract
Meiotic crossovers are required for accurate chromosome segregation and producing new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. Here, we reveal the tumor suppressor FANCM as a meiotic anti-crossover factor in mammals. We use unique large-scale crossover analyses with both single-gamete sequencing and pedigree-based bulk-sequencing datasets to identify a genome-wide increase in crossover frequencies in Fancm-deficient mice. Gametogenesis is heavily perturbed in Fancm loss-of-function mice, which is consistent with the reproductive defects reported in humans with biallelic FANCM mutations. A portion of the gametogenesis defects can be attributed to the cGAS-STING pathway after birth. Despite the gametogenesis phenotypes in Fancm mutants, both sexes are capable of producing offspring. We propose that the anti-crossover function and role in gametogenesis of Fancm are separable and will inform diagnostic pathways for human genomic instability disorders.
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Affiliation(s)
- Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Stevan Novakovic
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jessica M. Stringer
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Jessica E.M. Dunleavy
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Elissah Granger
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Tim Semple
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Anna Leichter
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Luciano G. Martelotto
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - D. Jo Merriner
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruijie Liu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Lucy McNeill
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Nadeen Zerafa
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Eva R. Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Moira K. O’Bryan
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Deans
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Genome Stability Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jörg Heierhorst
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Molecular Genetics Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
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7
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Draeger TN, Rey MD, Hayta S, Smedley M, Alabdullah AK, Moore G, Martín AC. ZIP4 is required for normal progression of synapsis and for over 95% of crossovers in wheat meiosis. FRONTIERS IN PLANT SCIENCE 2023; 14:1189998. [PMID: 37324713 PMCID: PMC10266424 DOI: 10.3389/fpls.2023.1189998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023]
Abstract
Tetraploid (AABB) and hexaploid (AABBDD) wheat have multiple sets of similar chromosomes, with successful meiosis and preservation of fertility relying on synapsis and crossover (CO) formation only taking place between homologous chromosomes. In hexaploid wheat, the major meiotic gene TaZIP4-B2 (Ph1) on chromosome 5B, promotes CO formation between homologous chromosomes, whilst suppressing COs between homeologous (related) chromosomes. In other species, ZIP4 mutations eliminate approximately 85% of COs, consistent with loss of the class I CO pathway. Tetraploid wheat has three ZIP4 copies: TtZIP4-A1 on chromosome 3A, TtZIP4-B1 on 3B and TtZIP4-B2 on 5B. Here, we have developed single, double and triple zip4 TILLING mutants and a CRISPR Ttzip4-B2 mutant, to determine the effect of ZIP4 genes on synapsis and CO formation in the tetraploid wheat cultivar 'Kronos'. We show that disruption of two ZIP4 gene copies in Ttzip4-A1B1 double mutants, results in a 76-78% reduction in COs when compared to wild-type plants. Moreover, when all three copies are disrupted in Ttzip4-A1B1B2 triple mutants, COs are reduced by over 95%, suggesting that the TtZIP4-B2 copy may also affect class II COs. If this is the case, the class I and class II CO pathways may be interlinked in wheat. When ZIP4 duplicated and diverged from chromosome 3B on wheat polyploidization, the new 5B copy, TaZIP4-B2, could have acquired an additional function to stabilize both CO pathways. In tetraploid plants deficient in all three ZIP4 copies, synapsis is delayed and does not complete, consistent with our previous studies in hexaploid wheat, when a similar delay in synapsis was observed in a 59.3 Mb deletion mutant, ph1b, encompassing the TaZIP4-B2 gene on chromosome 5B. These findings confirm the requirement of ZIP4-B2 for efficient synapsis, and suggest that TtZIP4 genes have a stronger effect on synapsis than previously described in Arabidopsis and rice. Thus, ZIP4-B2 in wheat accounts for the two major phenotypes reported for Ph1, promotion of homologous synapsis and suppression of homeologous COs.
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Affiliation(s)
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Azahara C. Martín
- Department of Plant Genetic Improvement, Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
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8
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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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9
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Kudryavtseva N, Ermolaev A, Pivovarov A, Simanovsky S, Odintsov S, Khrustaleva L. The Control of the Crossover Localization in Allium. Int J Mol Sci 2023; 24:ijms24087066. [PMID: 37108228 PMCID: PMC10138942 DOI: 10.3390/ijms24087066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Meiotic crossovers/chiasmata are not randomly distributed and strictly controlled. The mechanisms behind crossover (CO) patterning remain largely unknown. In Allium cepa, as in the vast majority of plants and animals, COs predominantly occur in the distal 2/3 of the chromosome arm, while in Allium fistulosum they are strictly localized in the proximal region. We investigated the factors that may contribute to the pattern of COs in A. cepa, A. fistulosum and their F1 diploid (2n = 2x = 8C + 8F) and F1 triploid (2n = 3x = 16F + 8C) hybrids. The genome structure of F1 hybrids was confirmed using genomic in situ hybridization (GISH). The analysis of bivalents in the pollen mother cells (PMCs) of the F1 triploid hybrid showed a significant shift in the localization of COs to the distal and interstitial regions. In F1 diploid hybrid, the COs localization was predominantly the same as that of the A. cepa parent. We found no differences in the assembly and disassembly of ASY1 and ZYP1 in PMCs between A. cepa and A. fistulosum, while F1 diploid hybrid showed a delay in chromosome pairing and a partial absence of synapsis in paired chromosomes. Immunolabeling of MLH1 (class I COs) and MUS81 (class II COs) proteins showed a significant difference in the class I/II CO ratio between A. fistulosum (50%:50%) and A. cepa (73%:27%). The MLH1:MUS81 ratio at the homeologous synapsis of F1 diploid hybrid (70%:30%) was the most similar to that of the A. cepa parent. F1 triploid hybrid at the A. fistulosum homologous synapsis showed a significant increase in MLH1:MUS81 ratio (60%:40%) compared to the A. fistulosum parent. The results suggest possible genetic control of CO localization. Other factors affecting the distribution of COs are discussed.
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Affiliation(s)
- Natalia Kudryavtseva
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Aleksey Ermolaev
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Anton Pivovarov
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Sergey Simanovsky
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prosp., Moscow 119071, Russia
| | - Sergey Odintsov
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Ludmila Khrustaleva
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
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10
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Mu N, Li Y, Li S, Shi W, Shen Y, Yang H, Zhang F, Tang D, Du G, You A, Cheng Z. MUS81 is required for atypical recombination intermediate resolution but not crossover designation in rice. THE NEW PHYTOLOGIST 2023; 237:2422-2434. [PMID: 36495065 DOI: 10.1111/nph.18668] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The endonuclease methyl methanesulfonate and UV-sensitive protein 81 (MUS81) has been reported to participate in DNA repair during mitosis and meiosis. However, the exact meiotic function of MUS81 in rice remains unclear. Here, we use a combination of physiological, cytological, and genetic approaches to provide evidence that MUS81 functions in atypical recombination intermediate resolution rather than crossover designation in rice. Cytological and genetic analysis revealed that the total chiasma numbers in mus81 mutants were indistinguishable from wild-type. The numbers of HEI10 foci (the sites of interference-sensitive crossovers) in mus81 were also similar to that of wild-type. Moreover, disruption of MUS81 in msh5 or msh4 msh5 background did not further decrease chiasmata frequency, suggesting that rice MUS81 did not function in crossover designation. Mutation of FANCM and ZEP1 could enhance recombination frequency. Unexpectedly, chromosome fragments and bridges were frequently observed in mus81 zep1 and mus81 fancm, illustrating that MUS81 may resolve atypical recombination intermediates. Taken together, our data suggest that MUS81 contributes little to crossover designation but plays a crucial role in the resolution of atypical meiotic intermediates by working together with other anti-crossover factors.
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Affiliation(s)
- Na Mu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 225009, Yangzhou, China
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yafei Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sanhe Li
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Wenqing Shi
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yi Shen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Han Yang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fanfan Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Ding Tang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Guijie Du
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Aiqing You
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zhukuan Cheng
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 225009, Yangzhou, China
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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11
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de Almeida BRR, Noronha RCR, Cardoso AL, Martins C, Martins JG, Procópio REDL, Nagamachi CY, Pieczarka JC. Kinetic Activity of Chromosomes and Expression of Recombination Genes in Achiasmatic Meiosis of Tityus (Archaeotityus) Scorpions. Int J Mol Sci 2022; 23:ijms23169179. [PMID: 36012447 PMCID: PMC9408970 DOI: 10.3390/ijms23169179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/18/2022] Open
Abstract
Several species of Tityus (Scorpiones, Buthidae) present multi-chromosomal meiotic associations and failures in the synaptic process, originated from reciprocal translocations. Holocentric chromosomes and achiasmatic meiosis in males are present in all members of this genus. In the present study, we investigated synapse dynamics, transcriptional silencing by γH2AX, and meiotic microtubule association in bivalents and a quadrivalent of the scorpion Tityus maranhensis. Additionally, we performed RT-PCR to verify the expression of mismatch repair enzymes involved in crossing-over formation in Tityus silvestris gonads. The quadrivalent association in T. maranhensis showed delay in the synaptic process and long asynaptic regions during pachytene. In this species, γH2AX was recorded only at the chromosome ends during early stages of prophase I; in metaphase I, bivalents and quadrivalents of T. maranhensis exhibited binding to microtubules along their entire length, while in metaphase II/anaphase II transition, spindle fibers interacted only with telomeric regions. Regarding T. silvestris, genes involved in the recombination process were transcribed in ovaries, testes and embryos, without significant difference between these tissues. The expression of these genes during T. silvestris achiasmatic meiosis is discussed in the present study. The absence of meiotic inactivation by γH2AX and holo/telokinetic behavior of the chromosomes are important factors for the maintenance of the quadrivalent in T. maranhensis and the normal continuation of the meiotic cycle in this species.
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Affiliation(s)
- Bruno Rafael Ribeiro de Almeida
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Avenida Perimetral da Ciência, km 01, Guamá, Belem 66075-750, PA, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Pará, Campus Itaituba, R. Universitário, s/n, Maria Magdalena, Itaituba 68183-300, PA, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Avenida Perimetral da Ciência, km 01, Guamá, Belem 66075-750, PA, Brazil
| | - Adauto Lima Cardoso
- Laboratório Genômica Integrativa, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Júnior, s/n, Rubião Júnior, Botucatu 18618970, SP, Brazil
| | - Cesar Martins
- Laboratório Genômica Integrativa, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Júnior, s/n, Rubião Júnior, Botucatu 18618970, SP, Brazil
| | - Jonas Gama Martins
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936-Petrópolis, Manaus 69067-375, AM, Brazil
| | - Rudi Emerson de Lima Procópio
- Programa de Pós-Graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas (UEA), Avenida Carvalho Leal, 1777-Cachoeirinha, Manaus 69065-170, AM, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Avenida Perimetral da Ciência, km 01, Guamá, Belem 66075-750, PA, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Avenida Perimetral da Ciência, km 01, Guamá, Belem 66075-750, PA, Brazil
- Correspondence:
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12
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Lorenz A, Mpaulo SJ. Gene conversion: a non-Mendelian process integral to meiotic recombination. Heredity (Edinb) 2022; 129:56-63. [PMID: 35393552 PMCID: PMC9273591 DOI: 10.1038/s41437-022-00523-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 12/30/2022] Open
Abstract
Meiosis is undoubtedly the mechanism that underpins Mendelian genetics. Meiosis is a specialised, reductional cell division which generates haploid gametes (reproductive cells) carrying a single chromosome complement from diploid progenitor cells harbouring two chromosome sets. Through this process, the hereditary material is shuffled and distributed into haploid gametes such that upon fertilisation, when two haploid gametes fuse, diploidy is restored in the zygote. During meiosis the transient physical connection of two homologous chromosomes (one originally inherited from each parent) each consisting of two sister chromatids and their subsequent segregation into four meiotic products (gametes), is what enables genetic marker assortment forming the core of Mendelian laws. The initiating events of meiotic recombination are DNA double-strand breaks (DSBs) which need to be repaired in a certain way to enable the homologous chromosomes to find each other. This is achieved by DSB ends searching for homologous repair templates and invading them. Ultimately, the repair of meiotic DSBs by homologous recombination physically connects homologous chromosomes through crossovers. These physical connections provided by crossovers enable faithful chromosome segregation. That being said, the DSB repair mechanism integral to meiotic recombination also produces genetic transmission distortions which manifest as postmeiotic segregation events and gene conversions. These processes are non-reciprocal genetic exchanges and thus non-Mendelian.
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Affiliation(s)
- Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK.
| | - Samantha J Mpaulo
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK
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13
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Hua Z, Fang Q, Zhang D, Luo Z, Yuan C, Lin Z. Crystal structure of the human MUS81-EME2 complex. Structure 2022; 30:743-752.e3. [DOI: 10.1016/j.str.2022.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/27/2022] [Accepted: 02/16/2022] [Indexed: 10/18/2022]
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14
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Oh JM, Myung K. Crosstalk between different DNA repair pathways for DNA double strand break repairs. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 873:503438. [PMID: 35094810 DOI: 10.1016/j.mrgentox.2021.503438] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022]
Abstract
DNA double strand breaks (DSBs) are the most threatening type of DNA lesions and must be repaired properly in order to inhibit severe diseases and cell death. There are four major repair pathways for DSBs: non-homologous end joining (NHEJ), homologous recombination (HR), single strand annealing (SSA) and alternative end joining (alt-EJ). Cells choose repair pathway depending on the cell cycle phase and the length of 3' end of the DNA when DSBs are generated. Blunt and short regions of the 5' or 3' overhang DNA are repaired by NHEJ, which uses direct ligation or limited resection processing of the broken DNA end. In contrast, HR, SSA and alt-EJ use the resected DNA generated by the MRN (MRE11-RAD50-NBS1) complex and C-terminal binding protein interacting protein (CtIP) activated during the S and G2 phases. Here, we review recent findings on each repair pathway and the choice of repair mechanism and highlight the role of mismatch repair (MMR) protein in HR.
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Affiliation(s)
- Jung-Min Oh
- Department of Oral Biochemistry, Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea.
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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15
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Carreira R, Aguado FJ, Hurtado-Nieves V, Blanco MG. Canonical and novel non-canonical activities of the Holliday junction resolvase Yen1. Nucleic Acids Res 2021; 50:259-280. [PMID: 34928393 PMCID: PMC8754655 DOI: 10.1093/nar/gkab1225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/12/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
Yen1 and GEN1 are members of the Rad2/XPG family of nucleases that were identified as the first canonical nuclear Holliday junction (HJ) resolvases in budding yeast and humans due to their ability to introduce two symmetric, coordinated incisions on opposite strands of the HJ, yielding nicked DNA products that could be readily ligated. While GEN1 has been extensively characterized in vitro, much less is known about the biochemistry of Yen1. Here, we have performed the first in-depth characterization of purified Yen1. We confirmed that Yen1 resembles GEN1 in many aspects, including range of substrates targeted, position of most incisions they produce or the increase in the first incision rate by assembly of a dimer on a HJ, despite minor differences. However, we demonstrate that Yen1 is endowed with additional nuclease activities, like a nick-specific 5′-3′ exonuclease or HJ arm-chopping that could apparently blur its classification as a canonical HJ resolvase. Despite this, we show that Yen1 fulfils the requirements of a canonical HJ resolvase and hypothesize that its wider array of nuclease activities might contribute to its function in the removal of persistent recombination or replication intermediates.
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Affiliation(s)
- Raquel Carreira
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - F Javier Aguado
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Vanesa Hurtado-Nieves
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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16
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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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17
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Bittmann J, Grigaitis R, Galanti L, Amarell S, Wilfling F, Matos J, Pfander B. An advanced cell cycle tag toolbox reveals principles underlying temporal control of structure-selective nucleases. eLife 2020; 9:e52459. [PMID: 32352375 PMCID: PMC7220381 DOI: 10.7554/elife.52459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/29/2020] [Indexed: 12/26/2022] Open
Abstract
Cell cycle tags allow to restrict target protein expression to specific cell cycle phases. Here, we present an advanced toolbox of cell cycle tag constructs in budding yeast with defined and compatible peak expression that allow comparison of protein functionality at different cell cycle phases. We apply this technology to the question of how and when Mus81-Mms4 and Yen1 nucleases act on DNA replication or recombination structures. Restriction of Mus81-Mms4 to M phase but not S phase allows a wildtype response to various forms of replication perturbation and DNA damage in S phase, suggesting it acts as a post-replicative resolvase. Moreover, we use cell cycle tags to reinstall cell cycle control to a deregulated version of Yen1, showing that its premature activation interferes with the response to perturbed replication. Curbing resolvase activity and establishing a hierarchy of resolution mechanisms are therefore the principal reasons underlying resolvase cell cycle regulation.
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Affiliation(s)
- Julia Bittmann
- Max Planck Institute of Biochemistry, DNA Replication and Genome IntegrityMartinsriedGermany
| | - Rokas Grigaitis
- Institute of Biochemistry, Eidgenössische Technische Hochschule, ZürichZürichSwitzerland
| | - Lorenzo Galanti
- Max Planck Institute of Biochemistry, DNA Replication and Genome IntegrityMartinsriedGermany
| | - Silas Amarell
- Max Planck Institute of Biochemistry, DNA Replication and Genome IntegrityMartinsriedGermany
| | - Florian Wilfling
- Max Planck Institute of Biochemistry, Molecular Cell BiologyMartinsriedGermany
| | - Joao Matos
- Institute of Biochemistry, Eidgenössische Technische Hochschule, ZürichZürichSwitzerland
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome IntegrityMartinsriedGermany
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18
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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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19
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Brown SD, Audoynaud C, Lorenz A. Intragenic meiotic recombination in Schizosaccharomyces pombe is sensitive to environmental temperature changes. Chromosome Res 2020; 28:195-207. [PMID: 32303869 PMCID: PMC7242256 DOI: 10.1007/s10577-020-09632-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 11/25/2022]
Abstract
Changes in environmental temperature influence cellular processes and their dynamics, and thus affect the life cycle of organisms that are unable to control their cell/body temperature. Meiotic recombination is the cellular process essential for producing healthy haploid gametes by providing physical links (chiasmata) between homologous chromosomes to guide their accurate segregation. Additionally, meiotic recombination—initiated by programmed DNA double-strand breaks (DSBs)—can generate genetic diversity and, therefore, is a driving force of evolution. Environmental temperature influencing meiotic recombination outcome thus may be a crucial determinant of reproductive success and genetic diversity. Indeed, meiotic recombination frequency in fungi, plants and invertebrates changes with temperature. In most organisms, these temperature-induced changes in meiotic recombination seem to be mediated through the meiosis-specific chromosome axis organization, the synaptonemal complex in particular. The fission yeast Schizosaccharomyces pombe does not possess a synaptonemal complex. Thus, we tested how environmental temperature modulates meiotic recombination frequency in the absence of a fully-fledged synaptonemal complex. We show that intragenic recombination (gene conversion) positively correlates with temperature within a certain range, especially at meiotic recombination hotspots. In contrast, crossover recombination, which manifests itself as chiasmata, is less affected. Based on our observations, we suggest that, in addition to changes in DSB frequency, DSB processing could be another temperature-sensitive step causing temperature-induced recombination rate alterations.
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Affiliation(s)
- Simon D Brown
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Charlotte Audoynaud
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- Institut Curie, PSL Research University, UMR3348-CNRS, 91405, Orsay, France
| | - Alexander Lorenz
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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20
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de Maagd RA, Loonen A, Chouaref J, Pelé A, Meijer‐Dekens F, Fransz P, Bai Y. CRISPR/Cas inactivation of RECQ4 increases homeologous crossovers in an interspecific tomato hybrid. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:805-813. [PMID: 31483929 PMCID: PMC7004904 DOI: 10.1111/pbi.13248] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/10/2019] [Accepted: 08/15/2019] [Indexed: 05/05/2023]
Abstract
Crossover formation during meiosis in plants is required for proper chromosome segregation and is essential for crop breeding as it allows an (optimal) combination of traits by mixing parental alleles on each chromosome. Crossover formation commences with the production of a large number of DNA double-strand breaks, of which only a few result in crossovers. A small number of genes, which drive the resolution of DNA crossover intermediate structures towards non-crossovers, have been identified in Arabidopisis thaliana. In order to explore the potential of modification of these genes in interspecific hybrids between crops and their wild relatives towards increased production of crossovers, we have used CRISPR/Cas9-mutagenesis in an interspecific tomato hybrid to knockout RecQ4. A biallelic recq4 mutant was obtained in the F1 hybrid of Solanum lycopersicum and S. pimpinellifolium. Compared with the wild-type F1 hybrid, the F1 recq4 mutant was shown to have a significant increase in crossovers: a 1.53-fold increase when directly observing ring bivalents in male meiocytes microscopically and a 1.8-fold extension of the genetic map when measured by analysing SNP markers in the progeny (F2) plants. This is one of the first demonstrations of increasing crossover frequency in interspecific hybrids by manipulating genes in crossover intermediate resolution pathways and the first to do so by directed mutagenesis. SIGNIFICANCE STATEMENT: Increasing crossover frequency during meiosis can speed up or simplify crop breeding that relies on meiotic crossovers to introduce favourable alleles controlling important traits from wild relatives into crops. Here we show for the first time that knocking out an inhibitor of crossovers in an interspecific hybrid between tomato and its relative wild species using CRISPR/Cas9-mutagenesis results in increased recombination between the two genomes.
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Affiliation(s)
- Ruud A. de Maagd
- BioscienceCluster Plant Developmental SystemsWageningen University & ResearchWageningenThe Netherlands
- Bioinformatics GroupWageningen University & ResearchWageningenThe Netherlands
| | - Annelies Loonen
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Jihed Chouaref
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - Alexandre Pelé
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | | | - Paul Fransz
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - Yuling Bai
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
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21
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Brown SD, Mpaulo SJ, Asogwa MN, Jézéquel M, Whitby MC, Lorenz A. DNA sequence differences are determinants of meiotic recombination outcome. Sci Rep 2019; 9:16446. [PMID: 31712578 PMCID: PMC6848502 DOI: 10.1038/s41598-019-52907-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/25/2019] [Indexed: 11/08/2022] Open
Abstract
Meiotic recombination is essential for producing healthy gametes, and also generates genetic diversity. DNA double-strand break (DSB) formation is the initiating step of meiotic recombination, producing, among other outcomes, crossovers between homologous chromosomes (homologs), which provide physical links to guide accurate chromosome segregation. The parameters influencing DSB position and repair are thus crucial determinants of reproductive success and genetic diversity. Using Schizosaccharomyces pombe, we show that the distance between sequence polymorphisms across homologs has a strong impact on meiotic recombination rate. The closer the sequence polymorphisms are to each other across the homologs the fewer recombination events were observed. In the immediate vicinity of DSBs, sequence polymorphisms affect the frequency of intragenic recombination events (gene conversions). Additionally, and unexpectedly, the crossover rate of flanking markers tens of kilobases away from the sequence polymorphisms was affected by their relative position to each other amongst the progeny having undergone intragenic recombination. A major regulator of this distance-dependent effect is the MutSα-MutLα complex consisting of Msh2, Msh6, Mlh1, and Pms1. Additionally, the DNA helicases Rqh1 and Fml1 shape recombination frequency, although the effects seen here are largely independent of the relative position of the sequence polymorphisms.
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Affiliation(s)
- Simon D Brown
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Samantha J Mpaulo
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Mimi N Asogwa
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Marie Jézéquel
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Alexander Lorenz
- The Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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22
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Palmer N, Talib SZA, Kaldis P. Diverse roles for CDK-associated activity during spermatogenesis. FEBS Lett 2019; 593:2925-2949. [PMID: 31566717 PMCID: PMC6900092 DOI: 10.1002/1873-3468.13627] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
The primary function of cyclin-dependent kinases (CDKs) in complex with their activating cyclin partners is to promote mitotic division in somatic cells. This canonical cell cycle-associated activity is also crucial for fertility as it allows the proliferation and differentiation of stem cells within the reproductive organs to generate meiotically competent cells. Intriguingly, several CDKs exhibit meiosis-specific functions and are essential for the completion of the two reductional meiotic divisions required to generate haploid gametes. These meiosis-specific functions are mediated by both known CDK/cyclin complexes and meiosis-specific CDK-regulators and are important for a variety of processes during meiotic prophase. The majority of meiotic defects observed upon deletion of these proteins occur during the extended prophase I of the first meiotic division. Importantly a lack of redundancy is seen within the meiotic arrest phenotypes described for many of these proteins, suggesting intricate layers of cell cycle control are required for normal meiotic progression. Using the process of male germ cell development (spermatogenesis) as a reference, this review seeks to highlight the diverse roles of selected CDKs their activators, and their regulators during gametogenesis.
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Affiliation(s)
- Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore.,Department of Biochemistry, National University of Singapore (NUS), Singapore, Singapore
| | - S Zakiah A Talib
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore.,Department of Biochemistry, National University of Singapore (NUS), Singapore, Singapore.,Department of Clinical Sciences, Clinical Research Centre (CRC), Lund University, Malmö, Sweden
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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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Ren Y, Chen D, Li W, Zhou D, Luo T, Yuan G, Zeng J, Cao Y, He Z, Zou T, Deng Q, Wang S, Zheng A, Zhu J, Liang Y, Liu H, Wang L, Li P, Li S. OsSHOC1 and OsPTD1 are essential for crossover formation during rice meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:315-328. [PMID: 30589140 DOI: 10.1111/tpj.14214] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Meiosis is essential for eukaryotic sexual reproduction and plant fertility, and crossovers (COs) are essential for meiosis and the formation of new allelic combinations in gametes. In this study, we report the isolation of a meiotic gene, OsSHOC1, and the identification of its partner, OsPTD1. Osshoc1 was sterile both in male and female gametophytes, and it showed a striking reduction in the number of meiotic COs, indicating that OsSHOC1 was required for normal CO formation. Further investigations showed that OsSHOC1 physically interacted with OsPTD1 and that the latter was also required for normal CO formation and plant fertility. Additionally, the expression profiles of both genes were consistent with their functions. Our results suggest that OsSHOC1 and OsPTD1 are essential for rice fertility and CO formation, possibly by stabilizing the recombinant intermediates during meiosis.
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Affiliation(s)
- Yun Ren
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
- Chongqing Key Laboratory of Economic Plant Biotechnology/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Dan Chen
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Wenjie Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Dan Zhou
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Tao Luo
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Guoqiang Yuan
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Jing Zeng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Ye Cao
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Zhongshan He
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Ting Zou
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Aiping Zheng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Yueyang Liang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Huainian Liu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Lingxia Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Shuangcheng Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, 611130, Sichuan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
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25
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Pai CC, Hsu KF, Durley SC, Keszthelyi A, Kearsey SE, Rallis C, Folkes LK, Deegan R, Wilkins SE, Pfister SX, De León N, Schofield CJ, Bähler J, Carr AM, Humphrey TC. An essential role for dNTP homeostasis following CDK-induced replication stress. J Cell Sci 2019; 132:jcs226969. [PMID: 30674555 PMCID: PMC6451416 DOI: 10.1242/jcs.226969] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/02/2019] [Indexed: 02/03/2023] Open
Abstract
Replication stress is a common feature of cancer cells, and thus a potentially important therapeutic target. Here, we show that cyclin-dependent kinase (CDK)-induced replication stress, resulting from Wee1 inactivation, is synthetic lethal with mutations disrupting dNTP homeostasis in fission yeast. Wee1 inactivation leads to increased dNTP demand and replication stress through CDK-induced firing of dormant replication origins. Subsequent dNTP depletion leads to inefficient DNA replication, DNA damage and to genome instability. Cells respond to this replication stress by increasing dNTP supply through histone methyltransferase Set2-dependent MBF-induced expression of Cdc22, the catalytic subunit of ribonucleotide reductase (RNR). Disrupting dNTP synthesis following Wee1 inactivation, through abrogating Set2-dependent H3K36 tri-methylation or DNA integrity checkpoint inactivation results in critically low dNTP levels, replication collapse and cell death, which can be rescued by increasing dNTP levels. These findings support a 'dNTP supply and demand' model in which maintaining dNTP homeostasis is essential to prevent replication catastrophe in response to CDK-induced replication stress.
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Affiliation(s)
- Chen-Chun Pai
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Kuo-Feng Hsu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Centre, Taipei 114, Taiwan
| | - Samuel C Durley
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex, BN1 9RQ, UK
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, Zoology Research & Administration Building, Mansfield Road, Oxford, OX1 3PS, UK
| | - Charalampos Rallis
- Research Department of Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
- School of Health, Sport and Bioscience, University of East London, Stratford Campus, E15 4LZ, London, UK
| | - Lisa K Folkes
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Rachel Deegan
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Sarah E Wilkins
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Sophia X Pfister
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Nagore De León
- Department of Zoology, University of Oxford, Zoology Research & Administration Building, Mansfield Road, Oxford, OX1 3PS, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex, BN1 9RQ, UK
| | - Timothy C Humphrey
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
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Bauer SL, Chen J, Åström SU. Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1. PLoS One 2019; 14:e0214102. [PMID: 30897139 PMCID: PMC6428284 DOI: 10.1371/journal.pone.0214102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/06/2019] [Indexed: 11/30/2022] Open
Abstract
Resolution of branched DNA structures is pivotal for repair of stalled replication forks and meiotic recombination intermediates. The Yen1 nuclease cleaves both Holliday junctions and replication forks. We show that Yen1 interacts physically with Uls1, a suggested SUMO-targeted ubiquitin ligase that also contains a SWI/SNF-family ATPase-domain. Yen1 is SUMO-modified in its noncatalytic carboxyl terminus and DNA damage induces SUMOylation. SUMO-modification of Yen1 strengthens the interaction to Uls1, and mutations in SUMO interaction motifs in Uls1 weakens the interaction. However, Uls1 does not regulate the steady-state level of SUMO-modified Yen1 or chromatin-associated Yen1. In addition, SUMO-modification of Yen1 does not affect the catalytic activity in vitro. Consistent with a shared function for Uls1 and Yen1, mutations in both genes display similar phenotypes. Both uls1 and yen1 display negative genetic interactions with the alternative HJ-cleaving nuclease Mus81, manifested both in hypersensitivity to DNA damaging agents and in meiotic defects. Point mutations in ULS1 (uls1K975R and uls1C1330S, C1333S) predicted to inactivate the ATPase and ubiquitin ligase activities, respectively, are as defective as the null allele, indicating that both functions of Uls1 are essential. A micrococcal nuclease sequencing experiment showed that Uls1 had minimal effects on global nucleosome positioning/occupancy. Moreover, increased gene dosage of YEN1 partially alleviates the mus81 uls1 sensitivity to DNA damage. We suggest a preliminary model in which Uls1 acts in the same pathway as Yen1 to resolve branched DNA structures.
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Affiliation(s)
- Stefanie L. Bauer
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jiang Chen
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Stefan U. Åström
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail:
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Li D, Roca M, Yuecel R, Lorenz A. Immediate visualization of recombination events and chromosome segregation defects in fission yeast meiosis. Chromosoma 2019; 128:385-396. [PMID: 30739171 PMCID: PMC6823302 DOI: 10.1007/s00412-019-00691-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 02/07/2023]
Abstract
Schizosaccharomyces pombe, also known as fission yeast, is an established model for studying chromosome biological processes. Over the years, research employing fission yeast has made important contributions to our knowledge about chromosome segregation during meiosis, as well as meiotic recombination and its regulation. Quantification of meiotic recombination frequency is not a straightforward undertaking, either requiring viable progeny for a genetic plating assay, or relying on laborious Southern blot analysis of recombination intermediates. Neither of these methods lends itself to high-throughput screens to identify novel meiotic factors. Here, we establish visual assays novel to Sz. pombe for characterizing chromosome segregation and meiotic recombination phenotypes. Genes expressing red, yellow, and/or cyan fluorophores from spore-autonomous promoters have been integrated into the fission yeast genomes, either close to the centromere of chromosome 1 to monitor chromosome segregation, or on the arm of chromosome 3 to form a genetic interval at which recombination frequency can be determined. The visual recombination assay allows straightforward and immediate assessment of the genetic outcome of a single meiosis by epi-fluorescence microscopy without requiring tetrad dissection. We also demonstrate that the recombination frequency analysis can be automatized by utilizing imaging flow cytometry to enable high-throughput screens. These assays have several advantages over traditional methods for analyzing meiotic phenotypes.
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Affiliation(s)
- Dmitriy Li
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- Iain Fraser Cytometry Centre (IFCC), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Marianne Roca
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, 06230, Villefranche-sur-Mer, France
| | - Raif Yuecel
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- Iain Fraser Cytometry Centre (IFCC), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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Marsolier-Kergoat MC, Khan MM, Schott J, Zhu X, Llorente B. Mechanistic View and Genetic Control of DNA Recombination during Meiosis. Mol Cell 2019; 70:9-20.e6. [PMID: 29625041 DOI: 10.1016/j.molcel.2018.02.032] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/07/2017] [Accepted: 02/26/2018] [Indexed: 10/17/2022]
Abstract
Meiotic recombination is essential for fertility and allelic shuffling. Canonical recombination models fail to capture the observed complexity of meiotic recombinants. Here, by combining genome-wide meiotic heteroduplex DNA patterns with meiotic DNA double-strand break (DSB) sites, we show that part of this complexity results from frequent template switching during synthesis-dependent strand annealing that yields noncrossovers and from branch migration of double Holliday junction (dHJ)-containing intermediates that mainly yield crossovers. This complexity also results from asymmetric positioning of crossover intermediates relative to the initiating DSB and Msh2-independent conversions promoted by the suspected dHJ resolvase Mlh1-3 as well as Exo1 and Sgs1. Finally, we show that dHJ resolution is biased toward cleavage of the pair of strands containing newly synthesized DNA near the junctions and that this bias can be decoupled from the crossover-biased dHJ resolution. These properties are likely conserved in eukaryotes containing ZMM proteins, which includes mammals.
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Affiliation(s)
- Marie-Claude Marsolier-Kergoat
- CEA/DRF, I2BC/UMR 9198, SBIGeM, Gif-sur-Yvette, France; CNRS-UMR 7206, Éco-anthropologie et Ethnobiologie, Musée de l'Homme, 17, Place du Trocadéro et du 11 Novembre, Paris, France.
| | - Md Muntaz Khan
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Jonathan Schott
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Xuan Zhu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center and Howard Hughes Medical Institute, New York, NY, USA
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France.
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Jimeno S, Mejías-Navarro F, Prados-Carvajal R, Huertas P. Controlling the balance between chromosome break repair pathways. DNA Repair (Amst) 2019; 115:95-134. [DOI: 10.1016/bs.apcsb.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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30
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Lahiri S, Li Y, Hingorani MM, Mukerji I. MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination. Biophys J 2018; 115:2087-2101. [PMID: 30467025 DOI: 10.1016/j.bpj.2018.10.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 01/11/2023] Open
Abstract
In many organisms, MutSγ plays a role in meiotic recombination, facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans result in infertility and birth defects. To improve current understanding of MutSγ function, this study investigates the binding affinities and structures of MutSγ in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSγ protein Saccharomyces cerevisiae (Sc) Msh4-Msh5. Sc Msh4-Msh5 binds Holliday junction (HJ)-like substrates, 3' overhangs, single-stranded (ss) forks, and the displacement loop with nanomolar affinity. The weakest binding affinities are detected for an intact duplex and open-junction construct. Similar to the human protein, Sc Msh4-Msh5 exhibits the highest affinity for the HJ with a Kd < 0.4 nM in solution. Energy-transfer experiments further demonstrate that DNA structure is modulated by the binding interaction with the largest changes associated with substrates containing an ss end. Upon binding, Sc Msh4-Msh5 displaces the ss away from the duplex in most of the ss-containing intermediates, potentially enabling the binding of RPA and other proteins. In the case of the junction-like intermediates, Msh4-Msh5 binding either stabilizes the existing stacked structure or induces formation of the stacked X conformation. Significantly, we find that upon binding, Msh4-Msh5 stacks an open-junction construct to the same extent as the standard junction. Stabilization of the junction in the stacked conformation is generally refractory to branch migration, which is consistent with a potential role for MutSγ to stabilize HJs and prevent branch migration until resolution by MutLγ. The different binding modalities observed suggest that Msh4-Msh5 not only binds to and stabilizes stacked junctions but also participates in meiotic recombination before junction formation through the stabilization of single-end invasion intermediates.
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Affiliation(s)
- Sudipta Lahiri
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Yan Li
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut.
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Arter M, Hurtado-Nieves V, Oke A, Zhuge T, Wettstein R, Fung JC, Blanco MG, Matos J. Regulated Crossing-Over Requires Inactivation of Yen1/GEN1 Resolvase during Meiotic Prophase I. Dev Cell 2018; 45:785-800.e6. [PMID: 29920281 DOI: 10.1016/j.devcel.2018.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/30/2018] [Accepted: 05/16/2018] [Indexed: 01/27/2023]
Abstract
During meiosis, crossover recombination promotes the establishment of physical connections between homologous chromosomes, enabling their bipolar segregation. To ensure that persistent recombination intermediates are disengaged prior to the completion of meiosis, the Yen1(GEN1) resolvase is strictly activated at the onset of anaphase II. Whether controlled activation of Yen1 is important for meiotic crossing-over is unknown. Here, we show that CDK-mediated phosphorylation of Yen1 averts its pervasive recruitment to recombination intermediates during prophase I. Yen1 mutants that are refractory to phosphorylation resolve DNA joint molecules prematurely and form crossovers independently of MutLγ, the central crossover resolvase during meiosis. Despite bypassing the requirement for MutLγ in joint molecule processing and promoting crossover-specific resolution, unrestrained Yen1 impairs the spatial distribution of crossover events, genome-wide. Thus, active suppression of Yen1 function, and by inference also of Mus81-Mms4(EME1) and Slx1-Slx4(BTBD12) resolvases, avoids precocious resolution of recombination intermediates to enable meiotic crossover patterning.
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Affiliation(s)
- Meret Arter
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Vanesa Hurtado-Nieves
- Departamento de Bioquímica e Bioloxía Molecular, CIMUS, Universidade de Santiago de Compostela - IDIS, 15706 Santiago de Compostela, Spain
| | - Ashwini Oke
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, CA, USA
| | - Tangna Zhuge
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, CA, USA
| | - Rahel Wettstein
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, CA, USA
| | - Miguel G Blanco
- Departamento de Bioquímica e Bioloxía Molecular, CIMUS, Universidade de Santiago de Compostela - IDIS, 15706 Santiago de Compostela, Spain.
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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Hong Y, Velkova M, Silva N, Jagut M, Scheidt V, Labib K, Jantsch V, Gartner A. The conserved LEM-3/Ankle1 nuclease is involved in the combinatorial regulation of meiotic recombination repair and chromosome segregation in Caenorhabditis elegans. PLoS Genet 2018; 14:e1007453. [PMID: 29879106 PMCID: PMC6007928 DOI: 10.1371/journal.pgen.1007453] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 06/19/2018] [Accepted: 05/29/2018] [Indexed: 11/23/2022] Open
Abstract
Homologous recombination is essential for crossover (CO) formation and accurate chromosome segregation during meiosis. It is of considerable importance to work out how recombination intermediates are processed, leading to CO and non-crossover (NCO) outcome. Genetic analysis in budding yeast and Caenorhabditis elegans indicates that the processing of meiotic recombination intermediates involves a combination of nucleases and DNA repair enzymes. We previously reported that in C. elegans meiotic joint molecule resolution is mediated by two redundant pathways, conferred by the SLX-1 and MUS-81 nucleases, and by the HIM-6 Bloom helicase in conjunction with the XPF-1 endonuclease, respectively. Both pathways require the scaffold protein SLX-4. However, in the absence of all these enzymes, residual processing of meiotic recombination intermediates still occurs and CO formation is reduced but not abolished. Here we show that the LEM-3 nuclease, mutation of which by itself does not have an overt meiotic phenotype, genetically interacts with slx-1 and mus-81 mutants, the respective double mutants displaying 100% embryonic lethality. The combined loss of LEM-3 and MUS-81 leads to altered processing of recombination intermediates, a delayed disassembly of foci associated with CO designated sites, and the formation of univalents linked by SPO-11 dependent chromatin bridges (dissociated bivalents). However, LEM-3 foci do not colocalize with ZHP-3, a marker that congresses into CO designated sites. In addition, neither CO frequency nor distribution is altered in lem-3 single mutants or in combination with mus-81 or slx-4 mutations. Finally, we found persistent chromatin bridges during meiotic divisions in lem-3; slx-4 double mutants. Supported by the localization of LEM-3 between dividing meiotic nuclei, this data suggest that LEM-3 is able to process erroneous recombination intermediates that persist into the second meiotic division.
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Affiliation(s)
- Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Maria Velkova
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Nicola Silva
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Marlène Jagut
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Viktor Scheidt
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Verena Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
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Sun L, Sun G, Shi C, Sun D. Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat. BMC Genomics 2018; 19:333. [PMID: 29739311 PMCID: PMC5941544 DOI: 10.1186/s12864-018-4727-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/25/2018] [Indexed: 11/16/2022] Open
Abstract
Background 337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory function of MicroRNAs (miRNAs) in reproductive development has been increasingly studied, their roles in pre-meiotic and meiotic cells formation of plants have not been clearly explored. Here, we explored the roles of miRNAs in regulating male sterility of 337S at short day length/low temperature condition. Results Small RNA sequencing and degradome analyses were employed to identify miRNAs and their targets in the 337S whose meiotic cells collapsed rapidly during male meiotic prophase, resulting in failure of meiosis at SL condition. A total of 102 unique miRNAs were detected. Noticeably, the largest miRNA family was MiR1122. The target CCR4-associated factor 1 (CAF1) of miR2275, a subunit of the Carbon Catabolite Repressed 4-Negative on TATA-less (CCR4-NOT) complex, contributes to the process of early meiosis, and was first identified here. Further studies showed that the expression of several pivotal anther-related miRNAs was altered in 337S at SL condition, especially tae-miR1127a, which may be related to male sterility of 337S. Here, we also identified a new member of SWI/SNF factors SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A, member 3-like 3 (SMARCA3L3) targeted by tae-miR1127a, whose function might be involved in faithful progression of meiosis in male reproductive cells. Conclusion The miRNA-target interactions of tae-miR2275-CAF1 and tae-miR1127a-SMARCA3L3 might be involved in regulating male fertility in 337S. Our results also implied that multiple roles for SMARCA3L3 and CAF1 in DNA repair and transcriptional regulation jointly orchestrated a tight and orderly system for maintaining chromatin and genome integrity during meiosis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4727-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Longqing Sun
- College of plant science & technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Chenxia Shi
- College of plant science & technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dongfa Sun
- College of plant science & technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, 434025, Hubei, China.
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Piazza A, Heyer WD. Multi-Invasion-Induced Rearrangements as a Pathway for Physiological and Pathological Recombination. Bioessays 2018; 40:e1700249. [PMID: 29578583 PMCID: PMC6072258 DOI: 10.1002/bies.201700249] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/08/2018] [Indexed: 01/24/2023]
Abstract
Cells mitigate the detrimental consequences of DNA damage on genome stability by attempting high fidelity repair. Homologous recombination templates DNA double-strand break (DSB) repair on an identical or near identical donor sequence in a process that can in principle access the entire genome. Other physiological processes, such as homolog recognition and pairing during meiosis, also harness the HR machinery using programmed DSBs to physically link homologs and generate crossovers. A consequence of the homology search process by a long nucleoprotein filament is the formation of multi-invasions (MI), a joint molecule in which the damaged ssDNA has invaded more than one donor molecule. Processing of MI joint molecules can compromise the integrity of both donor sites and lead to their rearrangement. Here, two mechanisms for the generation of rearrangements as a pathological consequence of MI processing are detailed and the potential relevance for non-allelic homologous recombination discussed. Finally, it is proposed that MI-induced crossover formation may be a feature of physiological recombination.
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Affiliation(s)
- Aurèle Piazza
- Department of Microbiology and Molecular Genetics, One Shields Avenue, University of California, Davis, CA, 95616, USA
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, One Shields Avenue, University of California, Davis, CA, 95616, USA
- Department of Molecular and Cellular Biology, One Shields Avenue, University of California, Davis, CA, 95616, USA
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Zhao H, Zhu M, Limbo O, Russell P. RNase H eliminates R-loops that disrupt DNA replication but is nonessential for efficient DSB repair. EMBO Rep 2018; 19:embr.201745335. [PMID: 29622660 DOI: 10.15252/embr.201745335] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/02/2018] [Accepted: 03/09/2018] [Indexed: 12/12/2022] Open
Abstract
In Saccharomyces cerevisiae, genome stability depends on RNases H1 and H2, which remove ribonucleotides from DNA and eliminate RNA-DNA hybrids (R-loops). In Schizosaccharomyces pombe, RNase H enzymes were reported to process RNA-DNA hybrids produced at a double-strand break (DSB) generated by I-PpoI meganuclease. However, it is unclear if RNase H is generally required for efficient DSB repair in fission yeast, or whether it has other genome protection roles. Here, we show that S. pombe rnh1∆ rnh201∆ cells, which lack the RNase H enzymes, accumulate R-loops and activate DNA damage checkpoints. Their viability requires critical DSB repair proteins and Mus81, which resolves DNA junctions formed during repair of broken replication forks. "Dirty" DSBs generated by ionizing radiation, as well as a "clean" DSB at a broken replication fork, are efficiently repaired in the absence of RNase H. RNA-DNA hybrids are not detected at a reparable DSB formed by fork collapse. We conclude that unprocessed R-loops collapse replication forks in rnh1∆ rnh201∆ cells, but RNase H is not generally required for efficient DSB repair.
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Affiliation(s)
- Hongchang Zhao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Min Zhu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Oliver Limbo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Russell
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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36
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Wright WD, Shah SS, Heyer WD. Homologous recombination and the repair of DNA double-strand breaks. J Biol Chem 2018; 293:10524-10535. [PMID: 29599286 DOI: 10.1074/jbc.tm118.000372] [Citation(s) in RCA: 410] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination enables the cell to access and copy intact DNA sequence information in trans, particularly to repair DNA damage affecting both strands of the double helix. Here, we discuss the DNA transactions and enzymatic activities required for this elegantly orchestrated process in the context of the repair of DNA double-strand breaks in somatic cells. This includes homology search, DNA strand invasion, repair DNA synthesis, and restoration of intact chromosomes. Aspects of DNA topology affecting individual steps are highlighted. Overall, recombination is a dynamic pathway with multiple metastable and reversible intermediates designed to achieve DNA repair with high fidelity.
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Affiliation(s)
| | | | - Wolf-Dietrich Heyer
- From the Departments of Microbiology and Molecular Genetics and .,Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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37
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Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants in Schizosaccharomyces pombe. Curr Genet 2018; 64:1089-1104. [PMID: 29550859 PMCID: PMC6153652 DOI: 10.1007/s00294-018-0827-7] [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: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 11/28/2022]
Abstract
Hop1 is a component of the meiosis-specific chromosome axis and belongs to the evolutionarily conserved family of HORMA domain proteins. Hop1 and its orthologs in higher eukaryotes are a major factor in promoting double-strand DNA break formation and inter-homolog recombination. In budding yeast and mammals, they are also involved in a meiotic checkpoint kinase cascade monitoring the completion of double-strand DNA break repair. We used the fission yeast, Schizosaccharomyces pombe, which lacks a canonical synaptonemal complex to test whether Hop1 has a role beyond supporting the generation of double-strand DNA breaks and facilitating inter-homolog recombination events. We determined how mutants of homologous recombination factors genetically interact with hop1, studied the role(s) of the HORMA domain of Hop1, and characterized a bio-informatically predicted interactor of Hop1, Aho1 (SPAC688.03c). Our observations indicate that in fission yeast, Hop1 does require its HORMA domain to support wild-type levels of meiotic recombination and localization to meiotic chromatin. Furthermore, we show that hop1∆ only weakly interacts genetically with mutants of homologous recombination factors, and in fission yeast likely has no major role beyond break formation and promoting inter-homolog events. We speculate that after the evolutionary loss of the synaptonemal complex, Hop1 likely has become less important for modulating recombination outcome during meiosis in fission yeast, and that this led to a concurrent rewiring of genetic pathways controlling meiotic recombination.
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Hum YF, Jinks-Robertson S. DNA strand-exchange patterns associated with double-strand break-induced and spontaneous mitotic crossovers in Saccharomyces cerevisiae. PLoS Genet 2018; 14:e1007302. [PMID: 29579095 PMCID: PMC5886692 DOI: 10.1371/journal.pgen.1007302] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/05/2018] [Accepted: 03/08/2018] [Indexed: 11/24/2022] Open
Abstract
Mitotic recombination can result in loss of heterozygosity and chromosomal rearrangements that shape genome structure and initiate human disease. Engineered double-strand breaks (DSBs) are a potent initiator of recombination, but whether spontaneous events initiate with the breakage of one or both DNA strands remains unclear. In the current study, a crossover (CO)-specific assay was used to compare heteroduplex DNA (hetDNA) profiles, which reflect strand exchange intermediates, associated with DSB-induced versus spontaneous events in yeast. Most DSB-induced CO products had the two-sided hetDNA predicted by the canonical DSB repair model, with a switch in hetDNA position from one product to the other at the position of the break. Approximately 40% of COs, however, had hetDNA on only one side of the initiating break. This anomaly can be explained by a modified model in which there is frequent processing of an early invasion (D-loop) intermediate prior to extension of the invading end. Finally, hetDNA tracts exhibited complexities consistent with frequent expansion of the DSB into a gap, migration of strand-exchange junctions, and template switching during gap-filling reactions. hetDNA patterns in spontaneous COs isolated in either a wild-type background or in a background with elevated levels of reactive oxygen species (tsa1Δ mutant) were similar to those associated with the DSB-induced events, suggesting that DSBs are the major instigator of spontaneous mitotic recombination in yeast.
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Affiliation(s)
- Yee Fang Hum
- Department of Molecular Genetics and Microbiology and the University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology and the University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
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39
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León-Ortiz AM, Panier S, Sarek G, Vannier JB, Patel H, Campbell PJ, Boulton SJ. A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination. Mol Cell 2018; 69:292-305.e6. [PMID: 29351848 PMCID: PMC5783719 DOI: 10.1016/j.molcel.2017.12.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/02/2017] [Accepted: 12/18/2017] [Indexed: 11/25/2022]
Abstract
Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses. Loss of vertebrate Rtel1 also causes a variety of unusually large and complex structural variations, including chromothripsis, breakage-fusion-bridge events, and tandem duplications with distant intra-chromosomal insertions, whose structure are consistent with a role for RTEL1 in preventing Ht-REC during break-induced replication. Our data establish Ht-REC as an unappreciated source of genome instability that underpins a novel class of complex genome rearrangements that likely arise during replication stress.
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Affiliation(s)
- Ana María León-Ortiz
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephanie Panier
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Grzegorz Sarek
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jean-Baptiste Vannier
- Telomere Replication and Stability Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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40
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Bhowmick R, Minocherhomji S, Hickson ID. RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress. Mol Cell 2017; 64:1117-1126. [PMID: 27984745 DOI: 10.1016/j.molcel.2016.10.037] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/06/2016] [Accepted: 10/28/2016] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is necessary to counteract DNA replication stress. Common fragile site (CFS) loci are particularly sensitive to replication stress and undergo pathological rearrangements in tumors. At these loci, replication stress frequently activates DNA repair synthesis in mitosis. This mitotic DNA synthesis, termed MiDAS, requires the MUS81-EME1 endonuclease and a non-catalytic subunit of the Pol-delta complex, POLD3. Here, we examine the contribution of HR factors in promoting MiDAS in human cells. We report that RAD51 and BRCA2 are dispensable for MiDAS but are required to counteract replication stress at CFS loci during S-phase. In contrast, MiDAS is RAD52 dependent, and RAD52 is required for the timely recruitment of MUS81 and POLD3 to CFSs in early mitosis. Our results provide further mechanistic insight into MiDAS and define a specific function for human RAD52. Furthermore, selective inhibition of MiDAS may comprise a potential therapeutic strategy to sensitize cancer cells undergoing replicative stress.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sheroy Minocherhomji
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark.
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41
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Zhao X, Wei C, Li J, Xing P, Li J, Zheng S, Chen X. Cell cycle-dependent control of homologous recombination. Acta Biochim Biophys Sin (Shanghai) 2017; 49:655-668. [PMID: 28541389 DOI: 10.1093/abbs/gmx055] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Indexed: 01/29/2023] Open
Abstract
DNA double-strand breaks (DSBs) are among the most deleterious type of DNA lesions threatening genome integrity. Homologous recombination (HR) and non-homologous end joining (NHEJ) are two major pathways to repair DSBs. HR requires a homologous template to direct DNA repair, and is generally recognized as a high-fidelity pathway. In contrast, NHEJ directly seals broken ends, but the repair product is often accompanied by sequence alterations. The choice of repair pathways is strictly controlled by the cell cycle. The occurrence of HR is restricted to late S to G2 phases while NHEJ operates predominantly in G1 phase, although it can act throughout most of the cell cycle. Deregulation of repair pathway choice can result in genotoxic consequences associated with cancers. How the cell cycle regulates the choice of HR and NHEJ has been extensively studied in the past decade. In this review, we will focus on the current progresses on how HR is controlled by the cell cycle in both Saccharomyces cerevisiae and mammals. Particular attention will be given to how cyclin-dependent kinases modulate DSB end resection, DNA damage checkpoint signaling, repair and processing of recombination intermediates. In addition, we will discuss recent findings on how HR is repressed in G1 and M phases by the cell cycle.
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Affiliation(s)
- Xin Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Chengwen Wei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jingjing Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Poyuan Xing
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jingyao Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Sihao Zheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
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42
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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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43
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Lorenz A. Modulation of meiotic homologous recombination by DNA helicases. Yeast 2017; 34:195-203. [PMID: 27930825 DOI: 10.1002/yea.3227] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/28/2016] [Accepted: 11/28/2016] [Indexed: 12/20/2022] Open
Abstract
DNA helicases are ATP-driven motor proteins which translocate along DNA capable of dismantling DNA-DNA interactions and/or removing proteins bound to DNA. These biochemical capabilities make DNA helicases main regulators of crucial DNA metabolic processes, including DNA replication, DNA repair, and genetic recombination. This budding topic will focus on reviewing the function of DNA helicases important for homologous recombination during meiosis, and discuss recent advances in how these modulators of meiotic recombination are themselves regulated. The emphasis is placed on work in the two model yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, which has vastly expanded our understanding of meiotic homologous recombination, a process whose correct execution is instrumental for healthy gamete formation, and thus functioning sexual reproduction. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alexander Lorenz
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
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44
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Shah Punatar R, Martin MJ, Wyatt HDM, Chan YW, West SC. Resolution of single and double Holliday junction recombination intermediates by GEN1. Proc Natl Acad Sci U S A 2017; 114:443-450. [PMID: 28049850 PMCID: PMC5255610 DOI: 10.1073/pnas.1619790114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genetic recombination provides an important mechanism for the repair of DNA double-strand breaks. Homologous pairing and strand exchange lead to the formation of DNA intermediates, in which sister chromatids or homologous chromosomes are covalently linked by four-way Holliday junctions (HJs). Depending on the type of recombination reaction that takes place, intermediates may have single or double HJs, and their resolution is essential for proper chromosome segregation. In mitotic cells, double HJs are primarily dissolved by the BLM helicase-TopoisomeraseIIIα-RMI1-RMI2 (BTR) complex, whereas single HJs (and double HJs that have escaped the attention of BTR) are resolved by structure-selective endonucleases known as HJ resolvases. These enzymes are ubiquitous in nature, because they are present in bacteriophage, bacteria, archaea, and simple and complex eukaryotes. The human HJ resolvase GEN1 is a member of the XPG/Rad2 family of 5'-flap endonucleases. Biochemical studies of GEN1 revealed that it cleaves synthetic DNA substrates containing a single HJ by a mechanism similar to that shown by the prototypic HJ resolvase, Escherichia coli RuvC protein, but it is unclear whether these substrates fully recapitulate the properties of recombination intermediates that arise within a physiological context. Here, we show that GEN1 efficiently cleaves both single and double HJs contained within large recombination intermediates. Moreover, we find that GEN1 exhibits a weak sequence preference for incision between two G residues that reside in a T-rich region of DNA. These results contrast with those obtained with RuvC, which exhibits a strict requirement for the consensus sequence 5'-A/TTTG/C-3'.
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Affiliation(s)
- Rajvee Shah Punatar
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Maria Jose Martin
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Haley D M Wyatt
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Ying Wai Chan
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephen C West
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
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45
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Reichman R, Alleva B, Smolikove S. Prophase I: Preparing Chromosomes for Segregation in the Developing Oocyte. Results Probl Cell Differ 2017; 59:125-173. [PMID: 28247048 DOI: 10.1007/978-3-319-44820-6_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Formation of an oocyte involves a specialized cell division termed meiosis. In meiotic prophase I (the initial stage of meiosis), chromosomes undergo elaborate events to ensure the proper segregation of their chromosomes into gametes. These events include processes leading to the formation of a crossover that, along with sister chromatid cohesion, forms the physical link between homologous chromosomes. Crossovers are formed as an outcome of recombination. This process initiates with programmed double-strand breaks that are repaired through the use of homologous chromosomes as a repair template. The accurate repair to form crossovers takes place in the context of the synaptonemal complex, a protein complex that links homologous chromosomes in meiotic prophase I. To allow proper execution of meiotic prophase I events, signaling processes connect different steps in recombination and synapsis. The events occurring in meiotic prophase I are a prerequisite for proper chromosome segregation in the meiotic divisions. When these processes go awry, chromosomes missegregate. These meiotic errors are thought to increase with aging and may contribute to the increase in aneuploidy observed in advanced maternal age female oocytes.
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Affiliation(s)
- Rachel Reichman
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Benjamin Alleva
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Sarit Smolikove
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA.
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46
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Onaka AT, Toyofuku N, Inoue T, Okita AK, Sagawa M, Su J, Shitanda T, Matsuyama R, Zafar F, Takahashi TS, Masukata H, Nakagawa T. Rad51 and Rad54 promote noncrossover recombination between centromere repeats on the same chromatid to prevent isochromosome formation. Nucleic Acids Res 2016; 44:10744-10757. [PMID: 27697832 PMCID: PMC5159554 DOI: 10.1093/nar/gkw874] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 09/06/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022] Open
Abstract
Centromeres consist of DNA repeats in many eukaryotes. Non-allelic homologous recombination (HR) between them can result in gross chromosomal rearrangements (GCRs). In fission yeast, Rad51 suppresses isochromosome formation that occurs between inverted repeats in the centromere. However, how the HR enzyme prevents homology-mediated GCRs remains unclear. Here, we provide evidence that Rad51 with the aid of the Swi/Snf-type motor protein Rad54 promotes non-crossover recombination between centromere repeats to prevent isochromosome formation. Mutations in Rad51 and Rad54 epistatically increased the rates of isochromosome formation and chromosome loss. In sharp contrast, these mutations decreased gene conversion between inverted repeats in the centromere. Remarkably, analysis of recombinant DNAs revealed that rad51 and rad54 increase the proportion of crossovers. In the absence of Rad51, deletion of the structure-specific endonuclease Mus81 decreased both crossovers and isochromosomes, while the cdc27/pol32-D1 mutation, which impairs break-induced replication, did not. We propose that Rad51 and Rad54 promote non-crossover recombination between centromere repeats on the same chromatid, thereby suppressing crossover between non-allelic repeats on sister chromatids that leads to chromosomal rearrangements. Furthermore, we found that Rad51 and Rad54 are required for gene silencing in centromeres, suggesting that HR also plays a role in the structure and function of 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
| | - Naoko Toyofuku
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takahiro Inoue
- 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
| | - Minami Sagawa
- 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
| | - Takeshi Shitanda
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Rei Matsuyama
- 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
| | - 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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47
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Xing M, Wang X, Palmai-Pallag T, Shen H, Helleday T, Hickson ID, Ying S. Acute MUS81 depletion leads to replication fork slowing and a constitutive DNA damage response. Oncotarget 2016; 6:37638-46. [PMID: 26415217 PMCID: PMC4741954 DOI: 10.18632/oncotarget.5497] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/11/2015] [Indexed: 11/25/2022] Open
Abstract
The MUS81 protein belongs to a conserved family of DNA structure-specific nucleases that play important roles in DNA replication and repair. Inactivation of the Mus81 gene in mice has no major deleterious consequences for embryonic development, although cancer susceptibility has been reported. We have investigated the role of MUS81 in human cells by acutely depleting the protein using shRNAs. We found that MUS81 depletion from human fibroblasts leads to accumulation of ssDNA and a constitutive DNA damage response that ultimately activates cellular senescence. Moreover, we show that MUS81 is required for efficient replication fork progression during an unperturbed S-phase, and for recovery of productive replication following replication stalling. These results demonstrate essential roles for the MUS81 nuclease in maintenance of replication fork integrity.
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Affiliation(s)
- Meichun Xing
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohui Wang
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Huahao Shen
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Institute of Respiratory Diseases, Zhejiang University School of Medicine, Hangzhou, China.,State Key Laboratory For Respiratory Diseases, Guangzhou, China
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ian D Hickson
- Center for Chromosome Stability and Nordea Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Songmin Ying
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China.,Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Institute of Respiratory Diseases, Zhejiang University School of Medicine, Hangzhou, China
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48
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Talhaoui I, Bernal M, Mazón G. The nucleolytic resolution of recombination intermediates in yeast mitotic cells. FEMS Yeast Res 2016; 16:fow065. [PMID: 27509904 DOI: 10.1093/femsyr/fow065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 12/20/2022] Open
Abstract
In mitotic cells, the repair of double-strand breaks by homologous recombination (HR) is important for genome integrity. HR requires the orchestration of a subset of pathways for timely removal of joint-molecule intermediates that would otherwise prevent segregation of chromosomes in mitosis. The use of nucleases to resolve recombination intermediates is important for chromosome segregation, but is hazardous because crossovers can result in loss of heterozygosity or chromosome rearrangements. Unregulated use of the nucleases involved in the resolution of recombination intermediates could also be a risk during replication. The yeast models (Saccharomyces cerevisae and Schizosaccharomyces pombe) have proven effective in determining the major nucleases involved in the processing of such intermediates: Mus81-Mms4 and Yen1. Mus81-Mms4 and Yen1 are regulated by the cell cycle in a gradual activation during G2/M to keep the crossing-over risk low while ensuring proper removal of HJ intermediates.
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Affiliation(s)
- Ibtissam Talhaoui
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS) UMR 8200 Genetic Stability and Oncogenesis, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Manuel Bernal
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS) UMR 8200 Genetic Stability and Oncogenesis, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Gerard Mazón
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS) UMR 8200 Genetic Stability and Oncogenesis, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
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Dbl2 Regulates Rad51 and DNA Joint Molecule Metabolism to Ensure Proper Meiotic Chromosome Segregation. PLoS Genet 2016; 12:e1006102. [PMID: 27304859 PMCID: PMC4909299 DOI: 10.1371/journal.pgen.1006102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/12/2016] [Indexed: 11/19/2022] Open
Abstract
To identify new proteins required for faithful meiotic chromosome segregation, we screened a Schizosaccharomyces pombe deletion mutant library and found that deletion of the dbl2 gene led to missegregation of chromosomes during meiosis. Analyses of both live and fixed cells showed that dbl2Δ mutant cells frequently failed to segregate homologous chromosomes to opposite poles during meiosis I. Removing Rec12 (Spo11 homolog) to eliminate meiotic DNA double-strand breaks (DSBs) suppressed the segregation defect in dbl2Δ cells, indicating that Dbl2 acts after the initiation of meiotic recombination. Analyses of DSBs and Holliday junctions revealed no significant defect in their formation or processing in dbl2Δ mutant cells, although some Rec12-dependent DNA joint molecules persisted late in meiosis. Failure to segregate chromosomes in the absence of Dbl2 correlated with persistent Rad51 foci, and deletion of rad51 or genes encoding Rad51 mediators also suppressed the segregation defect of dbl2Δ. Formation of foci of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments, was impaired in dbl2Δ cells. Our results suggest that Dbl2 is a novel regulator of Fbh1 and thereby Rad51-dependent DSB repair required for proper meiotic chromosome segregation and viable sex cell formation. The wide conservation of these proteins suggests that our results apply to many species. Meiosis produces haploid gametes from diploid precursor cells. This reduction of chromosome number is achieved by two successive divisions after only a single round of DNA replication. To identify novel regulators of meiosis, we screened a library of fission yeast deletion mutants and found that deletion of the dbl2 gene led to missegregation of chromosomes during meiosis. Analysis of live dbl2Δ cells by fluorescence microscopy showed that chromosomes frequently failed to segregate during the first meiotic division. Further cytological and biochemical analyses revealed that this segregation defect is due to persistent intermediates of DNA double-strand break repair, also called DNA joint molecules. Our results indicate that Dbl2 is required for formation of Fbh1 DNA helicase foci at the sites of DNA double-strand break repair in order to process DNA joint molecules and allow segregation of chromosomes during meiotic divisions. Our bioinformatics searches revealed that Dbl2 is highly conserved in fungi, animals and plants, suggesting that Dbl2 plays a similar role in other organisms–the formation of viable sex cells and healthy progeny.
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The RecQ DNA helicase Rqh1 constrains Exonuclease 1-dependent recombination at stalled replication forks. Sci Rep 2016; 6:22837. [PMID: 26957021 PMCID: PMC4783781 DOI: 10.1038/srep22837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 01/28/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) involves resection of the break to expose a 3' single-stranded DNA tail. In budding yeast, resection occurs in two steps: initial short-range resection, performed by Mre11-Rad50-Xrs2 and Sae2; and long-range resection catalysed by either Exo1 or Sgs1-Dna2. Here we use genetic assays to investigate the importance of Exo1 and the Sgs1 homologue Rqh1 for DNA repair and promotion of direct repeat recombination in the fission yeast Schizosaccharomyces pombe. We find that Exo1 and Rqh1 function in alternative redundant pathways for promoting survival following replication fork breakage. Exo1 promotes replication fork barrier-induced direct repeat recombination but intriguingly limits recombination induced by fork breakage. Direct repeat recombination induced by ultraviolet light depends on either Exo1 or Rqh1. Finally, we show that Rqh1 plays a major role in limiting Exo1-dependent direct repeat recombination induced by replication fork stalling but only a minor role in constraining recombination induced by fork breakage. The implications of our findings are discussed in the context of the benefits that long-range resection may bring to processing perturbed replication forks.
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