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Johnson D, Allison RM, Cannavo E, Cejka P, Harper JA, Neale MJ. Exploring the removal of Spo11 and topoisomerases from DNA breaks in S. cerevisiae by human Tyrosyl DNA Phosphodiesterase 2. DNA Repair (Amst) 2024; 142:103757. [PMID: 39236418 DOI: 10.1016/j.dnarep.2024.103757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/07/2024]
Abstract
Meiotic recombination is initiated by DNA double-strand breaks (DSBs) created by Spo11, a type-II topoisomerase-like protein that becomes covalently linked to DSB ends. Whilst Spo11 oligos-the products of nucleolytic removal by Mre11-have been detected in several organisms, the lifetime of the covalent Spo11-DSB precursor has not been determined and may be subject to alternative processing. Here, we explore the activity of human Tyrosyl DNA Phosphodiesterase, TDP2-a protein known to repair DNA ends arising from abortive topoisomerase activity-on Spo11 DSBs isolated from S. cerevisiae cells. We demonstrate that TDP2 can remove Spo11 peptides from ssDNA oligos and dsDNA ends even in the presence of competitor genomic DNA. Interestingly, TDP2-processed DSB ends are refractory to resection by Exo1, suggesting that ssDNA generated by Mre11 may be essential in vivo to facilitate HR at Spo11 DSBs even if TDP2 were active. Moreover, although TDP2 can remove Spo11 peptides in vitro, TDP2 expression in meiotic cells was unable to remove Spo11 in vivo-contrasting its ability to aid repair of topoisomerase-induced DNA lesions. These results suggest that Spo11-DNA, but not topoisomerase-DNA cleavage complexes, are inaccessible to the TDP2 enzyme, perhaps due to occlusion by higher-order protein complexes at sites of meiotic recombination.
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Affiliation(s)
- Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK
| | - Rachal M Allison
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK
| | - Elda Cannavo
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland
| | - Jon A Harper
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton UK.
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2
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Dutta A, Dutreux F, Garin M, Caradec C, Friedrich A, Brach G, Thiele P, Gaudin M, Llorente B, Schacherer J. Multiple independent losses of crossover interference during yeast evolutionary history. PLoS Genet 2024; 20:e1011426. [PMID: 39325820 DOI: 10.1371/journal.pgen.1011426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Meiotic recombination is essential for the accurate chromosome segregation and the generation of genetic diversity through crossover and gene conversion events. Although this process has been studied extensively in a few selected model species, understanding how its properties vary across species remains limited. For instance, the ancestral ZMM pathway that generates interference-dependent crossovers has undergone multiple losses throughout evolution, suggesting variations in the regulation of crossover formation. In this context, we first characterized the meiotic recombination landscape and properties of the Kluyveromyces lactis budding yeast. We then conducted a comprehensive analysis of 29,151 recombination events (19, 212 COs and 9, 939 NCOs) spanning 577 meioses in the five budding yeast species Saccharomyces cerevisiae, Saccharomyces paradoxus, Lachancea kluyveri, Lachancea waltii and K. lactis. Eventually, we found that the Saccharomyces yeasts displayed higher recombination rates compared to the non-Saccharomyces yeasts. In addition, bona fide crossover interference and associated crossover homeostasis were detected in the Saccharomyces species only, adding L. kluyveri and K. lactis to the list of budding yeast species that lost crossover interference. Finally, recombination hotspots, although highly conserved within the Saccharomyces yeasts are not conserved beyond the Saccharomyces genus. Overall, these results highlight great variability in the recombination landscape and properties through budding yeasts evolution.
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Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Marion Garin
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Gauthier Brach
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Pia Thiele
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, 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
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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3
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Blouin T, Saini N. Aldehyde-induced DNA-protein crosslinks- DNA damage, repair and mutagenesis. Front Oncol 2024; 14:1478373. [PMID: 39328207 PMCID: PMC11424613 DOI: 10.3389/fonc.2024.1478373] [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: 08/09/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
Aldehyde exposure has been shown to lead to the formation of DNA damage comprising of DNA-protein crosslinks (DPCs), base adducts and interstrand or intrastrand crosslinks. DPCs have recently drawn more attention because of recent advances in detection and quantification of these adducts. DPCs are highly deleterious to genome stability and have been shown to block replication forks, leading to wide-spread mutagenesis. Cellular mechanisms to prevent DPC-induced damage include excision repair pathways, homologous recombination, and specialized proteases involved in cleaving the covalently bound proteins from DNA. These pathways were first discovered in formaldehyde-treated cells, however, since then, various other aldehydes have been shown to induce formation of DPCs in cells. Defects in DPC repair or aldehyde clearance mechanisms lead to various diseases including Ruijs-Aalfs syndrome and AMeD syndrome in humans. Here, we discuss recent developments in understanding how aldehydes form DPCs, how they are repaired, and the consequences of defects in these repair pathways.
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Affiliation(s)
- Thomas Blouin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
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4
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Weng Q, Wan L, Straker GC, Deegan TD, Duncker BP, Neiman AM, Luk E, Hollingsworth NM. An acidic loop in the forkhead-associated domain of the yeast meiosis-specific kinase Mek1 interacts with a specific motif in a subset of Mek1 substrates. Genetics 2024; 228:iyae106. [PMID: 38979911 PMCID: PMC11373509 DOI: 10.1093/genetics/iyae106] [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: 05/24/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/10/2024] Open
Abstract
The meiosis-specific kinase Mek1 regulates key steps in meiotic recombination in the budding yeast, Saccharomyces cerevisiae. MEK1 limits resection at double-strand break (DSB) ends and is required for preferential strand invasion into homologs, a process known as interhomolog bias. After strand invasion, MEK1 promotes phosphorylation of the synaptonemal complex protein Zip1 that is necessary for DSB repair mediated by a crossover-specific pathway that enables chromosome synapsis. In addition, Mek1 phosphorylation of the meiosis-specific transcription factor, Ndt80, regulates the meiotic recombination checkpoint that prevents exit from pachytene when DSBs are present. Mek1 interacts with Ndt80 through a 5-amino acid sequence, RPSKR, located between the DNA-binding and activation domains of Ndt80. AlphaFold Multimer modeling of a fragment of Ndt80 containing the RPSKR motif and full-length Mek1 indicated that RPSKR binds to an acidic loop located in the Mek1 FHA domain, a noncanonical interaction with this motif. A second protein, the 5'-3' helicase Rrm3, similarly interacts with Mek1 through an RPAKR motif and is an in vitro substrate of Mek1. Genetic analysis using various mutants in the MEK1 acidic loop validated the AlphaFold model, in that they specifically disrupt 2-hybrid interactions with Ndt80 and Rrm3. Phenotypic analyses further showed that the acidic loop mutants are defective in the meiotic recombination checkpoint and, in certain circumstances, exhibit more severe phenotypes compared to the NDT80 mutant with the RPSKR sequence deleted, suggesting that additional, as yet unknown, substrates of Mek1 also bind to Mek1 using an RPXKR motif.
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Affiliation(s)
- Qixuan Weng
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Lihong Wan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Geburah C Straker
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Tom D Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Bernard P Duncker
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Aaron M Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Nancy M Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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Tamai T, Reginato G, Ojiri R, Morita I, Avrutis A, Cejka P, Shinohara M, Sugimoto K. Sae2 controls Mre11 endo- and exonuclease activities by different mechanisms. Nat Commun 2024; 15:7221. [PMID: 39174552 PMCID: PMC11341764 DOI: 10.1038/s41467-024-51493-5] [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: 10/12/2023] [Accepted: 08/09/2024] [Indexed: 08/24/2024] Open
Abstract
DNA double-strand breaks (DSBs) must be repaired to ensure cell survival and genomic integrity. In yeast, the Mre11-Rad50-Xrs2 complex (MRX) collaborates with Sae2 to initiate DSB repair. Sae2 stimulates two MRX nuclease activities, endonuclease and 3'-5' exonuclease. However, how Sae2 controls the two nuclease activities remains enigmatic. Using a combined genetic and biochemical approach, we identified a separation-of-function rad50 mutation, rad50-C47, that causes a defect in Sae2-dependent MRX 3'-5' exonuclease activity, but not endonuclease activity. We found that both the endo- and 3'-5' exonuclease activities are essential to release Spo11 from DNA ends, whereas only the endonuclease activity is required for hairpin removal. We also uncovered that MRX-Sae2 endonuclease introduces a cleavage at defined distances from the Spo11-blocked end with gradually decreasing efficiency. Our findings demonstrate that Sae2 stimulates the MRX endo- and exonuclease activities via Rad50 by different mechanisms, ensuring diverse actions of MRX-Sae2 nuclease at DNA ends.
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Affiliation(s)
- Tomoki Tamai
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Giordano Reginato
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ryusei Ojiri
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Issei Morita
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Alexandra Avrutis
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ, 07103, USA
| | - Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland.
| | - Miki Shinohara
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara City, Nara, 631-8505, Japan.
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ, 07103, USA.
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Kim S, Yamada S, Li T, Canasto-Chibuque C, Kim JH, Marcet-Ortega M, Xu J, Eng DY, Feeney L, Petrini JHJ, Keeney S. The MRE11-RAD50-NBS1 complex both starts and extends DNA end resection in mouse meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.17.608390. [PMID: 39185212 PMCID: PMC11343206 DOI: 10.1101/2024.08.17.608390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Nucleolytic resection of DNA ends is critical for homologous recombination, but its mechanism is not fully understood, particularly in mammalian meiosis. Here we examine roles of the conserved MRN complex (MRE11, RAD50, and NBS1) through genome-wide analysis of meiotic resection in mice with various MRN mutations, including several that cause chromosomal instability in humans. Meiotic DSBs form at elevated levels but remain unresected if Mre11 is conditionally deleted, thus MRN is required for both resection initiation and regulation of DSB numbers. Resection lengths are reduced to varying degrees in MRN hypomorphs or if MRE11 nuclease activity is attenuated in a conditional nuclease-dead Mre11 model. These findings unexpectedly establish that MRN is needed for longer-range extension of resection, not just resection initiation. Finally, resection defects are additively worsened by combining MRN and Exo1 mutations, and mice that are unable to initiate resection or have greatly curtailed resection lengths experience catastrophic spermatogenic failure. Our results elucidate multiple functions of MRN in meiotic recombination, uncover unanticipated relationships between short- and long-range resection, and establish the importance of resection for mammalian meiosis.
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Affiliation(s)
- Soonjoung Kim
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Shintaro Yamada
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- The HAKUBI Center for Advanced Research, and Department of Aging Science and Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tao Li
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Claudia Canasto-Chibuque
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jun Hyun Kim
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Marina Marcet-Ortega
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jiaqi Xu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Weill Cornell Graduate School of Medical Sciences
| | - Diana Y. Eng
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Laura Feeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - John H. J. Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Weill Cornell Graduate School of Medical Sciences
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Weill Cornell Graduate School of Medical Sciences
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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7
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Feng Y, Zhao S, Ju R, Li J, Pan C, Tang Q, Zou Z, Jing J, Xu Y, Ding H, Ma J, Li Z, Tang T, Shao Y, Chen L, Huang X, Wang X, Yao B. The therapeutic effect and metabolic mechanism analysis of Guilingji on idiopathic oligo-asthenoteratozoospermia. J Tradit Complement Med 2024; 14:403-413. [PMID: 39035689 PMCID: PMC11259704 DOI: 10.1016/j.jtcme.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/29/2023] [Accepted: 01/05/2024] [Indexed: 07/23/2024] Open
Abstract
Introduction Guilingji, a famous traditional Chinese medicine (TCM) formula, has been used to combat aging and male sexual dysfunction in China for centuries. To date, there has been little evidence-based clinical research on the use of Guilingji to treat idiopathic oligo-asthenoteratozoospermia (OAT), and the therapeutic mechanism from a metabolic perspective needs to be investigated further. Methods This was a multicenter, double-blind, randomized controlled clinical study of 240 patients with idiopathic OAT recruited from four hospitals between January 2020 and January 2022. Patients were randomly assigned in a 1꞉1 ratio to receive oral Guilingji capsules or placebo for 12 weeks. The total progressive motile sperm count (TPMSC) was considered the primary outcome, and the other sperm parameters, seminal plasma parameters and serum hormones were considered the secondary outcome. A nontargeted metabolomics analysis of serum from OAT patients before and after Guilingji administration was performed by HPLC-MS to identify key metabolites. Furthermore, we used a rat model to show spermatogenesis phenotypes to validate the effect of the key metabolites screened from the patients. Results At weeks 4, 8 and 12, TPMSC and other sperm parameters were significantly improved in the Guilingji group compared with the placebo group (P < 0.05 for all comparisons). At week 4, superoxide dismutase (SOD) and acrosomal enzyme activity of seminal plasma were significantly elevated in the Guilingji group compared with the placebo group, while reactive oxygen species (ROS) levels were significantly reduced (P < 0.05). Lactate dehydrogenase-X (LDHX) levels appeared to be significantly increased after 12 weeks continuous medication compared with Placebo group (P = 0.032). The metabolomics analysis of serum from OAT patients before and after Guilingji administration showed that the glucose-6-phosphate (G6P) concentration in patients' serum was significantly elevated after Guilingji treatment. Compared to the control, when Kidney-Yang deficiency model rats were treated with Guilingji or its key intermediate metabolite G6P, their sperm concentration and spermatozoic activity were improved similarly, and their structural damage of rat's testicular and epididymal tissues were recovered. Conclusion This study provided valuable clinical evidence for the utility of Guilingji as a treatment for OAT. These findings thus demonstrate that G6P is involved in the therapeutic mechanism of Guilingji in OAT treatment based on clinical and rat intervention studies.
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Affiliation(s)
- Yuming Feng
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Shanmeizi Zhao
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Rong Ju
- Department of Obstetrics and Gynecology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, 211100, Jiangsu, China
| | - Jianbo Li
- Center for Reproductive Medicine of Obstetrics and Gynecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Chengshuang Pan
- Reproductive Medicine Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Qinglai Tang
- Department of Urology, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211100, Jiangsu, China
| | - Zhichuan Zou
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Jun Jing
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Yao Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211116, Jiangsu, China
| | - Hualong Ding
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Jinzhao Ma
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Zhou Li
- Department of Reproductive Medicine, Nanjing Jinling Hospital, School of Medicine, Jiangsu University, Zhenjiang, 212000, Jiangsu, China
| | - Ting Tang
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Yong Shao
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Li Chen
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
| | - Xuefeng Huang
- Reproductive Medicine Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Xiaohong Wang
- Center for Reproductive Medicine of Obstetrics and Gynecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Bing Yao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, Jiangsu, China
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
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8
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Nicolas Y, Bret H, Cannavo E, Acharya A, Cejka P, Borde V, Guerois R. Molecular insights into the activation of Mre11-Rad50 endonuclease activity by Sae2/CtIP. Mol Cell 2024; 84:2223-2237.e4. [PMID: 38870937 DOI: 10.1016/j.molcel.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 02/25/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
In Saccharomyces cerevisiae (S. cerevisiae), Mre11-Rad50-Xrs2 (MRX)-Sae2 nuclease activity is required for the resection of DNA breaks with secondary structures or protein blocks, while in humans, the MRE11-RAD50-NBS1 (MRN) homolog with CtIP is needed to initiate DNA end resection of all breaks. Phosphorylated Sae2/CtIP stimulates the endonuclease activity of MRX/N. Structural insights into the activation of the Mre11 nuclease are available only for organisms lacking Sae2/CtIP, so little is known about how Sae2/CtIP activates the nuclease ensemble. Here, we uncover the mechanism of Mre11 activation by Sae2 using a combination of AlphaFold2 structural modeling of biochemical and genetic assays. We show that Sae2 stabilizes the Mre11 nuclease in a conformation poised to cleave substrate DNA. Several designs of compensatory mutations establish how Sae2 activates MRX in vitro and in vivo, supporting the structural model. Finally, our study uncovers how human CtIP, despite considerable sequence divergence, employs a similar mechanism to activate MRN.
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Affiliation(s)
- Yoann Nicolas
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France
| | - Hélène Bret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Elda Cannavo
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland.
| | - Valérie Borde
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005 Paris, France.
| | - Raphaël Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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9
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Tang Z, Liang Z, Zhang B, Xu X, Li P, Li L, Lu LY, Liu Y. MRE11 is essential for the long-term viability of undifferentiated spermatogonia. Cell Prolif 2024:e13685. [PMID: 38894566 DOI: 10.1111/cpr.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
In the meiotic prophase, programmed SPO11-linked DNA double-strand breaks (DSBs) are repaired by homologous recombination (HR). The MRE11-RAD50-NBS1 (MRN) complex is essential for initiating DNA end resection, the first step of HR. However, residual DNA end resection still occurs in Nbs1 knockout (KO) spermatocytes for unknown reasons. Here, we show that DNA end resection is completely abolished in Mre11 KO spermatocytes. In addition, Mre11 KO, but not Nbs1 KO, undifferentiated spermatogonia are rapidly exhausted due to DSB accumulation, proliferation defects, and elevated apoptosis. Cellular studies reveal that a small amount of MRE11 retained in the nucleus of Nbs1 KO cells likely underlies the differences between Mre11 and Nbs1 KO cells. Taken together, our study not only demonstrates an irreplaceable role of the MRE11 in DNA end resection at SPO11-linked DSBs but also unveils a unique function of MRE11 in maintaining the long-term viability of undifferentiated spermatogonia.
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Affiliation(s)
- Zhenghui Tang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongyang Liang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohui Xu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Li
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lejun Li
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lin-Yu Lu
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, China
| | - Yidan Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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10
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Weng Q, Wan L, Straker GC, Deegan TD, Duncker BP, Neiman AM, Luk E, Hollingsworth NM. An acidic loop in the FHA domain of the yeast meiosis-specific kinase Mek1 interacts with a specific motif in a subset of Mek1 substrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595751. [PMID: 38826409 PMCID: PMC11142242 DOI: 10.1101/2024.05.24.595751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The meiosis-specific kinase Mek1 regulates key steps in meiotic recombination in the budding yeast, Saccharomyces cerevisiae. MEK1 limits resection at the double strand break (DSB) ends and is required for preferential strand invasion into homologs, a process known as interhomolog bias. After strand invasion, MEK1 promotes phosphorylation of the synaptonemal complex protein Zip1 that is necessary for DSB repair mediated by a crossover specific pathway that enables chromosome synapsis. In addition, Mek1 phosphorylation of the meiosis-specific transcription factor, Ndt80, regulates the meiotic recombination checkpoint that prevents exit from pachytene when DSBs are present. Mek1 interacts with Ndt80 through a five amino acid sequence, RPSKR, located between the DNA binding and activation domains of Ndt80. AlphaFold Multimer modeling of a fragment of Ndt80 containing the RPSKR motif and full length Mek1 indicated that RPSKR binds to an acidic loop located in the Mek1 FHA domain, a non-canonical interaction with this motif. A second protein, the 5'-3' helicase Rrm3, similarly interacts with Mek1 through an RPAKR motif and is an in vitro substrate of Mek1. Genetic analysis using various mutants in the MEK1 acidic loop validated the AlphaFold model, in that they specifically disrupt two-hybrid interactions with Ndt80 and Rrm3. Phenotypic analyses further showed that the acidic loop mutants are defective in the meiotic recombination checkpoint, and in certain circumstances exhibit more severe phenotypes compared to the NDT80 mutant with the RPSKR sequence deleted, suggesting that additional, as yet unknown, substrates of Mek1 also bind to Mek1 using an RPXKR motif.
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Affiliation(s)
- Qixuan Weng
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Lihong Wan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Geburah C. Straker
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Tom. D. Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK DD1 5EH, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Bernard P. Duncker
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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11
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Aithal R, Nangalia K, Spirek M, Chen D, Klein F, Krejci L. Physical interaction with Spo11 mediates the localisation of Mre11 to chromatin in meiosis and promotes its nuclease activity. Nucleic Acids Res 2024; 52:4328-4343. [PMID: 38407383 PMCID: PMC11077076 DOI: 10.1093/nar/gkae111] [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: 04/21/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
Meiotic recombination is of central importance for the proper segregation of homologous chromosomes, but also for creating genetic diversity. It is initiated by the formation of double-strand breaks (DSBs) in DNA catalysed by evolutionarily conserved Spo11, together with additional protein partners. Difficulties in purifying the Spo11 protein have limited the characterization of its biochemical properties and of its interactions with other DSB proteins. In this study, we have purified fragments of Spo11 and show for the first time that Spo11 can physically interact with Mre11 and modulates its DNA binding, bridging, and nuclease activities. The interaction of Mre11 with Spo11 requires its far C-terminal region, which is in line with the severe meiotic phenotypes of various mre11 mutations located at the C-terminus. Moreover, calibrated ChIP for Mre11 shows that Spo11 promotes Mre11 recruitment to chromatin, independent of DSB formation. A mutant deficient in Spo11 interaction severely reduces the association of Mre11 with meiotic chromatin. Consistent with the reduction of Mre11 foci in this mutant, it strongly impedes DSB formation, leading to spore death. Our data provide evidence that physical interaction between Spo11 and Mre11, together with end-bridging, promote normal recruitment of Mre11 to hotspots and DSB formation.
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Affiliation(s)
- Rakesh Aithal
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Kuldeep Nangalia
- Department of Chromosome Biology, Center for Molecular Biology, University of Vienna
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030Vienna, Austria
| | - Mario Spirek
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Doris Chen
- Department of Chromosome Biology, Center for Molecular Biology, University of Vienna
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030Vienna, Austria
| | - Franz Klein
- Department of Chromosome Biology, Center for Molecular Biology, University of Vienna
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030Vienna, Austria
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Department of Biology, Masaryk University, Brno, Czech Republic
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12
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Chen HW, Yeh HY, Chang CC, Kuo WC, Lin SW, Vrielynck N, Grelon M, Chan NL, Chi P. Biochemical characterization of the meiosis-essential yet evolutionarily divergent topoisomerase VIB-like protein MTOPVIB from Arabidopsis thaliana. Nucleic Acids Res 2024; 52:4541-4555. [PMID: 38499490 PMCID: PMC11077084 DOI: 10.1093/nar/gkae181] [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: 09/06/2023] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Formation of programmed DNA double-strand breaks is essential for initiating meiotic recombination. Genetic studies on Arabidopsis thaliana and Mus musculus have revealed that assembly of a type IIB topoisomerase VI (Topo VI)-like complex, composed of SPO11 and MTOPVIB, is a prerequisite for generating DNA breaks. However, it remains enigmatic if MTOPVIB resembles its Topo VI subunit B (VIB) ortholog in possessing robust ATPase activity, ability to undergo ATP-dependent dimerization, and activation of SPO11-mediated DNA cleavage. Here, we successfully prepared highly pure A. thaliana MTOPVIB and MTOPVIB-SPO11 complex. Contrary to expectations, our findings highlight that MTOPVIB differs from orthologous Topo VIB by lacking ATP-binding activity and independently forming dimers without ATP. Most significantly, our study reveals that while MTOPVIB lacks the capability to stimulate SPO11-mediated DNA cleavage, it functions as a bona fide DNA-binding protein and plays a substantial role in facilitating the dsDNA binding capacity of the MOTOVIB-SPO11 complex. Thus, we illustrate mechanistic divergence between the MTOPVIB-SPO11 complex and classical type IIB topoisomerases.
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Affiliation(s)
- Hsin-Wen Chen
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
| | - Chih-Chiang Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Wei-Chen Kuo
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan
| | - Nathalie Vrielynck
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000,Versailles, France
| | - Mathilde Grelon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000,Versailles, France
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan
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13
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Arter M, Keeney S. Divergence and conservation of the meiotic recombination machinery. Nat Rev Genet 2024; 25:309-325. [PMID: 38036793 DOI: 10.1038/s41576-023-00669-8] [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] [Accepted: 10/03/2023] [Indexed: 12/02/2023]
Abstract
Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost universally conserved in its broad strokes, but specific molecular details often differ considerably between taxa, and the proteins that constitute the recombination machinery show substantial sequence variability. The extent of this variation is becoming increasingly clear because of recent increases in genomic resources and advances in protein structure prediction. We discuss the tension between functional conservation and rapid evolutionary change with a focus on the proteins that are required for the formation and repair of meiotic DNA double-strand breaks. We highlight phylogenetic relationships on different time scales and propose that this remarkable evolutionary plasticity is a fundamental property of meiotic recombination that shapes our understanding of molecular mechanisms in reproductive biology.
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Affiliation(s)
- Meret Arter
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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14
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Joo JH, Hong S, Higashide MT, Choi EH, Yoon S, Lee MS, Kang HA, Shinohara A, Kleckner N, Kim KP. RPA interacts with Rad52 to promote meiotic crossover and noncrossover recombination. Nucleic Acids Res 2024; 52:3794-3809. [PMID: 38340339 DOI: 10.1093/nar/gkae083] [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: 02/19/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Meiotic recombination is initiated by programmed double-strand breaks (DSBs). Studies in Saccharomyces cerevisiae have shown that, following rapid resection to generate 3' single-stranded DNA (ssDNA) tails, one DSB end engages a homolog partner chromatid and is extended by DNA synthesis, whereas the other end remains associated with its sister. Then, after regulated differentiation into crossover- and noncrossover-fated types, the second DSB end participates in the reaction by strand annealing with the extended first end, along both pathways. This second-end capture is dependent on Rad52, presumably via its known capacity to anneal two ssDNAs. Here, using physical analysis of DNA recombination, we demonstrate that this process is dependent on direct interaction of Rad52 with the ssDNA binding protein, replication protein A (RPA). Furthermore, the absence of this Rad52-RPA joint activity results in a cytologically-prominent RPA spike, which emerges from the homolog axes at sites of crossovers during the pachytene stage of the meiotic prophase. Our findings suggest that this spike represents the DSB end of a broken chromatid caused by either the displaced leading DSB end or the second DSB end, which has been unable to engage with the partner homolog-associated ssDNA. These and other results imply a close correspondence between Rad52-RPA roles in meiotic recombination and mitotic DSB repair.
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Affiliation(s)
- Jeong H Joo
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Soogil Hong
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Mika T Higashide
- Institute for Protein Research, Graduate School of Science, Osaka University, Osaka 565-0871, Japan
| | - Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Deagu 41061, South Korea
| | - Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Min-Su Lee
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Akira Shinohara
- Institute for Protein Research, Graduate School of Science, Osaka University, Osaka 565-0871, Japan
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge 02138, USA
| | - Keun P Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
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15
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Huang PC, Hong S, Mimitou EP, Kim KP, Murakami H, Keeney S. Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589955. [PMID: 38659928 PMCID: PMC11042300 DOI: 10.1101/2024.04.17.589955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
DNA double-strand breaks (DSBs) are nucleolytically processed to generate single-stranded DNA tails for homologous recombination. In Saccharomyces cerevisiae meiosis, this 5'-to-3' resection involves initial nicking by the Mre11-Rad50-Xrs2 complex (MRX) plus Sae2, then exonucleolytic digestion by Exo1. Chromatin remodeling adjacent to meiotic DSBs is thought to be necessary for resection, but the relevant remodeling activity was unknown. Here we show that the SWI/SNF-like ATPase Fun30 plays a major, non-redundant role in resecting meiotic DSBs. A fun30 null mutation shortened resection tract lengths almost as severely as an exo1-nd (nuclease-dead) mutation, and resection was further shortened in the fun30 exo1-nd double mutant. Fun30 associates with chromatin in response to meiotic DSBs, and the constitutive positioning of nucleosomes governs resection endpoint locations in the absence of Fun30. We infer that Fun30 directly promotes both the MRX- and Exo1-dependent steps in resection, possibly by removing nucleosomes from broken chromatids. Moreover, we found that the extremely short resection in the fun30 exo1-nd double mutant is accompanied by compromised interhomolog recombination bias, leading to defects in recombination and chromosome segregation. Thus, this study also provides insight about the minimal resection lengths needed for robust recombination.
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Affiliation(s)
- Pei-Ching Huang
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Soogil Hong
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Eleni P. Mimitou
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Keun P. Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
- Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 06974, South Korea
| | - Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Scott Keeney
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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16
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Dereli I, Telychko V, Papanikos F, Raveendran K, Xu J, Boekhout M, Stanzione M, Neuditschko B, Imjeti NS, Selezneva E, Tuncay H, Demir S, Giannattasio T, Gentzel M, Bondarieva A, Stevense M, Barchi M, Schnittger A, Weir JR, Herzog F, Keeney S, Tóth A. Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes. Nat Commun 2024; 15:2941. [PMID: 38580643 PMCID: PMC10997794 DOI: 10.1038/s41467-024-47020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
Programmed DNA double-strand break (DSB) formation is a crucial feature of meiosis in most organisms. DSBs initiate recombination-mediated linking of homologous chromosomes, which enables correct chromosome segregation in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We uncover in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms. Both IHO1 phosphorylation and formation of axial IHO1 platforms are diminished by chemical inhibition of DBF4-dependent kinase (DDK), suggesting that DDK contributes to the control of the axial DSB-machinery. Furthermore, we show that axial IHO1 platforms are based on an interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.
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Affiliation(s)
- Ihsan Dereli
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Vladyslav Telychko
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Frantzeskos Papanikos
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Kavya Raveendran
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Jiaqi Xu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Michiel Boekhout
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Marcello Stanzione
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Benjamin Neuditschko
- Institute Krems Bioanalytics, IMC University of Applied Sciences, 3500, Krems, Austria
| | - Naga Sailaja Imjeti
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Elizaveta Selezneva
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hasibe Tuncay
- Department of Developmental Biology, University of Hamburg, 22609, Hamburg, Germany
| | - Sevgican Demir
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Teresa Giannattasio
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Marc Gentzel
- Core Facility Mass Spectrometry & Proteomics, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Anastasiia Bondarieva
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Michelle Stevense
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Marco Barchi
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
- Saint Camillus International University of Health Sciences, Rome, Italy
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, 22609, Hamburg, Germany
| | - John R Weir
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Franz Herzog
- Institute Krems Bioanalytics, IMC University of Applied Sciences, 3500, Krems, Austria
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Attila Tóth
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany.
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17
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Zou M, Shabala S, Zhao C, Zhou M. Molecular mechanisms and regulation of recombination frequency and distribution in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:86. [PMID: 38512498 PMCID: PMC10957645 DOI: 10.1007/s00122-024-04590-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
KEY MESSAGE Recent developments in understanding the distribution and distinctive features of recombination hotspots are reviewed and approaches are proposed to increase recombination frequency in coldspot regions. Recombination events during meiosis provide the foundation and premise for creating new varieties of crops. The frequency of recombination in different genomic regions differs across eukaryote species, with recombination generally occurring more frequently at the ends of chromosomes. In most crop species, recombination is rare in centromeric regions. If a desired gene variant is linked in repulsion with an undesired variant of a second gene in a region with a low recombination rate, obtaining a recombinant plant combining two favorable alleles will be challenging. Traditional crop breeding involves combining desirable genes from parental plants into offspring. Therefore, understanding the mechanisms of recombination and factors affecting the occurrence of meiotic recombination is important for crop breeding. Here, we review chromosome recombination types, recombination mechanisms, genes and proteins involved in the meiotic recombination process, recombination hotspots and their regulation systems and discuss how to increase recombination frequency in recombination coldspot regions.
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Affiliation(s)
- Meilin Zou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, 6009, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia.
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18
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Pizzul P, Casari E, Rinaldi C, Gnugnoli M, Mangiagalli M, Tisi R, Longhese MP. Rif2 interaction with Rad50 counteracts Tel1 functions in checkpoint signalling and DNA tethering by releasing Tel1 from MRX binding. Nucleic Acids Res 2024; 52:2355-2371. [PMID: 38180815 PMCID: PMC10954470 DOI: 10.1093/nar/gkad1246] [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: 07/15/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
The yeast Rif2 protein is known to inhibit Mre11 nuclease and the activation of Tel1 kinase through a short motif termed MIN, which binds the Rad50 subunit and simulates its ATPase activity in vitro. The mechanism by which Rif2 restrains Tel1 activation and the consequences of this inhibition at DNA double-strand breaks (DSBs) are poorly understood. In this study, we employed AlphaFold-Multimer modelling to pinpoint and validate the interaction surface between Rif2 MIN and Rad50. We also engineered the rif2-S6E mutation that enhances the inhibitory effect of Rif2 by increasing Rif2-Rad50 interaction. Unlike rif2Δ, the rif2-S6E mutation impairs hairpin cleavage. Furthermore, it diminishes Tel1 activation by inhibiting Tel1 binding to DSBs while leaving MRX association unchanged, indicating that Rif2 can directly inhibit Tel1 recruitment to DSBs. Additionally, Rif2S6E reduces Tel1-MRX interaction and increases stimulation of ATPase by Rad50, indicating that Rif2 binding to Rad50 induces an ADP-bound MRX conformation that is not suitable for Tel1 binding. The decreased Tel1 recruitment to DSBs in rif2-S6E cells impairs DSB end-tethering and this bridging defect is suppressed by expressing a Tel1 mutant variant that increases Tel1 persistence at DSBs, suggesting a direct role for Tel1 in the bridging of DSB ends.
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Affiliation(s)
- Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Marco Gnugnoli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Marco Mangiagalli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
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19
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Legrand S, Saifudeen A, Bordelet H, Vernerey J, Guille A, Bignaud A, Thierry A, Acquaviva L, Gaudin M, Sanchez A, Johnson D, Friedrich A, Schacherer J, Neale MJ, Borde V, Koszul R, Llorente B. Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri. Proc Natl Acad Sci U S A 2024; 121:e2312820121. [PMID: 38478689 PMCID: PMC10962940 DOI: 10.1073/pnas.2312820121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/24/2024] [Indexed: 03/27/2024] Open
Abstract
Meiotic recombination shows broad variations across species and along chromosomes and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here, we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence of recruitment of the two chromosome axis proteins Red1 and Hop1, essential for proper Spo11-DSBs formation. Furthermore, cytological observation of spread pachytene meiotic chromosomes reveals that Lakl0C-left does not undergo synapsis. However, we show that the behavior of Lakl0C-left is independent of its particularly early replication timing and is not accompanied by any peculiar chromosome structure as detectable by Hi-C in this yet poorly studied yeast. Finally, we observed an accumulation of heterozygous mutations on Lakl0C-left and a sexual dimorphism of the haploid meiotic offspring, supporting a direct effect of this absence of meiotic recombination on L. kluyveri genome evolution and fitness. Because suppression of meiotic recombination on sex chromosomes is widely observed across eukaryotes, the mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.
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Affiliation(s)
- Sylvain Legrand
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Asma Saifudeen
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Hélène Bordelet
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Julien Vernerey
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Arnaud Guille
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Laurent Acquaviva
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Maxime Gaudin
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Aurore Sanchez
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Anne Friedrich
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Valérie Borde
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Bertrand Llorente
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
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20
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López Ruiz LM, Johnson D, Gittens WH, Brown GGB, Allison RM, Neale MJ. Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference. PLoS Genet 2024; 20:e1011140. [PMID: 38427688 PMCID: PMC10936813 DOI: 10.1371/journal.pgen.1011140] [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: 04/27/2023] [Revised: 03/13/2024] [Accepted: 01/17/2024] [Indexed: 03/03/2024] Open
Abstract
During meiosis, genetic recombination is initiated by the formation of many DNA double-strand breaks (DSBs) catalysed by the evolutionarily conserved topoisomerase-like enzyme, Spo11, in preferred genomic sites known as hotspots. DSB formation activates the Tel1/ATM DNA damage responsive (DDR) kinase, locally inhibiting Spo11 activity in adjacent hotspots via a process known as DSB interference. Intriguingly, in S. cerevisiae, over short genomic distances (<15 kb), Spo11 activity displays characteristics of concerted activity or clustering, wherein the frequency of DSB formation in adjacent hotspots is greater than expected by chance. We have proposed that clustering is caused by a limited number of sub-chromosomal domains becoming primed for DSB formation. Here, we provide evidence that DSB clustering is abolished when meiotic prophase timing is extended via deletion of the NDT80 transcription factor. We propose that extension of meiotic prophase enables most cells, and therefore most chromosomal domains within them, to reach an equilibrium state of similar Spo11-DSB potential, reducing the impact that priming has on estimates of coincident DSB formation. Consistent with this view, when Tel1 is absent but Ndt80 is present and thus cells are able to rapidly exit meiotic prophase, genome-wide maps of Spo11-DSB formation are skewed towards pericentromeric regions and regions that load pro-DSB factors early-revealing regions of preferential priming-but this effect is abolished when NDT80 is deleted. Our work highlights how the stochastic nature of Spo11-DSB formation in individual cells within the limited temporal window of meiotic prophase can cause localised DSB clustering-a phenomenon that is exacerbated in tel1Δ cells due to the dual roles that Tel1 has in DSB interference and meiotic prophase checkpoint control.
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Affiliation(s)
- Luz María López Ruiz
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - William H. Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - George G. B. Brown
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rachal M. Allison
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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21
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Essawy MM, Campbell C. Enzymatic Processing of DNA-Protein Crosslinks. Genes (Basel) 2024; 15:85. [PMID: 38254974 PMCID: PMC10815813 DOI: 10.3390/genes15010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).
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Affiliation(s)
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA;
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22
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Brown GGB, Gittens WH, Allison RM, Oliver AW, Neale MJ. CC-seq: Nucleotide-Resolution Mapping of Spo11 DNA Double-Strand Breaks in S. cerevisiae Cells. Methods Mol Biol 2024; 2818:3-22. [PMID: 39126464 DOI: 10.1007/978-1-0716-3906-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
During meiosis, Spo11 generates DNA double-strand breaks to induce recombination, becoming covalently attached to the 5' ends on both sides of the break during this process. Such Spo11 "covalent complexes" are transient in wild-type cells, but accumulate in nuclease mutants unable to initiate repair. The CC-seq method presented here details how to map the location of these Spo11 complexes genome-wide with strand-specific nucleotide-resolution accuracy in synchronized Saccharomyces cerevisiae meiotic cells.
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Affiliation(s)
- George G B Brown
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Will H Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Rachal M Allison
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
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23
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Saha LK, Pommier Y. TOP3A coupling with replication forks and repair of TOP3A cleavage complexes. Cell Cycle 2024; 23:115-130. [PMID: 38341866 PMCID: PMC11037291 DOI: 10.1080/15384101.2024.2314440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 02/13/2024] Open
Abstract
Humans have two Type IA topoisomerases, topoisomerase IIIα (TOP3A) and topoisomerase IIIβ (TOP3B). In this review, we focus on the role of human TOP3A in DNA replication and highlight the recent progress made in understanding TOP3A in the context of replication. Like other topoisomerases, TOP3A acts by a reversible mechanism of cleavage and rejoining of DNA strands allowing changes in DNA topology. By cleaving and resealing single-stranded DNA, it generates TOP3A-linked single-strand breaks as TOP3A cleavage complexes (TOP3Accs) with a TOP3A molecule covalently bound to the 5´-end of the break. TOP3A is critical for both mitochondrial and for nuclear DNA replication. Here, we discuss the formation and repair of irreversible TOP3Accs, as their presence compromises genome integrity as they form TOP3A DNA-protein crosslinks (TOP3A-DPCs) associated with DNA breaks. We discuss the redundant pathways that repair TOP3A-DPCs, and how their defects are a source of DNA damage leading to neurological diseases and mitochondrial disorders.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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24
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Tian Y, Liu L, Gao J, Wang R. Homologous chromosome pairing: The linchpin of accurate segregation in meiosis. J Cell Physiol 2024; 239:3-19. [PMID: 38032002 DOI: 10.1002/jcp.31166] [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: 09/09/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
Meiosis is a specialized cell division that occurs in sexually reproducing organisms, generating haploid gametes containing half the chromosome number through two rounds of cell division. Homologous chromosomes pair and prepare for their proper segregation in subsequent divisions. How homologous chromosomes recognize each other and achieve pairing is an important question. Early studies showed that in most organisms, homologous pairing relies on homologous recombination. However, pairing mechanisms differ across species. Evidence indicates that chromosomes are dynamic and move during early meiotic stages, facilitating pairing. Recent studies in various model organisms suggest conserved mechanisms and key regulators of homologous chromosome pairing. This review summarizes these findings and compare similarities and differences in homologous chromosome pairing mechanisms across species.
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Affiliation(s)
- Yuqi Tian
- Center for Cell Structure and Function, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, China
| | - Libo Liu
- Center for Cell Structure and Function, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, China
| | - Jinmin Gao
- Center for Cell Structure and Function, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, China
| | - Ruoxi Wang
- Center for Cell Structure and Function, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, China
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25
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Hernández I, Álvarez-Melo D, de Lacoba MG, Carballo JA. SPO-Seq: An Accessible Method for Efficient Evaluation of Spo11 Catalytic Activity and Profiling Meiotic DSB Hotspots in Saccharomyces cerevisiae. Methods Mol Biol 2024; 2818:23-43. [PMID: 39126465 DOI: 10.1007/978-1-0716-3906-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
Meiotic recombination is a key process facilitating the formation of crossovers and the exchange of genetic material between homologous chromosomes in early meiosis. This involves controlled double-strand breaks (DSBs) formation catalyzed by Spo11. DSBs exhibit a preferential location in specific genomic regions referred to as hotspots, and their variability is tied to varying Spo11 activity levels. We have refined a ChIP-Seq technique, called SPO-Seq, to map Spo11-specific DSB formation in Saccharomyces cerevisiae. The chapter describes our streamlined approach and the developed bioinformatic tools for processing data and comparing with existing DSB hotspot maps. Through this combined experimental and computational approach, we aim to enhance our understanding of meiotic recombination and genetic exchange processes in budding yeast, with the potential to expand this methodology to other organisms by applying a few modifications.
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Affiliation(s)
- Iván Hernández
- Gene Therapy Unit, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - David Álvarez-Melo
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
| | | | - Jesús A Carballo
- Institute of Functional Biology and Genomics, (CSIC - USAL), Salamanca, Spain.
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26
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Essawy M, Chesner L, Alshareef D, Ji S, Tretyakova N, Campbell C. Ubiquitin signaling and the proteasome drive human DNA-protein crosslink repair. Nucleic Acids Res 2023; 51:12174-12184. [PMID: 37843153 PMCID: PMC10711432 DOI: 10.1093/nar/gkad860] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are large cytotoxic DNA lesions that form following exposure to chemotherapeutic drugs and environmental chemicals. Nucleotide excision repair (NER) and homologous recombination (HR) promote survival following exposure to DPC-inducing agents. However, it is not known how cells recognize DPC lesions, or what mechanisms selectively target DPC lesions to these respective repair pathways. To address these questions, we examined DPC recognition and repair by transfecting a synthetic DPC lesion comprised of the human oxoguanine glycosylase (OGG1) protein crosslinked to double-stranded M13MP18 into human cells. In wild-type cells, this lesion is efficiently repaired, whereas cells deficient in NER can only repair this lesion if an un-damaged homologous donor is co-transfected. Transfected DPC is subject to rapid K63 polyubiquitination. In NER proficient cells, the DPC is subject to K48 polyubiquitination, and is removed via a proteasome-dependent mechanism. In NER-deficient cells, the DNA-conjugated protein is not subject to K48 polyubiquitination. Instead, the K63 tag remains attached, and is only lost when a homologous donor molecule is present. Taken together, these results support a model in which selective addition of polyubiquitin chains to DNA-crosslinked protein leads to selective recruitment of the proteasome and the cellular NER and recombinational DNA repair machinery.
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Affiliation(s)
- Maram Essawy
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Lisa Chesner
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Duha Alshareef
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
| | - Shaofei Ji
- Department of Medicinal Chemistry, University of Minnesota, Minnesota, MN 55455, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minnesota, MN 55455, USA
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minnesota, MN 55455, USA
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27
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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28
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Dereli I, Telychko V, Papanikos F, Raveendran K, Xu J, Boekhout M, Stanzione M, Neuditschko B, Imjeti NS, Selezneva E, Erbasi HT, Demir S, Giannattasio T, Gentzel M, Bondarieva A, Stevense M, Barchi M, Schnittger A, Weir JR, Herzog F, Keeney S, Tóth A. Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568863. [PMID: 38077023 PMCID: PMC10705248 DOI: 10.1101/2023.11.27.568863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Programmed DNA double-strand break (DSB) formation is a unique meiotic feature that initiates recombination-mediated linking of homologous chromosomes, thereby enabling chromosome number halving in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We discovered in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms, which are based on a DBF4-dependent kinase (DDK)-modulated interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.
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29
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Allison RM, Johnson DJ, Neale MJ, Gray S. Recombinase-independent chromosomal rearrangements between dispersed inverted repeats in Saccharomyces cerevisiae meiosis. Nucleic Acids Res 2023; 51:9703-9715. [PMID: 37548404 PMCID: PMC10570019 DOI: 10.1093/nar/gkad650] [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: 10/29/2021] [Revised: 07/16/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) uses a DNA template with similar sequence to restore genetic identity. Allelic DNA repair templates can be found on the sister chromatid or homologous chromosome. During meiotic recombination, DSBs preferentially repair from the homologous chromosome, with a proportion of HR events generating crossovers. Nevertheless, regions of similar DNA sequence exist throughout the genome, providing potential DNA repair templates. When DSB repair occurs at these non-allelic loci (termed ectopic recombination), chromosomal duplications, deletions and rearrangements can arise. Here, we characterize in detail ectopic recombination arising between a dispersed pair of inverted repeats in wild-type Saccharomyces cerevisiae at both a local and a chromosomal scale-the latter identified via gross chromosomal acentric and dicentric chromosome rearrangements. Mutation of the DNA damage checkpoint clamp loader Rad24 and the RecQ helicase Sgs1 causes an increase in ectopic recombination. Unexpectedly, additional mutation of the RecA orthologues Rad51 and Dmc1 alters-but does not abolish-the type of ectopic recombinants generated, revealing a novel class of inverted chromosomal rearrangement driven by the single-strand annealing pathway. These data provide important insights into the role of key DNA repair proteins in regulating DNA repair pathway and template choice during meiosis.
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Affiliation(s)
- Rachal M Allison
- Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, UK
| | - Dominic J Johnson
- Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, UK
| | - Stephen Gray
- School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
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30
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Börner GV, Hochwagen A, MacQueen AJ. Meiosis in budding yeast. Genetics 2023; 225:iyad125. [PMID: 37616582 PMCID: PMC10550323 DOI: 10.1093/genetics/iyad125] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/13/2023] [Indexed: 08/26/2023] Open
Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
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Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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31
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Giannattasio T, Testa E, Faieta M, Lampitto M, Nardozi D, di Cecca S, Russo A, Barchi M. The proper interplay between the expression of Spo11 splice isoforms and the structure of the pseudoautosomal region promotes XY chromosomes recombination. Cell Mol Life Sci 2023; 80:279. [PMID: 37682311 PMCID: PMC10491539 DOI: 10.1007/s00018-023-04912-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023]
Abstract
XY chromosome missegregation is relatively common in humans and can lead to sterility or the generation of aneuploid spermatozoa. A leading cause of XY missegregation in mammals is the lack of formation of double-strand breaks (DSBs) in the pseudoautosomal region (PAR), a defect that may occur in mice due to faulty expression of Spo11 splice isoforms. Using a knock-in (ki) mouse that expresses only the single Spo11β splice isoform, here we demonstrate that by varying the genetic background of mice, the length of chromatin loops extending from the PAR axis and the XY recombination proficiency varies. In spermatocytes of C57Spo11βki/- mice, in which loops are relatively short, recombination/synapsis between XY is fairly normal. In contrast, in cells of C57/129Spo11βki/- males where PAR loops are relatively long, formation of DSBs in the PAR (more frequently the Y-PAR) and XY synapsis fails at a high rate, and mice produce sperm with sex-chromosomal aneuploidy. However, if the entire set of Spo11 splicing isoforms is expressed by a wild type allele in the C57/129 background, XY recombination and synapsis is recovered. By generating a Spo11αki mouse model, we prove that concomitant expression of SPO11β and SPO11α isoforms, boosts DSB formation in the PAR. Based on these findings, we propose that SPO11 splice isoforms cooperate functionally in promoting recombination in the PAR, constraining XY asynapsis defects that may arise due to differences in the conformation of the PAR between mouse strains.
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Affiliation(s)
- Teresa Giannattasio
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, Rome, Italy
| | - Erika Testa
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, Rome, Italy
| | - Monica Faieta
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, Rome, Italy
| | - Matteo Lampitto
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, Rome, Italy
| | - Daniela Nardozi
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, Rome, Italy
| | - Stefano di Cecca
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, Rome, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Marco Barchi
- Department of Biomedicine and Prevention, Section of Anatomy, University of Rome Tor Vergata, Rome, Italy.
- Department of Biomedical Science, Lady of Good Counsel University, Tirana, Albania.
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32
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Dickinson L, Yuan W, LeBlanc C, Thomson G, Wang S, Jacob Y. Regulation of gene editing using T-DNA concatenation. NATURE PLANTS 2023; 9:1398-1408. [PMID: 37653336 PMCID: PMC11193869 DOI: 10.1038/s41477-023-01495-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Transformation via Agrobacterium tumefaciens is the predominant method used to introduce exogenous DNA into plant genomes1,2. Transfer DNA (T-DNA) originating from Agrobacterium can be integrated as a single copy or in complex concatenated forms3,4, but the mechanisms affecting final T-DNA structure remain unknown. Here we demonstrate that inclusion of retrotransposon (RT)-derived sequences in T-DNA can increase T-DNA copy number by more than 50-fold in Arabidopsis thaliana. These additional T-DNA copies are organized into large concatemers, an effect primarily induced by the long terminal repeats (LTRs) of RTs that can be replicated using non-LTR DNA repeats. We found that T-DNA concatenation is dependent on the activity of the DNA repair proteins MRE11, RAD17 and ATR. Finally, we show that T-DNA concatenation can be used to increase the frequency of targeted mutagenesis and gene targeting. Overall, this work uncovers molecular determinants that modulate T-DNA copy number in Arabidopsis and demonstrates the utility of inducing T-DNA concatenation for plant gene editing.
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Affiliation(s)
- Lauren Dickinson
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Wenxin Yuan
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Chantal LeBlanc
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Geoffrey Thomson
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
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Bradley RA, Wolff ID, Cohen PE, Gray S. Dynamic regulatory phosphorylation of mouse CDK2 occurs during meiotic prophase I. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550435. [PMID: 37546989 PMCID: PMC10402020 DOI: 10.1101/2023.07.24.550435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
During prophase I of meiosis, DNA double-strand breaks form throughout the genome, with a subset repairing as crossover events, enabling the accurate segregation of homologous chromosomes during the first meiotic division. The mechanism by which DSBs become selected to repair as crossovers is unknown, although the crossover positioning and levels in each cell indicate it is a highly regulated process. One of the proteins that localises to crossover sites is the serine/threonine cyclin-dependent kinase CDK2. Regulation of CDK2 occurs via phosphorylation at tyrosine 15 (Y15) and threonine 160 (T160) inhibiting and activating the kinase, respectively. In this study we use a combination of immunofluorescence staining on spread spermatocytes and fixed testis sections, and STA-PUT gravitational sedimentation to isolate cells at different developmental stages to further investigate the temporal phospho regulation of CDK2 during prophase I. Western blotting reveals differential levels of the two CDK2 isoforms (CDK233kDa and CDK239kDa) throughout prophase I, with inhibitory phosphorylation of CDK2 at Y15 occurring early in prophase I, localising to telomeres and diminishing as cells enter pachynema. Conversely, the activatory phosphorylation on T160 occurs later, specifically the CDK233kDa isoform, and T160 signal is detected in spermatogonia and pachytene spermatocytes, where it co-localises with the Class I crossover protein MLH3. Taken together, our data reveals intricate control of CDK2 both with regards to levels of the two CDK2 isoforms, and differential regulation via inhibitory and activatory phosphorylation.
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Affiliation(s)
- Rachel A. Bradley
- Department of Biomedical Sciences and Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, 14853, United States of America
| | - Ian D. Wolff
- Department of Biomedical Sciences and Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, 14853, United States of America
| | - Paula E. Cohen
- Department of Biomedical Sciences and Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, 14853, United States of America
| | - Stephen Gray
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
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Yudkina A, Bulgakov N, Kim D, Baranova S, Ishchenko A, Saparbaev M, Koval V, Zharkov D. Abasic site-peptide cross-links are blocking lesions repaired by AP endonucleases. Nucleic Acids Res 2023; 51:6321-6336. [PMID: 37216593 PMCID: PMC10325907 DOI: 10.1093/nar/gkad423] [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: 12/20/2022] [Revised: 04/18/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023] Open
Abstract
Apurinic/apyrimidinic (AP) sites are abundant DNA lesions arising from spontaneous hydrolysis of the N-glycosidic bond and as base excision repair (BER) intermediates. AP sites and their derivatives readily trap DNA-bound proteins, resulting in DNA-protein cross-links. Those are subject to proteolysis but the fate of the resulting AP-peptide cross-links (APPXLs) is unclear. Here, we report two in vitro models of APPXLs synthesized by cross-linking of DNA glycosylases Fpg and OGG1 to DNA followed by trypsinolysis. The reaction with Fpg produces a 10-mer peptide cross-linked through its N-terminus, while OGG1 yields a 23-mer peptide attached through an internal lysine. Both adducts strongly blocked Klenow fragment, phage RB69 polymerase, Saccharolobus solfataricus Dpo4, and African swine fever virus PolX. In the residual lesion bypass, mostly dAMP and dGMP were incorporated by Klenow and RB69 polymerases, while Dpo4 and PolX used primer/template misalignment. Of AP endonucleases involved in BER, Escherichia coli endonuclease IV and its yeast homolog Apn1p efficiently hydrolyzed both adducts. In contrast, E. coli exonuclease III and human APE1 showed little activity on APPXL substrates. Our data suggest that APPXLs produced by proteolysis of AP site-trapped proteins may be removed by the BER pathway, at least in bacterial and yeast cells.
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Affiliation(s)
- Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikita A Bulgakov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Daria V Kim
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Svetlana V Baranova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Groupe “Mechanisms of DNA Repair and Carcinogenesis”, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France
| | - Murat K Saparbaev
- Groupe “Mechanisms of DNA Repair and Carcinogenesis”, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France
| | - Vladimir V Koval
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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35
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Xu W, Liu C, Zhang Z, Sun C, Li Q, Li K, Jiang H, Li W, Sun Q. DEtail-seq is an ultra-efficient and convenient method for meiotic DNA break profiling in multiple organisms. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1392-1407. [PMID: 36723795 DOI: 10.1007/s11427-022-2277-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/02/2023] [Indexed: 06/15/2023]
Abstract
Programmed DNA double-strand break (DSB) formation is a crucial step in meiotic recombination, yet techniques for high-efficiency and precise mapping of the 3' ends of DSBs are still in their infancy. Here, we report a novel technique, named DNA End tailing and sequencing (DEtail-seq), which can directly and ultra-efficiently characterize the 3' ends of meiotic DSBs with near single-nucleotide resolution in a variety of species, including yeast, mouse, and human. We find that the 3' ends of meiotic DSBs are stable without significant resection in budding yeast. Meiotic DSBs are strongly enriched in de novo H3K4me3 peaks in the mouse genome at leptotene stage. We also profile meiotic DSBs in human and find DSB hotspots are enriched near the common fragile sites during human meiosis, especially at CCCTC-binding factor (CTCF)-associated enhancers. Therefore, DEtail-seq provides a powerful method to detect DSB ends in various species, and our results provide new insights into the distribution and regulation of meiotic DSB hotspots.
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Affiliation(s)
- Wei Xu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Zhe Zhang
- Department of Urology, Department of Andrology, Department of Reproductive Medicine Center, and Department of Human Sperm Bank, Peking University Third Hospital, Beijing, 100191, China
| | - Changbin Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qin Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Hui Jiang
- Department of Urology, Department of Andrology, Department of Reproductive Medicine Center, and Department of Human Sperm Bank, Peking University Third Hospital, Beijing, 100191, China.
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
| | - Qianwen Sun
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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36
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Liu C, Xu W, Wang L, Yang Z, Li K, Hu J, Chen Y, Zhang R, Xiao S, Liu W, Wei H, Chen JY, Sun Q, Li W. Dual roles of R-loops in the formation and processing of programmed DNA double-strand breaks during meiosis. Cell Biosci 2023; 13:82. [PMID: 37170281 PMCID: PMC10173651 DOI: 10.1186/s13578-023-01026-2] [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: 01/03/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Meiotic recombination is initiated by Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions called hotspots; however, the factor(s) that specify the positions of meiotic DSB hotspots remain unclear. RESULTS Here, we examined the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, during budding yeast meiosis and found that the R-loops were changed dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage and found that these R-loops were associated with meiotic recombination during yeast meiosis. We show that transcription-replication head-on collisions could promote R-loop formation during meiotic DNA replication, and these R-loops are associated with Spo11. Furthermore, meiotic recombination hotspots can be eliminated by reversing the direction of transcription or replication, and reversing both of these directions can reconstitute the hotspots. CONCLUSIONS Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.
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Affiliation(s)
- Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liying Wang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yinghong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruidan Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sai Xiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenwen Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huafang Wei
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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37
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Giannattasio T, Testa E, Palombo R, Chellini L, Franceschini F, Crevenna Á, Petkov PM, Paronetto MP, Barchi M. The RNA-binding protein FUS/TLS interacts with SPO11 and PRDM9 and localize at meiotic recombination hotspots. Cell Mol Life Sci 2023; 80:107. [PMID: 36967403 PMCID: PMC10040399 DOI: 10.1007/s00018-023-04744-5] [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: 01/24/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
In mammals, meiotic recombination is initiated by the introduction of DNA double strand breaks (DSBs) into narrow segments of the genome, defined as hotspots, which is carried out by the SPO11/TOPOVIBL complex. A major player in the specification of hotspots is PRDM9, a histone methyltransferase that, following sequence-specific DNA binding, generates trimethylation on lysine 4 (H3K4me3) and lysine 36 (H3K36me3) of histone H3, thus defining the hotspots. PRDM9 activity is key to successful meiosis, since in its absence DSBs are redirected to functional sites and synapsis between homologous chromosomes fails. One protein factor recently implicated in guiding PRDM9 activity at hotspots is EWS, a member of the FET family of proteins that also includes TAF15 and FUS/TLS. Here, we demonstrate that FUS/TLS partially colocalizes with PRDM9 on the meiotic chromosome axes, marked by the synaptonemal complex component SYCP3, and physically interacts with PRDM9. Furthermore, we show that FUS/TLS also interacts with REC114, one of the axis-bound SPO11-auxiliary factors essential for DSB formation. This finding suggests that FUS/TLS is a component of the protein complex that promotes the initiation of meiotic recombination. Accordingly, we document that FUS/TLS coimmunoprecipitates with SPO11 in vitro and in vivo. The interaction occurs with both SPO11β and SPO11α splice isoforms, which are believed to play distinct functions in the formation of DSBs in autosomes and male sex chromosomes, respectively. Finally, using chromatin immunoprecipitation experiments, we show that FUS/TLS is localized at H3K4me3-marked hotspots in autosomes and in the pseudo-autosomal region, the site of genetic exchange between the XY chromosomes.
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Affiliation(s)
- Teresa Giannattasio
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Erika Testa
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Ramona Palombo
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy
| | - Flavia Franceschini
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Álvaro Crevenna
- European Molecular Biology Laboratory, Neurobiology and Epigenetics Unit, Monterotondo, Italy
| | | | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy.
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135, Rome, Italy.
| | - Marco Barchi
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy.
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38
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Kawashima Y, Oda AH, Hikida Y, Ohta K. Chromosome-dependent aneuploid formation in Spo11-less meiosis. Genes Cells 2023; 28:129-148. [PMID: 36530025 PMCID: PMC10107155 DOI: 10.1111/gtc.12998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/21/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Deficiency in meiotic recombination leads to aberrant chromosome disjunction during meiosis, often resulting in the lethality of gametes or genetic disorders due to aneuploidy formation. Budding yeasts lacking Spo11, which is essential for initiation of meiotic recombination, produce many inviable spores in meiosis, while very rarely all sets of 16 chromosomes are coincidentally assorted into gametes to form viable spores. We induced meiosis in a spo11∆ diploid, in which homolog pairs can be distinguished by single nucleotide polymorphisms and determined whole-genome sequences of their exceptionally viable spores. We detected no homologous recombination in the viable spores of spo11∆ diploid. Point mutations were fewer in spo11∆ than in wild-type. We observed spo11∆ viable spores carrying a complete diploid set of homolog pairs or haploid spores with a complete haploid set of homologs but with aneuploidy in some chromosomes. In the latter, we found the chromosome-dependence in the aneuploid incidence, which was positively and negatively influenced by the chromosome length and the impact of dosage-sensitive genes, respectively. Selection of aneuploidy during meiosis II or mitosis after spore germination was also chromosome dependent. These results suggest a pathway by which specific chromosomes are more prone to cause aneuploidy, as observed in Down syndrome.
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Affiliation(s)
- Yuri Kawashima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Arisa H Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasushi Hikida
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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39
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Soniat MM, Nguyen G, Kuo HC, Finkelstein IJ. The MRN complex and topoisomerase IIIa-RMI1/2 synchronize DNA resection motor proteins. J Biol Chem 2023; 299:102802. [PMID: 36529288 PMCID: PMC9971906 DOI: 10.1016/j.jbc.2022.102802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
DNA resection-the nucleolytic processing of broken DNA ends-is the first step of homologous recombination. Resection is catalyzed by the resectosome, a multienzyme complex that includes bloom syndrome helicase (BLM), DNA2 or exonuclease 1 nucleases, and additional DNA-binding proteins. Although the molecular players have been known for over a decade, how the individual proteins work together to regulate DNA resection remains unknown. Using single-molecule imaging, we characterized the roles of the MRE11-RAD50-NBS1 complex (MRN) and topoisomerase IIIa (TOP3A)-RMI1/2 during long-range DNA resection. BLM partners with TOP3A-RMI1/2 to form the BTRR (BLM-TOP3A-RMI1/2) complex (or BLM dissolvasome). We determined that TOP3A-RMI1/2 aids BLM in initiating DNA unwinding, and along with MRN, stimulates DNA2-mediated resection. Furthermore, we found that MRN promotes the association between BTRR and DNA and synchronizes BLM and DNA2 translocation to prevent BLM from pausing during resection. Together, this work provides direct observation of how MRN and DNA2 harness the BTRR complex to resect DNA efficiently and how TOP3A-RMI1/2 regulates the helicase activity of BLM to promote efficient DNA repair.
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Affiliation(s)
- Michael M Soniat
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.
| | - Giaochau Nguyen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.
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40
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Huang Y, Roig I. Genetic control of meiosis surveillance mechanisms in mammals. Front Cell Dev Biol 2023; 11:1127440. [PMID: 36910159 PMCID: PMC9996228 DOI: 10.3389/fcell.2023.1127440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Meiosis is a specialized cell division that generates haploid gametes and is critical for successful sexual reproduction. During the extended meiotic prophase I, homologous chromosomes progressively pair, synapse and desynapse. These chromosomal dynamics are tightly integrated with meiotic recombination (MR), during which programmed DNA double-strand breaks (DSBs) are formed and subsequently repaired. Consequently, parental chromosome arms reciprocally exchange, ultimately ensuring accurate homolog segregation and genetic diversity in the offspring. Surveillance mechanisms carefully monitor the MR and homologous chromosome synapsis during meiotic prophase I to avoid producing aberrant chromosomes and defective gametes. Errors in these critical processes would lead to aneuploidy and/or genetic instability. Studies of mutation in mouse models, coupled with advances in genomic technologies, lead us to more clearly understand how meiosis is controlled and how meiotic errors are linked to mammalian infertility. Here, we review the genetic regulations of these major meiotic events in mice and highlight our current understanding of their surveillance mechanisms. Furthermore, we summarize meiotic prophase genes, the mutations that activate the surveillance system leading to meiotic prophase arrest in mouse models, and their corresponding genetic variants identified in human infertile patients. Finally, we discuss their value for the diagnosis of causes of meiosis-based infertility in humans.
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Affiliation(s)
- Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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41
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Brinkmeier J, Coelho S, de Massy B, Bourbon HM. Evolution and Diversity of the TopoVI and TopoVI-like Subunits With Extensive Divergence of the TOPOVIBL subunit. Mol Biol Evol 2022; 39:msac227. [PMID: 36256608 PMCID: PMC9665070 DOI: 10.1093/molbev/msac227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Type II DNA topoisomerases regulate topology by double-stranded DNA cleavage and ligation. The TopoVI family of DNA topoisomerase, first identified and biochemically characterized in Archaea, represents, with TopoVIII and mini-A, the type IIB family. TopoVI has several intriguing features in terms of function and evolution. TopoVI has been identified in some eukaryotes, and a global view is lacking to understand its evolutionary pattern. In addition, in eukaryotes, the two TopoVI subunits (TopoVIA and TopoVIB) have been duplicated and have evolved to give rise to Spo11 and TopoVIBL, forming TopoVI-like (TopoVIL), a complex essential for generating DNA breaks that initiate homologous recombination during meiosis. TopoVIL is essential for sexual reproduction. How the TopoVI subunits have evolved to ensure this meiotic function is unclear. Here, we investigated the phylogenetic conservation of TopoVI and TopoVIL. We demonstrate that BIN4 and RHL1, potentially interacting with TopoVIB, have co-evolved with TopoVI. Based on model structures, this observation supports the hypothesis for a role of TopoVI in decatenation of replicated chromatids and predicts that in eukaryotes the TopoVI catalytic complex includes BIN4 and RHL1. For TopoVIL, the phylogenetic analysis of Spo11, which is highly conserved among Eukarya, highlighted a eukaryal-specific N-terminal domain that may be important for its regulation. Conversely, TopoVIBL was poorly conserved, giving rise to ATP hydrolysis-mutated or -truncated protein variants, or was undetected in some species. This remarkable plasticity of TopoVIBL provides important information for the activity and function of TopoVIL during meiosis.
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Affiliation(s)
- Julia Brinkmeier
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Susana Coelho
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Henri-Marc Bourbon
- Centre de Biologie Intégrative, CNRS, Université de Toulouse, Toulouse 31400, France
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McCarthy-Leo C, Darwiche F, Tainsky MA. DNA Repair Mechanisms, Protein Interactions and Therapeutic Targeting of the MRN Complex. Cancers (Basel) 2022; 14:5278. [PMID: 36358700 PMCID: PMC9656488 DOI: 10.3390/cancers14215278] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
Repair of a DNA double-strand break relies upon a pathway of proteins to identify damage, regulate cell cycle checkpoints, and repair the damage. This process is initiated by a sensor protein complex, the MRN complex, comprised of three proteins-MRE11, RAD50, and NBS1. After a double-stranded break, the MRN complex recruits and activates ATM, in-turn activating other proteins such as BRCA1/2, ATR, CHEK1/2, PALB2 and RAD51. These proteins have been the focus of many studies for their individual roles in hereditary cancer syndromes and are included on several genetic testing panels. These panels have enabled us to acquire large amounts of genetic data, much of which remains a challenge to interpret due to the presence of variants of uncertain significance (VUS). While the primary aim of clinical testing is to accurately and confidently classify variants in order to inform medical management, the presence of VUSs has led to ambiguity in genetic counseling. Pathogenic variants within MRN complex genes have been implicated in breast, ovarian, prostate, colon cancers and gliomas; however, the hundreds of VUSs within MRE11, RAD50, and NBS1 precludes the application of these data in genetic guidance of carriers. In this review, we discuss the MRN complex's role in DNA double-strand break repair, its interactions with other cancer predisposing genes, the variants that can be found within the three MRN complex genes, and the MRN complex's potential as an anti-cancer therapeutic target.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Fatima Darwiche
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael A. Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Karmanos Cancer Institute at Wayne State University School of Medicine, Detroit, MI 48201, USA
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Sun Y, Soans E, Mishina M, Petricci E, Pommier Y, Nitiss KC, Nitiss JL. Requirements for MRN endonuclease processing of topoisomerase II-mediated DNA damage in mammalian cells. Front Mol Biosci 2022; 9:1007064. [PMID: 36213114 PMCID: PMC9537633 DOI: 10.3389/fmolb.2022.1007064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
During a normal topoisomerase II (TOP2) reaction, the enzyme forms a covalent enzyme DNA intermediate consisting of a 5′ phosphotyrosyl linkage between the enzyme and DNA. While the enzyme typically rejoins the transient breakage after strand passage, a variety of conditions including drugs targeting TOP2 can inhibit DNA resealing, leading to enzyme-mediated DNA damage. A critical aspect of the repair of TOP2-mediated damage is the removal of the TOP2 protein covalently bound to DNA. While proteolysis plays a role in repairing this damage, nucleolytic enzymes must remove the phosphotyrosyl-linked peptide bound to DNA. The MRN complex has been shown to participate in the removal of TOP2 protein from DNA following cellular treatment with TOP2 poisons. In this report we used an optimized ICE (In vivo Complex of Enzyme) assay to measure covalent TOP2/DNA complexes. In agreement with previous independent reports, we find that the absence or inhibition of the MRE11 endonuclease results in elevated levels of both TOP2α and TOP2β covalent complexes. We also examined levels of TOP2 covalent complexes in cells treated with the proteasome inhibitor MG132. Although MRE11 inhibition plus MG132 was not synergistic in etoposide-treated cells, ectopic overexpression of MRE11 resulted in removal of TOP2 even in the presence of MG132. We also found that VCP/p97 inhibition led to elevated TOP2 covalent complexes and prevented the removal of TOP2 covalent complexes by MRE11 overexpression. Our results demonstrate the existence of multiple pathways for proteolytic processing of TOP2 prior to nucleolytic processing, and that MRE11 can process TOP2 covalent complexes even when the proteasome is inhibited. The interactions between VCP/p97 and proteolytic processing of TOP2 covalent complexes merit additional investigation.
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Affiliation(s)
- Yilun Sun
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
| | - Eroica Soans
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | - Margarita Mishina
- St. Jude Children’s Research Hospital Memphis, Memphis, TN, United States
| | | | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karin C. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, Rockford, IL, United States
- *Correspondence: Yilun Sun, ; John L. Nitiss,
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Yuan S, Huang T, Bao Z, Wang S, Wu X, Liu J, Liu H, Chen ZJ. The histone modification reader ZCWPW1 promotes double-strand break repair by regulating cross-talk of histone modifications and chromatin accessibility at meiotic hotspots. Genome Biol 2022; 23:187. [PMID: 36068616 PMCID: PMC9446545 DOI: 10.1186/s13059-022-02758-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The PRDM9-dependent histone methylation H3K4me3 and H3K36me3 function in assuring accurate homologous recombination at recombination hotspots in mammals. Beyond histone methylation, H3 lysine 9 acetylation (H3K9ac) is also greatly enriched at recombination hotspots. Previous work has indicated the potential cross-talk between H3K4me3 and H3K9ac at recombination hotspots, but it is still unknown what molecular mechanisms mediate the cross-talk between the two histone modifications at hotspots or how the cross-talk regulates homologous recombination in meiosis. RESULTS Here, we find that the histone methylation reader ZCWPW1 is essential for maintaining H3K9ac by antagonizing HDAC proteins' deacetylation activity and further promotes chromatin openness at recombination hotspots thus preparing the way for homologous recombination during meiotic double-strand break repair. Interestingly, ectopic expression of the germ-cell-specific protein ZCWPW1 in human somatic cells enhances double-strand break repair via homologous recombination. CONCLUSIONS Taken together, our findings provide new insights into how histone modifications and their associated regulatory proteins collectively regulate meiotic homologous recombination.
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Affiliation(s)
- Shenli Yuan
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, China National Center for Bioinformation, and Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Huang
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China.
| | - Ziyou Bao
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Shiyu Wang
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Xinyue Wu
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, China National Center for Bioinformation, and Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China.
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China.
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China.
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OsRAD51 Plays a Vital Role in Promoting Homologous Recombination in Rice Meiosis. Int J Mol Sci 2022; 23:ijms23179906. [PMID: 36077304 PMCID: PMC9456343 DOI: 10.3390/ijms23179906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Meiotic recombination plays a pivotal role in achieving accurate chromosomal segregation and increasing genetic diversity. In the homologous recombination pathway, the detailed mechanisms of how OsRAD51 and OsDMC1 work in rice meiosis remain to be explored. Here, we obtained different types of mutants for Osrad51a1, Osrad51a2, Osdmc1a, and Osdmc1b through CRISPR/Cas9. Both Osrad51a1 and Osrad51a2 exhibited normal vegetative growth and fertility. Osrad51 (Osrad51a1 Osrad51a2) mutant plants show normal vegetative growth but exhibit complete sterility, indicating that OsRAD51A1 and OsRAD51A2 are functionally redundant in rice fertility. In contrast to the wild type, Osrad51 chromosomes are not paired perfectly at pachytene and synaptonemal complex (SC) formation is deficient. Moreover, univalents and multivalent associations were observed at metaphase I, chromosome fragments presented at anaphase I, and crossover formation is basically suppressed in Osrad51 pollen mother cells (PMCs). OsRAD51 foci emerge at leptotene and disappear from late pachytene and chromosome localization of OsRAD51 depends on the formation of double-strand breaks (DSBs). Most OsRAD51 foci can co-localize with OsDMC1 signals. OsRAD51 is essential for the loading of OsDMC1 onto chromosomes, and vice versa. In addition, both OsRAD51 and OsDMC1 can interact with OsFIGL1 and OsBRCA2, two important components in rice meiosis. Moreover, the Osrad51 Osdmc1 (Osrad51a1 Osrad51a2 Osdmc1a Osdmc1b) quadruple mutant PMCs exhibited similar defective phenotypes as Osrad51 in homologous pairing, synapsis, and DSB repair. Taken together, our results suggest that the recombinases DMC1 and RAD51 may functionally depend on each other and play important roles in meiotic recombination during meiosis in rice.
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Xie H, Wang X, Jin M, Li L, Zhu J, Kang Y, Chen Z, Sun Y, Zhao C. Cilia regulate meiotic recombination in zebrafish. J Mol Cell Biol 2022; 14:6671532. [PMID: 35981808 PMCID: PMC9764210 DOI: 10.1093/jmcb/mjac049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/16/2022] [Accepted: 08/15/2022] [Indexed: 01/14/2023] Open
Abstract
Meiosis is essential for evolution and genetic diversity in almost all sexual eukaryotic organisms. The mechanisms of meiotic recombination, such as synapsis, have been extensively investigated. However, it is still unclear whether signals from the cytoplasm or even from outside of the cell can regulate the meiosis process. Cilia are microtubule-based structures that protrude from the cell surface and function as signaling hubs to sense extracellular signals. Here, we reported an unexpected and critical role of cilia during meiotic recombination. During gametogenesis of zebrafish, cilia were specifically present in the prophase stages of both primary spermatocytes and primary oocytes. By developing a germ cell-specific CRISPR/Cas9 system, we demonstrated that germ cell-specific depletion of ciliary genes resulted in compromised double-strand break repair, reduced crossover formation, and increased germ cell apoptosis. Our study reveals a previously undiscovered role for cilia during meiosis and suggests that extracellular signals may regulate meiotic recombination via this particular organelle.
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Affiliation(s)
| | | | - Minjun Jin
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Sars-Fang Centre, Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lanqin Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Sars-Fang Centre, Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Junwen Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan 430072, China,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunsi Kang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Sars-Fang Centre, Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhe Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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Differentiated function and localisation of SPO11-1 and PRD3 on the chromosome axis during meiotic DSB formation in Arabidopsis thaliana. PLoS Genet 2022; 18:e1010298. [PMID: 35857772 PMCID: PMC9342770 DOI: 10.1371/journal.pgen.1010298] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 08/01/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022] Open
Abstract
During meiosis, DNA double-strand breaks (DSBs) occur throughout the genome, a subset of which are repaired to form reciprocal crossovers between chromosomes. Crossovers are essential to ensure balanced chromosome segregation and to create new combinations of genetic variation. Meiotic DSBs are formed by a topoisomerase-VI-like complex, containing catalytic (e.g. SPO11) proteins and auxiliary (e.g. PRD3) proteins. Meiotic DSBs are formed in chromatin loops tethered to a linear chromosome axis, but the interrelationship between DSB-promoting factors and the axis is not fully understood. Here, we study the localisation of SPO11-1 and PRD3 during meiosis, and investigate their respective functions in relation to the chromosome axis. Using immunocytogenetics, we observed that the localisation of SPO11-1 overlaps relatively weakly with the chromosome axis and RAD51, a marker of meiotic DSBs, and that SPO11-1 recruitment to chromatin is genetically independent of the axis. In contrast, PRD3 localisation correlates more strongly with RAD51 and the chromosome axis. This indicates that PRD3 likely forms a functional link between SPO11-1 and the chromosome axis to promote meiotic DSB formation. We also uncovered a new function of SPO11-1 in the nucleation of the synaptonemal complex protein ZYP1. We demonstrate that chromosome co-alignment associated with ZYP1 deposition can occur in the absence of DSBs, and is dependent on SPO11-1, but not PRD3. Lastly, we show that the progression of meiosis is influenced by the presence of aberrant chromosomal connections, but not by the absence of DSBs or synapsis. Altogether, our study provides mechanistic insights into the control of meiotic DSB formation and reveals diverse functional interactions between SPO11-1, PRD3 and the chromosome axis. Most eukaryotes rely on the formation of gametes with half the number of chromosomes for sexual reproduction. Meiosis is a specialised type of cell division essential for the transition between a diploid and a haploid stage during gametogenesis. In early meiosis, programmed-DNA double strand breaks (DSBs) occur across the genome. These DSBs are processed by a set of proteins and the broken ends are repaired using the genetic information from the homologous chromosomes. These reciprocal exchanges of information between two chromosomes are called crossovers. Crossovers physical link chromosomes in pairs which is essential to ensure their correct segregation during the two rounds of meiotic division. Crossovers are also essential for the creation of genetic diversity as they break genetic linkages to form novel allelic blocks. The formation of DSBs is not completely understood in plants. Here we studied the function of SPO11-1 and PRD3, two proteins involved in the formation of DSBs in Arabidopsis. We discovered functional differences in their respective mode of recruitment to the chromosomes, their interactions with proteins forming the chromosome core and their roles in chromosome co-alignment. These indicate that, although SPO11-1 and PRD3 share a role in the formation of DSBs, the two proteins have additional and distinct roles beside DSB formation.
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Yelina NE, Holland D, Gonzalez-Jorge S, Hirsz D, Yang Z, Henderson IR. Coexpression of MEIOTIC-TOPOISOMERASE VIB-dCas9 with guide RNAs specific to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis. G3 (BETHESDA, MD.) 2022; 12:jkac105. [PMID: 35485960 PMCID: PMC9258527 DOI: 10.1093/g3journal/jkac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022]
Abstract
During meiosis, homologous chromosomes pair and recombine, which can result in reciprocal crossovers that increase genetic diversity. Crossovers are unevenly distributed along eukaryote chromosomes and show repression in heterochromatin and the centromeres. Within the chromosome arms, crossovers are often concentrated in hotspots, which are typically in the kilobase range. The uneven distribution of crossovers along chromosomes, together with their low number per meiosis, creates a limitation during crop breeding, where recombination can be beneficial. Therefore, targeting crossovers to specific genome locations has the potential to accelerate crop improvement. In plants, meiotic crossovers are initiated by DNA double-strand breaks that are catalyzed by SPO11 complexes, which consist of 2 catalytic (SPO11-1 and SPO11-2) and 2 noncatalytic subunits (MTOPVIB). We used the model plant Arabidopsis thaliana to coexpress an MTOPVIB-dCas9 fusion protein with guide RNAs specific to the 3a crossover hotspot. We observed that this was insufficient to significantly change meiotic crossover frequency or pattern within 3a. We discuss the implications of our findings for targeting meiotic recombination within plant genomes.
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Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
- Department of Plant Sciences, Crop Science Centre, University of Cambridge, Cambridge CB3 0LE, UK
| | - Daniel Holland
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Dominique Hirsz
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Ziyi Yang
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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Leng X, Duxin JP. Targeting DNA-Protein Crosslinks via Post-Translational Modifications. Front Mol Biosci 2022; 9:944775. [PMID: 35860355 PMCID: PMC9289515 DOI: 10.3389/fmolb.2022.944775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.
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50
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Perry M, Ghosal G. Mechanisms and Regulation of DNA-Protein Crosslink Repair During DNA Replication by SPRTN Protease. Front Mol Biosci 2022; 9:916697. [PMID: 35782873 PMCID: PMC9240642 DOI: 10.3389/fmolb.2022.916697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are deleterious DNA lesions that occur when proteins are covalently crosslinked to the DNA by the action of variety of agents like reactive oxygen species, aldehydes and metabolites, radiation, and chemotherapeutic drugs. Unrepaired DPCs are blockades to all DNA metabolic processes. Specifically, during DNA replication, replication forks stall at DPCs and are vulnerable to fork collapse, causing DNA breakage leading to genome instability and cancer. Replication-coupled DPC repair involves DPC degradation by proteases such as SPRTN or the proteasome and the subsequent removal of DNA-peptide adducts by nucleases and canonical DNA repair pathways. SPRTN is a DNA-dependent metalloprotease that cleaves DPC substrates in a sequence-independent manner and is also required for translesion DNA synthesis following DPC degradation. Biallelic mutations in SPRTN cause Ruijs-Aalfs (RJALS) syndrome, characterized by hepatocellular carcinoma and segmental progeria, indicating the critical role for SPRTN and DPC repair pathway in genome maintenance. In this review, we will discuss the mechanism of replication-coupled DPC repair, regulation of SPRTN function and its implications in human disease and cancer.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States,Fred and Pamela Buffett Cancer Center, Omaha, NE, United States,*Correspondence: Gargi Ghosal,
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