1
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Clot CR, Klein D, Koopman J, Schuit C, Engelen CJM, Hutten RCB, Brouwer M, Visser RGF, Jurani M, van Eck HJ. Crossover shortage in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility. Genetics 2024; 226:iyad194. [PMID: 37943687 PMCID: PMC10763545 DOI: 10.1093/genetics/iyad194] [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: 09/04/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers (COs). A strong reduction of CO number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation of univalents during meiosis I and ultimately to the production of unbalanced and sterile gametes. However, if CO shortage is combined with another meiotic alteration that restitutes the first meiotic division, then uniform and balanced unreduced male gametes, essentially composed of nonrecombinant homologs, are produced. This mitosis-like division is of interest to breeders because it transmits most of the parental heterozygosity to the gametes. In potato, CO shortage, a recessive trait previously referred to as desynapsis, was tentatively mapped to chromosome 8. In this article, we have fine-mapped the position of the CO shortage locus and identified StMSH4, an essential component of the class I CO pathway, as the most likely candidate gene. A 7 base-pair insertion in the second exon of StMSH4 was found to be associated with CO shortage in our mapping population. We also identified a second allele with a 3,820 base-pair insertion and confirmed that both alleles cannot complement each other. Such nonfunctional alleles appear to be common in potato cultivars. More than half of the varieties we tested are carriers of mutational load at the StMSH4 locus. With this new information, breeders can choose to remove alleles associated with CO shortage from their germplasm to improve fertility or to use them to produce highly uniform unreduced male gametes in alternative breeding schemes.
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Affiliation(s)
- Corentin R Clot
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Dennis Klein
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Joey Koopman
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Cees Schuit
- Bejo Zaden B.V., Warmenhuizen, 1749 CZ, The Netherlands
| | - Christel J M Engelen
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Ronald C B Hutten
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Martina Jurani
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
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2
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Hwang HY, Wang J. Effect of recombination on genetic diversity of Caenorhabditis elegans. Sci Rep 2023; 13:16425. [PMID: 37777524 PMCID: PMC10542817 DOI: 10.1038/s41598-023-42600-5] [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: 07/20/2022] [Accepted: 09/12/2023] [Indexed: 10/02/2023] Open
Abstract
Greater molecular divergence and genetic diversity are present in regions of high recombination in many species. Studies describing the correlation between variant abundance and recombination rate have long focused on recombination in the context of linked selection models, whereby interference between linked sites under positive or negative selection reduces genetic diversity in regions of low recombination. Here, we show that indels, especially those of intermediate sizes, are enriched relative to single nucleotide polymorphisms in regions of high recombination in C. elegans. To explain this phenomenon, we reintroduce an alternative model that emphasizes the mutagenic effect of recombination. To extend the analysis, we examine the variants with a phylogenetic context and discuss how different models could be examined together. The number of variants generated by recombination in natural populations could be substantial including possibly the majority of some indel subtypes. Our work highlights the potential importance of a mutagenic effect of recombination, which could have a significant role in the shaping of natural genetic diversity.
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Affiliation(s)
- Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
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3
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Girard C, Zwicker D, Mercier R. The regulation of meiotic crossover distribution: a coarse solution to a century-old mystery? Biochem Soc Trans 2023:233030. [PMID: 37145037 DOI: 10.1042/bst20221329] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Meiotic crossovers, which are exchanges of genetic material between homologous chromosomes, are more evenly and distantly spaced along chromosomes than expected by chance. This is because the occurrence of one crossover reduces the likelihood of nearby crossover events - a conserved and intriguing phenomenon called crossover interference. Although crossover interference was first described over a century ago, the mechanism allowing coordination of the fate of potential crossover sites half a chromosome away remains elusive. In this review, we discuss the recently published evidence supporting a new model for crossover patterning, coined the coarsening model, and point out the missing pieces that are still needed to complete this fascinating puzzle.
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Affiliation(s)
- Chloe Girard
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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4
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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: 2] [Impact Index Per Article: 2.0] [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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5
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Genetic aetiology of Down syndrome birth: novel variants of maternal DNMT3B and RFC1 genes increase risk of meiosis II nondisjunction in the oocyte. Mol Genet Genomics 2023; 298:293-313. [PMID: 36447056 DOI: 10.1007/s00438-022-01981-4] [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: 06/30/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022]
Abstract
The aim of the present work was to explore the intriguing association of maternal folate regulator gene polymorphisms and mutations with the incidence of chromosome 21 nondisjunction and Down syndrome birth. We tested polymorphisms/mutations of DNMT3B and RFC1 genes for their association with meiotic errors in oocyte among the 1215 Down syndrome child-bearing women and 900 controls. We observed that 23 out of 31 variants of DNMT3B and RFC1 exhibited an association with meiosis II nondisjunction in maternal age-independent manner. Additionally, we have reported 17 novel mutations and 1 novel polymorphic variant that are unique to the Indian Bengali speaking cohort and increased odds in favour of meiosis II nondisjunction. We hypothesize that the risk variants and mutations of DNMT3B and RFC1 genes may cause reduction in two or more recombination events and also cause peri-centromeric single exchange that increases the risk of nondisjunction at any age of women. In silico analyses predicted the probable damages of the transcripts or proteins from the respective genes owing to the said polymorphisms. These findings from the largest population sample tested ever revealed that mutations/polymorphisms of the genes DNMT3B and RFC1 impair recombination that leads to chromosome 21 nondisjunction in the oocyte at meiosis II stage and bring us a significant step closer towards understanding the aetiology of chromosome 21 nondisjunction and birth of a child with Down syndrome to women at any age.
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6
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Tóth A, Székvölgyi L, Vellai T. The genome loading model for the origin and maintenance of sex in eukaryotes. Biol Futur 2022; 73:345-357. [PMID: 36534301 DOI: 10.1007/s42977-022-00148-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Understanding why sexual reproduction-which involves syngamy (union of gametes) and meiosis-emerged and how it has subsisted for millions of years remains a fundamental problem in biology. Considered as the essence of sex, meiotic recombination is initiated by a DNA double-strand break (DSB) that forms on one of the pairing homologous chromosomes. This DNA lesion is subsequently repaired by gene conversion, the non-reciprocal transfer of genetic information from the intact homolog. A major issue is which of the pairing homologs undergoes DSB formation. Accumulating evidence shows that chromosomal sites where the pairing homologs locally differ in size, i.e., are heterozygous for an insertion or deletion, often display disparity in gene conversion. Biased conversion tends to duplicate insertions and lose deletions. This suggests that DSB is preferentially formed on the "shorter" homologous region, which thereby acts as the recipient for DNA transfer. Thus, sex primarily functions as a genome (re)loading mechanism. It ensures the restoration of formerly lost DNA sequences (deletions) and allows the efficient copying and, mainly in eukaryotes, subsequent spreading of newly emerged sequences (insertions) arising initially in an individual genome, even if they confer no advantage to the host. In this way, sex simultaneously repairs deletions and increases genetic variability underlying adaptation. The model explains a remarkable increase in DNA content during the evolution of eukaryotic genomes.
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Affiliation(s)
- András Tóth
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary.
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7
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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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8
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Wang Y, Zhai B, Tan T, Yang X, Zhang J, Song M, Tan Y, Yang X, Chu T, Zhang S, Wang S, Zhang L. ESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4. Nucleic Acids Res 2021; 49:9353-9373. [PMID: 34417612 PMCID: PMC8450111 DOI: 10.1093/nar/gkab722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Meiotic recombination is integrated into and regulated by meiotic chromosomes, which is organized as loop/axis architecture. However, the regulation of chromosome organization is poorly understood. Here, we show Esa1, the NuA4 complex catalytic subunit, is constitutively expressed and localizes on chromatin loops during meiosis. Esa1 plays multiple roles including homolog synapsis, sporulation efficiency, spore viability, and chromosome segregation in meiosis. Detailed analyses show the meiosis-specific depletion of Esa1 results in decreased chromosome axis length independent of another axis length regulator Pds5, which further leads to a decreased number of Mer2 foci, and consequently a decreased number of DNA double-strand breaks, recombination intermediates, and crossover frequency. However, Esa1 depletion does not impair the occurrence of the obligatory crossover required for faithful chromosome segregation, or the strength of crossover interference. Further investigations demonstrate Esa1 regulates chromosome axis length via acetylating the N-terminal tail of histone H4 but not altering transcription program. Therefore, we firstly show a non-chromosome axis component, Esa1, acetylates histone H4 on chromatin loops to regulate chromosome axis length and consequently recombination frequency but does not affect the basic meiotic recombination process. Additionally, Esa1 depletion downregulates middle induced meiotic genes, which probably causing defects in sporulation and chromosome segregation.
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Affiliation(s)
- Ying Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Binyuan Zhai
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Taicong Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Xiao Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Jiaming Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Meihui Song
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Yingjin Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Xuan Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Tingting Chu
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Shuxian Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong250001, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China
| | - Liangran Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University, China.,Advanced Medical Research Institute, Shandong University, Jinan, Shandong250012, China.,Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan250014, Shandong, China
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9
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Abstract
Meiotic recombination is triggered by programmed DNA double-strand breaks (DSBs), catalyzed by the type II topoisomerase-like Spo11 protein. Meiotic DSBs are repaired by homologous recombination, which produces either crossovers or noncrossovers, this decision being linked to the binding of proteins specific of each pathway. Mapping the binding of these proteins along chromosomes in wild type or mutant yeast background is extremely useful to understand how and at which step the decision to repair a DSB with a crossover is taken. It is now possible to obtain highly synchronous yeast meiotic populations, which, combined with appropriate negative controls, enable to detect by chromatin immunoprecipitation followed by sequencing (ChIP-Seq) the transient binding of diverse recombination proteins with high sensitivity and resolution.
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Affiliation(s)
- Aurore Sanchez
- Institut Curie - Research Center, UMR3244 CNRS, Pavillon Trouillet Rossignol, PSL Research University, Paris Cedex 05, France
- Paris Sorbonne Université, Paris, France
| | - Valérie Borde
- Institut Curie - Research Center, UMR3244 CNRS, Pavillon Trouillet Rossignol, PSL Research University, Paris Cedex 05, France.
- Paris Sorbonne Université, Paris, France.
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10
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Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation. Proc Natl Acad Sci U S A 2020; 117:30577-30588. [PMID: 33199619 DOI: 10.1073/pnas.2013012117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Crossovers generated during the repair of programmed meiotic double-strand breaks must be tightly regulated to promote accurate homolog segregation without deleterious outcomes, such as aneuploidy. The Mlh1-Mlh3 (MutLγ) endonuclease complex is critical for crossover resolution, which involves mechanistically unclear interplay between MutLγ and Exo1 and polo kinase Cdc5. Using budding yeast to gain temporal and genetic traction on crossover regulation, we find that MutLγ constitutively interacts with Exo1. Upon commitment to crossover repair, MutLγ-Exo1 associate with recombination intermediates, followed by direct Cdc5 recruitment that triggers MutLγ crossover activity. We propose that Exo1 serves as a central coordinator in this molecular interplay, providing a defined order of interaction that prevents deleterious, premature activation of crossovers. MutLγ associates at a lower frequency near centromeres, indicating that spatial regulation across chromosomal regions reduces risky crossover events. Our data elucidate the temporal and spatial control surrounding a constitutive, potentially harmful, nuclease. We also reveal a critical, noncatalytic role for Exo1, through noncanonical interaction with polo kinase. These mechanisms regulating meiotic crossovers may be conserved across species.
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11
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Janisiw E, Raices M, Balmir F, Paulin LF, Baudrimont A, von Haeseler A, Yanowitz JL, Jantsch V, Silva N. Poly(ADP-ribose) glycohydrolase coordinates meiotic DNA double-strand break induction and repair independent of its catalytic activity. Nat Commun 2020; 11:4869. [PMID: 32978394 PMCID: PMC7519143 DOI: 10.1038/s41467-020-18693-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Poly(ADP-ribosyl)ation is a reversible post-translational modification synthetized by ADP-ribose transferases and removed by poly(ADP-ribose) glycohydrolase (PARG), which plays important roles in DNA damage repair. While well-studied in somatic tissues, much less is known about poly(ADP-ribosyl)ation in the germline, where DNA double-strand breaks are introduced by a regulated program and repaired by crossover recombination to establish a tether between homologous chromosomes. The interaction between the parental chromosomes is facilitated by meiotic specific adaptation of the chromosome axes and cohesins, and reinforced by the synaptonemal complex. Here, we uncover an unexpected role for PARG in coordinating the induction of meiotic DNA breaks and their homologous recombination-mediated repair in Caenorhabditis elegans. PARG-1/PARG interacts with both axial and central elements of the synaptonemal complex, REC-8/Rec8 and the MRN/X complex. PARG-1 shapes the recombination landscape and reinforces the tightly regulated control of crossover numbers without requiring its catalytic activity. We unravel roles in regulating meiosis, beyond its enzymatic activity in poly(ADP-ribose) catabolism. Poly(ADP-ribose) glycohydrolase (PARG) is involved in different cellular processes including DNA repair. Here the authors reveal a role for PARG in regulating meiotic DNA double strand break induction and repair in Caenorhabditis elegans.
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Affiliation(s)
- Eva Janisiw
- Department of Chromosome Biology, Max Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria.,Centre for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Marilina Raices
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fabiola Balmir
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,AHN Center for Reproductive Medicine, AHN McCandless, Pittsburgh, PA, USA
| | - Luis F Paulin
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Laboratories, Medical University of Vienna, Vienna BioCenter, University of Vienna, Vienna, Austria
| | - Antoine Baudrimont
- Department of Chromosome Biology, Max Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Laboratories, Medical University of Vienna, Vienna BioCenter, University of Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Judith L Yanowitz
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Verena Jantsch
- Department of Chromosome Biology, Max Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Nicola Silva
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
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12
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Benyahya F, Nadaud I, Da Ines O, Rimbert H, White C, Sourdille P. SPO11.2 is essential for programmed double-strand break formation during meiosis in bread wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:30-43. [PMID: 32603485 DOI: 10.1111/tpj.14903] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 05/20/2023]
Abstract
Meiotic recombination is initiated by formation of DNA double-strand breaks (DSBs). This involves a protein complex that includes in plants the two similar proteins, SPO11-1 and SPO11-2. We analysed the sequences of SPO11-2 in hexaploid bread wheat (Triticum aestivum), as well as in its diploid and tetraploid progenitors. We investigated its role during meiosis using single, double and triple mutants. The three homoeologous SPO11-2 copies of hexaploid wheat exhibit high nucleotide and amino acid similarities with those of the diploids, tetraploids and Arabidopsis. Interestingly, however, two nucleotides deleted in exon-2 of the A copy lead to a premature stop codon and suggest that it encodes a non-functional protein. Remarkably, the mutation was absent from the diploid A-relative Triticum urartu, but present in the tetraploid Triticum dicoccoides and in different wheat cultivars indicating that the mutation occurred after the first polyploidy event and has since been conserved. We further show that triple mutants with all three copies (A, B, D) inactivated are sterile. Cytological analyses of these mutants show synapsis defects, accompanied by severe reductions in bivalent formation and numbers of DMC1 foci, thus confirming the essential role of TaSPO11-2 in meiotic recombination in wheat. In accordance with its 2-nucleotide deletion in exon-2, double mutants for which only the A copy remained are also sterile. Notwithstanding, some DMC1 foci remain visible in this mutant, suggesting a residual activity of the A copy, albeit not sufficient to restore fertility.
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Affiliation(s)
- Fatiha Benyahya
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Isabelle Nadaud
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, UMR CNRS 6293 - Université Clermont Auvergne - INSERM U1103, Clermont-Ferrand, 63001, France
| | - Hélène Rimbert
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Charles White
- Génétique, Reproduction et Développement, UMR CNRS 6293 - Université Clermont Auvergne - INSERM U1103, Clermont-Ferrand, 63001, France
| | - Pierre Sourdille
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
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13
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Yao Y, Li X, Chen W, Liu H, Mi L, Ren D, Mo A, Lu P. ATM Promotes RAD51-Mediated Meiotic DSB Repair by Inter-Sister-Chromatid Recombination in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:839. [PMID: 32670319 PMCID: PMC7329986 DOI: 10.3389/fpls.2020.00839] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/26/2020] [Indexed: 05/17/2023]
Abstract
Meiotic recombination ensures accurate homologous chromosome segregation during meiosis and generates novel allelic combinations among gametes. During meiosis, DNA double strand breaks (DSBs) are generated to facilitate recombination. To maintain genome integrity, meiotic DSBs must be repaired using appropriate DNA templates. Although the DNA damage response protein kinase Ataxia-telangiectasia mutated (ATM) has been shown to be involved in meiotic recombination in Arabidopsis, its mechanistic role is still unclear. In this study, we performed cytological analysis in Arabidopsis atm mutant, we show that there are fewer γH2AX foci, but more RAD51 and DMC1 foci on atm meiotic chromosomes. Furthermore, we observed an increase in meiotic Type I crossovers (COs) in atm. Our genetic analysis shows that the meiotic phenotype of atm rad51 double mutants is similar to the rad51 single mutant. Whereas, the atm dmc1 double mutant has a more severe chromosome fragmentation phenotype compared to both single mutants, suggesting that ATM functions in concert with RAD51, but in parallel to DMC1. Lastly, we show that atm asy1 double mutants also have more severe meiotic recombination defects. These data lead us to propose a model wherein ATM promotes RAD51-mediated meiotic DSB repair by inter-sister-chromatid (IS) recombination in Arabidopsis.
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Affiliation(s)
- Yuan Yao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaojing Li
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wanli Chen
- School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Liu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Limin Mi
- School of Life Sciences, Fudan University, Shanghai, China
| | - Ding Ren
- School of Life Sciences, Fudan University, Shanghai, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai, China
| | - Pingli Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- *Correspondence: Pingli Lu, ;
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14
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Kawakami T, Wallberg A, Olsson A, Wintermantel D, de Miranda JR, Allsopp M, Rundlöf M, Webster MT. Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees. Genetics 2019; 212:1101-1119. [PMID: 31152071 PMCID: PMC6707477 DOI: 10.1534/genetics.119.302008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/30/2019] [Indexed: 12/30/2022] Open
Abstract
Meiotic recombination shuffles genetic variation and promotes correct segregation of chromosomes. Rates of recombination vary on several scales, both within genomes and between individuals, and this variation is affected by both genetic and environmental factors. Social insects have extremely high rates of recombination, although the evolutionary causes of this are not known. Here, we estimate rates of crossovers and gene conversions in 22 colonies of the honeybee, Apis mellifera, and 9 colonies of the bumblebee, Bombus terrestris, using direct sequencing of 299 haploid drone offspring. We confirm that both species have extremely elevated crossover rates, with higher rates measured in the highly eusocial honeybee than the primitively social bumblebee. There are also significant differences in recombination rate between subspecies of honeybee. There is substantial variation in genome-wide recombination rate between individuals of both A. mellifera and B. terrestris and the distribution of these rates overlap between species. A large proportion of interindividual variation in recombination rate is heritable, which indicates the presence of variation in trans-acting factors that influence recombination genome-wide. We infer that levels of crossover interference are significantly lower in honeybees compared to bumblebees, which may be one mechanism that contributes to higher recombination rates in honeybees. We also find a significant increase in recombination rate with distance from the centromere, mirrored by methylation differences. We detect a strong transmission bias due to GC-biased gene conversion associated with noncrossover gene conversions. Our results shed light on the mechanistic causes of extreme rates of recombination in social insects and the genetic architecture of recombination rate variation.
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Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, 752 36, Sweden
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, United Kingdom
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
| | - Dimitry Wintermantel
- INRA, UE 1255 APIS, Le Magneraud, 17700 Surgères, France
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS and Université de La Rochelle, 79360 Villiers-en-Bois, France
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Mike Allsopp
- Plant Protection Research Institute, Agricultural Research Council, Stellenbosch, 7608, South Africa
| | - Maj Rundlöf
- Department of Biology, Lund University, 223 62, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
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15
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Pyatnitskaya A, Borde V, De Muyt A. Crossing and zipping: molecular duties of the ZMM proteins in meiosis. Chromosoma 2019; 128:181-198. [PMID: 31236671 DOI: 10.1007/s00412-019-00714-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 11/25/2022]
Abstract
Accurate segregation of homologous chromosomes during meiosis depends on the ability of meiotic cells to promote reciprocal exchanges between parental DNA strands, known as crossovers (COs). For most organisms, including budding yeast and other fungi, mammals, nematodes, and plants, the major CO pathway depends on ZMM proteins, a set of molecular actors specifically devoted to recognize and stabilize CO-specific DNA intermediates that are formed during homologous recombination. The progressive implementation of ZMM-dependent COs takes place within the context of the synaptonemal complex (SC), a proteinaceous structure that polymerizes between homologs and participates in close homolog juxtaposition during prophase I of meiosis. While SC polymerization starts from ZMM-bound sites and ZMM proteins are required for SC polymerization in budding yeast and the fungus Sordaria, other organisms differ in their requirement for ZMM in SC elongation. This review provides an overview of ZMM functions and discusses their collaborative tasks for CO formation and SC assembly, based on recent findings and on a comparison of different model organisms.
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Affiliation(s)
- Alexandra Pyatnitskaya
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Paris Sorbonne Université, Paris, France
| | - Valérie Borde
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France.
- Paris Sorbonne Université, Paris, France.
| | - Arnaud De Muyt
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France.
- Paris Sorbonne Université, Paris, France.
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16
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Faridounnia M, Folkers GE, Boelens R. Function and Interactions of ERCC1-XPF in DNA Damage Response. Molecules 2018; 23:E3205. [PMID: 30563071 PMCID: PMC6320978 DOI: 10.3390/molecules23123205] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/27/2018] [Accepted: 12/01/2018] [Indexed: 12/28/2022] Open
Abstract
Numerous proteins are involved in the multiple pathways of the DNA damage response network and play a key role to protect the genome from the wide variety of damages that can occur to DNA. An example of this is the structure-specific endonuclease ERCC1-XPF. This heterodimeric complex is in particular involved in nucleotide excision repair (NER), but also in double strand break repair and interstrand cross-link repair pathways. Here we review the function of ERCC1-XPF in various DNA repair pathways and discuss human disorders associated with ERCC1-XPF deficiency. We also overview our molecular and structural understanding of XPF-ERCC1.
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Affiliation(s)
- Maryam Faridounnia
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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17
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Okagaki RJ, Dukowic-Schulze S, Eggleston WB, Muehlbauer GJ. A Critical Assessment of 60 Years of Maize Intragenic Recombination. FRONTIERS IN PLANT SCIENCE 2018; 9:1560. [PMID: 30420864 PMCID: PMC6215864 DOI: 10.3389/fpls.2018.01560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/04/2018] [Indexed: 06/09/2023]
Abstract
Until the mid-1950s, it was believed that genetic crossovers did not occur within genes. Crossovers occurred between genes, the "beads on a string" model. Then in 1956, Seymour Benzer published his classic paper describing crossing over within a gene, intragenic recombination. This result from a bacteriophage gene prompted Oliver Nelson to study intragenic recombination in the maize Waxy locus. His studies along with subsequent work by others working with maize and other organisms described the outcomes of intragenic recombination and provided some of the earliest evidence that genes, not intergenic regions, were recombination hotspots. High-throughput genotyping approaches have since replaced single gene intragenic studies for characterizing the outcomes of recombination. These large-scale studies confirm that genes, or more generally genic regions, are the most active recombinogenic regions, and suggested a pattern of crossovers similar to the budding yeast Saccharomyces cerevisiae. In S. cerevisiae recombination is initiated by double-strand breaks (DSBs) near transcription start sites (TSSs) of genes producing a polarity gradient where crossovers preferentially resolve at the 5' end of genes. Intragenic studies in maize yielded less evidence for either polarity or for DSBs near TSSs initiating recombination and in certain respects resembled Schizosaccharomyces pombe or mouse. These different perspectives highlight the need to draw upon the strengths of different approaches and caution against relying on a single model system or approach for understanding recombination.
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Affiliation(s)
- Ron J. Okagaki
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | | | - William B. Eggleston
- Department of Biology, Virginia Commonwealth University, St. Paul, MN, United States
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
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18
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Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize. Proc Natl Acad Sci U S A 2017; 114:12231-12236. [PMID: 29087335 DOI: 10.1073/pnas.1713225114] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.
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19
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Singh G, Da Ines O, Gallego ME, White CI. Analysis of the impact of the absence of RAD51 strand exchange activity in Arabidopsis meiosis. PLoS One 2017; 12:e0183006. [PMID: 28797117 PMCID: PMC5552350 DOI: 10.1371/journal.pone.0183006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/27/2017] [Indexed: 11/21/2022] Open
Abstract
The ploidy of eukaryote gametes must be halved to avoid doubling of numbers of chromosomes with each generation and this is carried out by meiosis, a specialized cell division in which a single chromosomal replication phase is followed by two successive nuclear divisions. With some exceptions, programmed recombination ensures the proper pairing and distribution of homologous pairs of chromosomes in meiosis and recombination defects thus lead to sterility. Two highly related recombinases are required to catalyse the key strand-invasion step of meiotic recombination and it is the meiosis-specific DMC1 which is generally believed to catalyse the essential non-sister chromatid crossing-over, with RAD51 catalysing sister-chromatid and non-cross-over events. Recent work in yeast and plants has however shown that in the absence of RAD51 strand-exchange activity, DMC1 is able to repair all meiotic DNA breaks and surprisingly, that this does not appear to affect numbers of meiotic cross-overs. In this work we confirm and extend this conclusion. Given that more than 95% of meiotic homologous recombination in Arabidopsis does not result in inter-homologue crossovers, Arabidopsis is a particularly sensitive model for testing the relative importance of the two proteins-even minor effects on the non-crossover event population should produce detectable effects on crossing-over. Although the presence of RAD51 protein provides essential support for the action of DMC1, our results show no significant effect of the absence of RAD51 strand-exchange activity on meiotic crossing-over rates or patterns in different chromosomal regions or across the whole genome of Arabidopsis, strongly supporting the argument that DMC1 catalyses repair of all meiotic DNA breaks, not only non-sister cross-overs.
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Affiliation(s)
- Gunjita Singh
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Olivier Da Ines
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Charles I. White
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
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20
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Modulating Crossover Frequency and Interference for Obligate Crossovers in Saccharomyces cerevisiae Meiosis. G3-GENES GENOMES GENETICS 2017; 7:1511-1524. [PMID: 28315832 PMCID: PMC5427503 DOI: 10.1534/g3.117.040071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Meiotic crossover frequencies show wide variation among organisms. But most organisms maintain at least one crossover per homolog pair (obligate crossover). In Saccharomyces cerevisiae, previous studies have shown crossover frequencies are reduced in the mismatch repair related mutant mlh3Δ and enhanced in a meiotic checkpoint mutant pch2Δ by up to twofold at specific chromosomal loci, but both mutants maintain high spore viability. We analyzed meiotic recombination events genome-wide in mlh3Δ, pch2Δ, and mlh3Δ pch2Δ mutants to test the effect of variation in crossover frequency on obligate crossovers. mlh3Δ showed ∼30% genome-wide reduction in crossovers (64 crossovers per meiosis) and loss of the obligate crossover, but nonexchange chromosomes were efficiently segregated. pch2Δ showed ∼50% genome-wide increase in crossover frequency (137 crossovers per meiosis), elevated noncrossovers as well as loss of chromosome size dependent double-strand break formation. Meiotic defects associated with pch2∆ did not cause significant increase in nonexchange chromosome frequency. Crossovers were restored to wild-type frequency in the double mutant mlh3Δ pch2Δ (100 crossovers per meiosis), but obligate crossovers were compromised. Genetic interference was reduced in mlh3Δ, pch2Δ, and mlh3Δ pch2Δ. Triple mutant analysis of mlh3Δ pch2Δ with other resolvase mutants showed that most of the crossovers in mlh3Δ pch2Δ are made through the Mus81-Mms4 pathway. These results are consistent with a requirement for increased crossover frequencies in the absence of genetic interference for obligate crossovers. In conclusion, these data suggest crossover frequencies and the strength of genetic interference in an organism are mutually optimized to ensure obligate crossovers.
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21
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Shodhan A, Kataoka K, Mochizuki K, Novatchkova M, Loidl J. A Zip3-like protein plays a role in crossover formation in the SC-less meiosis of the protist Tetrahymena. Mol Biol Cell 2017; 28:825-833. [PMID: 28100637 PMCID: PMC5349789 DOI: 10.1091/mbc.e16-09-0678] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/21/2016] [Accepted: 01/09/2017] [Indexed: 11/11/2022] Open
Abstract
When programmed meiotic DNA double-strand breaks (DSBs) undergo recombinational repair, genetic crossovers (COs) may be formed. A certain level of this is required for the faithful segregation of chromosomes, but the majority of DSBs are processed toward a safer alternative, namely noncrossovers (NCOs), via nonreciprocal DNA exchange. At the crossroads between these two DSB fates is the Msh4-Msh5 (MutSγ) complex, which stabilizes CO-destined recombination intermediates and members of the Zip3/RNF212 family of RING finger proteins, which in turn stabilize MutSγ. These proteins function in the context of the synaptonemal complex (SC) and mainly act on SC-dependent COs. Here we show that in the SC-less ciliate Tetrahymena, Zhp3 (a protein distantly related to Zip3/RNF212), together with MutSγ, is responsible for the majority of COs. This activity of Zhp3 suggests an evolutionarily conserved SC-independent strategy for balancing CO:NCO ratios. Moreover, we report a novel meiosis-specific protein, Sa15, as an interacting partner of Zhp3. Sa15 forms linear structures in meiotic prophase nuclei to which Zhp3 localizes. Sa15 is required for a wild-type level of CO formation. Its linear organization suggests the existence of an underlying chromosomal axis that serves as a scaffold for Zhp3 and other recombination proteins.
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Affiliation(s)
- Anura Shodhan
- Department of Chromosome Biology, University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Kensuke Kataoka
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences and
| | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences and
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences and
- Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
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22
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Hwang HY, Wang J. Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans. PLoS Comput Biol 2017; 13:e1005369. [PMID: 28135268 PMCID: PMC5305269 DOI: 10.1371/journal.pcbi.1005369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 02/13/2017] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
Genetic diversity is maintained by continuing generation and removal of variants. While examining over 800,000 DNA variants in wild isolates of Caenorhabditis elegans, we made a discovery that the proportions of variant types are not constant across the C. elegans genome. The variant proportion is defined as the fraction of a specific variant type (e.g. single nucleotide polymorphism (SNP) or indel) within a broader set of variants (e.g. all variants or all non-SNPs). The proportions of most variant types show a correlation with the recombination rate. These correlations can be explained as a result of a concerted action of two mutation mechanisms, which we named Morgan and Sanger mechanisms. The two proposed mechanisms act according to the distinct components of the recombination rate, specifically the genetic and physical distance. Regression analysis was used to explore the characteristics and contributions of the two mutation mechanisms. According to our model, ~20-40% of all mutations in C. elegans wild populations are derived from programmed meiotic double strand breaks, which precede chromosomal crossovers and thus may be the point of origin for the Morgan mechanism. A substantial part of the known correlation between the recombination rate and variant distribution appears to be caused by the mutations generated by the Morgan mechanism. Mathematically integrating the mutation model with background selection model gives a more complete depiction of how the variant landscape is shaped in C. elegans. Similar analysis should be possible in other species by examining the correlation between the recombination rate and variant landscape within the context of our mutation model.
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Affiliation(s)
- Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
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23
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Calvente A, Santos JL, Rufas JS. Do Exogenous DNA Double-Strand Breaks Change Incomplete Synapsis and Chiasma Localization in the Grasshopper Stethophyma grossum? PLoS One 2016; 11:e0168499. [PMID: 28005992 PMCID: PMC5179137 DOI: 10.1371/journal.pone.0168499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
Meiotic recombination occurs as a programmed event that initiates by the formation of DNA double-strand breaks (DSBs) that give rise to the formation of crossovers that are observed as chiasmata. Chiasmata are essential for the accurate chromosome segregation and the generation of new combinations of parental alleles. Some treatments that provoke exogenous DSBs also lead to alterations in the recombination pattern of some species in which full homologous synapsis is achieved at pachytene. We have carried out a similar approach in males of the grasshopper Stethophyma grossum, whose homologues show incomplete synapsis and proximal chiasma localization. After irradiating males with γ rays we have studied the distribution of both the histone variant γ-H2AX and the recombinase RAD51. These proteins are cytological markers of DSBs at early prophase I. We have inferred synaptonemal complex (SC) formation via identification of SMC3 and RAD 21 cohesin subunits. Whereas thick and thin SMC3 filaments would correspond to synapsed and unsynapsed regions, the presence of RAD21 is only restricted to synapsed regions. Results show that irradiated spermatocytes maintain restricted synapsis between homologues. However, the frequency and distribution of chiasmata in metaphase I bivalents is slightly changed and quadrivalents were also observed. These results could be related to the singular nuclear polarization displayed by the spermatocytes of this species.
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Affiliation(s)
- Adela Calvente
- Departamento de Biología, Edificio de Biológicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Luis Santos
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Julio S. Rufas
- Departamento de Biología, Edificio de Biológicas, Universidad Autónoma de Madrid, Madrid, Spain
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24
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Abstract
Comparisons among a variety of eukaryotes have revealed considerable variability in the structures and processes involved in their meiosis. Nevertheless, conventional forms of meiosis occur in all major groups of eukaryotes, including early-branching protists. This finding confirms that meiosis originated in the common ancestor of all eukaryotes and suggests that primordial meiosis may have had many characteristics in common with conventional extant meiosis. However, it is possible that the synaptonemal complex and the delicate crossover control related to its presence were later acquisitions. Later still, modifications to meiotic processes occurred within different groups of eukaryotes. Better knowledge on the spectrum of derived and uncommon forms of meiosis will improve our understanding of many still mysterious aspects of the meiotic process and help to explain the evolutionary basis of functional adaptations to the meiotic program.
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Affiliation(s)
- Josef Loidl
- Department of Chromosome Biology and Vienna Biocenter, University of Vienna, A-1030 Vienna, Austria;
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25
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Hong Y, Sonneville R, Agostinho A, Meier B, Wang B, Blow JJ, Gartner A. The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis. PLoS Genet 2016; 12:e1005872. [PMID: 27010650 PMCID: PMC4807058 DOI: 10.1371/journal.pgen.1005872] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/25/2016] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.
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Affiliation(s)
- Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Remi Sonneville
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Ana Agostinho
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Bin Wang
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - J. Julian Blow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
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26
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Nambiar M, Smith GR. Repression of harmful meiotic recombination in centromeric regions. Semin Cell Dev Biol 2016; 54:188-97. [PMID: 26849908 DOI: 10.1016/j.semcdb.2016.01.042] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/27/2016] [Indexed: 11/16/2022]
Abstract
During the first division of meiosis, segregation of homologous chromosomes reduces the chromosome number by half. In most species, sister chromatid cohesion and reciprocal recombination (crossing-over) between homologous chromosomes are essential to provide tension to signal proper chromosome segregation during the first meiotic division. Crossovers are not distributed uniformly throughout the genome and are repressed at and near the centromeres. Rare crossovers that occur too near or in the centromere interfere with proper segregation and can give rise to aneuploid progeny, which can be severely defective or inviable. We review here how crossing-over occurs and how it is prevented in and around the centromeres. Molecular mechanisms of centromeric repression are only now being elucidated. However, rapid advances in understanding crossing-over, chromosome structure, and centromere functions promise to explain how potentially deleterious crossovers are avoided in certain chromosomal regions while allowing beneficial crossovers in others.
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Affiliation(s)
- Mridula Nambiar
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, United States.
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, United States.
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27
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Burri R, Nater A, Kawakami T, Mugal CF, Olason PI, Smeds L, Suh A, Dutoit L, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Res 2015; 25:1656-65. [PMID: 26355005 PMCID: PMC4617962 DOI: 10.1101/gr.196485.115] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/30/2015] [Indexed: 12/19/2022]
Abstract
Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation (“differentiation islands”) widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (dxy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.
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Affiliation(s)
- Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Pall I Olason
- Wallenberg Advanced Bioinformatics Infrastructure (WABI), Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden
| | - Linnea Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Stanislav Bureš
- Laboratory of Ornithology, Department of Zoology, Palacky University, 77146 Olomouc, Czech Republic
| | - Laszlo Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, 41092 Seville, Spain
| | - Silje Hogner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway; Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Juan Moreno
- Museo Nacional de Ciencias Naturales-CSIC, 28006 Madrid, Spain
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Milan Ružić
- Bird Protection and Study Society of Serbia, Radnička 20a, 21000 Novi Sad, Serbia
| | - Stein-Are Sæther
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway; Norwegian Institute for Nature Research (NINA), 7034 Trondheim, Norway
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
| | - Janos Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
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28
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Varas J, Sánchez-Morán E, Copenhaver GP, Santos JL, Pradillo M. Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant. PLoS Genet 2015; 11:e1005301. [PMID: 26147458 PMCID: PMC4492999 DOI: 10.1371/journal.pgen.1005301] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/27/2015] [Indexed: 01/06/2023] Open
Abstract
Chromatin Assembly Factor 1 (CAF-1) is a histone chaperone that assembles acetylated histones H3/H4 onto newly synthesized DNA, allowing the de novo assembly of nucleosomes during replication. CAF-1 is an evolutionary conserved heterotrimeric protein complex. In Arabidopsis, the three CAF-1 subunits are encoded by FAS1, FAS2 and MSI1. Atfas1-4 mutants have reduced fertility due to a decrease in the number of cells that enter meiosis. Interestingly, the number of DNA double-strand breaks (DSBs), measured by scoring the presence of γH2AX, AtRAD51 and AtDMC1 foci, is higher than in wild-type (WT) plants, and meiotic recombination genes such AtCOM1/SAE2, AtBRCA1, AtRAD51 and AtDMC1 are overexpressed. An increase in DSBs in this mutant does not have a significant effect in the mean chiasma frequency at metaphase I, nor a different number of AtMLH1 nor AtMUS81 foci per cell compared to WT at pachytene. Nevertheless, this mutant does show a higher gene conversion (GC) frequency. To examine how an increase in DSBs influences meiotic recombination and synaptonemal complex (SC) formation, we analyzed double mutants defective for AtFAS1 and different homologous recombination (HR) proteins. Most showed significant increases in both the mean number of synapsis initiation points (SIPs) and the total length of AtZYP1 stretches in comparison with the corresponding single mutants. These experiments also provide new insight into the relationships between the recombinases in Arabidopsis, suggesting a prominent role for AtDMC1 versus AtRAD51 in establishing interhomolog interactions. In Arabidopsis an increase in the number of DSBs does not translate to an increase in the number of crossovers (COs) but instead in a higher GC frequency. We discuss different mechanisms to explain these results including the possible existence of CO homeostasis in plants.
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Affiliation(s)
- Javier Varas
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Gregory P. Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Juan L. Santos
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Mónica Pradillo
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
- * E-mail:
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29
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Zickler D, Kleckner N. Recombination, Pairing, and Synapsis of Homologs during Meiosis. Cold Spring Harb Perspect Biol 2015; 7:cshperspect.a016626. [PMID: 25986558 DOI: 10.1101/cshperspect.a016626] [Citation(s) in RCA: 490] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recombination is a prominent feature of meiosis in which it plays an important role in increasing genetic diversity during inheritance. Additionally, in most organisms, recombination also plays mechanical roles in chromosomal processes, most notably to mediate pairing of homologous chromosomes during prophase and, ultimately, to ensure regular segregation of homologous chromosomes when they separate at the first meiotic division. Recombinational interactions are also subject to important spatial patterning at both early and late stages. Recombination-mediated processes occur in physical and functional linkage with meiotic axial chromosome structure, with interplay in both directions, before, during, and after formation and dissolution of the synaptonemal complex (SC), a highly conserved meiosis-specific structure that links homolog axes along their lengths. These diverse processes also are integrated with recombination-independent interactions between homologous chromosomes, nonhomology-based chromosome couplings/clusterings, and diverse types of chromosome movement. This review provides an overview of these diverse processes and their interrelationships.
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Affiliation(s)
- Denise Zickler
- Institut de Génétique et Microbiologie, UMR 8621, Université Paris-Sud, 91405 Orsay, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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Mézard C, Jahns MT, Grelon M. Where to cross? New insights into the location of meiotic crossovers. Trends Genet 2015; 31:393-401. [PMID: 25907025 DOI: 10.1016/j.tig.2015.03.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
During meiosis, the repair of induced DNA double-strand breaks (DSBs) produces crossovers (COs). COs are essential for the proper segregation of homologous chromosomes at the first meiotic division. In addition, COs generate new combinations of genetic markers in the progeny. CO localization is tightly controlled, giving rise to patterns that are specific to each species. The underlying mechanisms governing CO location, however, are poorly understood. Recent studies highlight the complexity of the multiple interconnected factors involved in shaping the CO landscape and demonstrate that the mechanisms that control CO distribution can vary from species to species. Here, we provide an overview of the recent findings related to CO distribution and discuss their impact on our understanding of the control of meiotic recombination.
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Affiliation(s)
- Christine Mézard
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, France
| | - Marina Tagliaro Jahns
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, France
| | - Mathilde Grelon
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, France.
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31
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Lam I, Keeney S. Mechanism and regulation of meiotic recombination initiation. Cold Spring Harb Perspect Biol 2014; 7:a016634. [PMID: 25324213 DOI: 10.1101/cshperspect.a016634] [Citation(s) in RCA: 279] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Meiotic recombination involves the formation and repair of programmed DNA double-strand breaks (DSBs) catalyzed by the conserved Spo11 protein. This review summarizes recent studies pertaining to the formation of meiotic DSBs, including the mechanism of DNA cleavage by Spo11, proteins required for break formation, and mechanisms that control the location, timing, and number of DSBs. Where appropriate, findings in different organisms are discussed to highlight evolutionary conservation or divergence.
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Affiliation(s)
- Isabel Lam
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Scott Keeney
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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32
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Dong CB, Mao JF, Suo YJ, Shi L, Wang J, Zhang PD, Kang XY. A strategy for characterization of persistent heteroduplex DNA in higher plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:282-291. [PMID: 25073546 DOI: 10.1111/tpj.12631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus-centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.
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Affiliation(s)
- Chun-Bo Dong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
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33
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Humphryes N, Hochwagen A. A non-sister act: recombination template choice during meiosis. Exp Cell Res 2014; 329:53-60. [PMID: 25158281 DOI: 10.1016/j.yexcr.2014.08.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/12/2014] [Accepted: 08/18/2014] [Indexed: 11/30/2022]
Abstract
Meiotic recombination has two key functions: the faithful assortment of chromosomes into gametes and the creation of genetic diversity. Both processes require that meiotic recombination occurs between homologous chromosomes, rather than sister chromatids. Accordingly, a host of regulatory factors are activated during meiosis to distinguish sisters from homologs, suppress recombination between sister chromatids and promote the chromatids of the homologous chromosome as the preferred recombination partners. Here, we discuss the recent advances in our understanding of the mechanistic basis of meiotic recombination template choice, focusing primarily on developments in the budding yeast, Saccharomyces cerevisiae, where the regulation is currently best understood.
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Affiliation(s)
- Neil Humphryes
- Department of Biology, New York University, New York, USA
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34
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Pradillo M, Varas J, Oliver C, Santos JL. On the role of AtDMC1, AtRAD51 and its paralogs during Arabidopsis meiosis. FRONTIERS IN PLANT SCIENCE 2014; 5:23. [PMID: 24596572 PMCID: PMC3925842 DOI: 10.3389/fpls.2014.00023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/20/2014] [Indexed: 05/02/2023]
Abstract
Meiotic recombination plays a critical role in achieving accurate chromosome segregation and increasing genetic diversity. Many studies, mostly in yeast, have provided important insights into the coordination and interplay between the proteins involved in the homologous recombination pathway, especially the recombinase RAD51 and the meiosis-specific DMC1. Here we summarize the current progresses on the function of both recombinases and the CX3 complex encoded by AtRAD51 paralogs, in the plant model species Arabidopsis thaliana. Similarities and differences respect to the function of these proteins in other organisms are also indicated.
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Affiliation(s)
- Mónica Pradillo
- Departamento de Genética, Facultad de Biología, Universidad Complutense de MadridMadrid, Spain
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35
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Marston AL. Chromosome segregation in budding yeast: sister chromatid cohesion and related mechanisms. Genetics 2014; 196:31-63. [PMID: 24395824 PMCID: PMC3872193 DOI: 10.1534/genetics.112.145144] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/28/2022] Open
Abstract
Studies on budding yeast have exposed the highly conserved mechanisms by which duplicated chromosomes are evenly distributed to daughter cells at the metaphase-anaphase transition. The establishment of proteinaceous bridges between sister chromatids, a function provided by a ring-shaped complex known as cohesin, is central to accurate segregation. It is the destruction of this cohesin that triggers the segregation of chromosomes following their proper attachment to microtubules. Since it is irreversible, this process must be tightly controlled and driven to completion. Furthermore, during meiosis, modifications must be put in place to allow the segregation of maternal and paternal chromosomes in the first division for gamete formation. Here, I review the pioneering work from budding yeast that has led to a molecular understanding of the establishment and destruction of cohesion.
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Affiliation(s)
- Adele L Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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36
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Meiotic recombination in Arabidopsis is catalysed by DMC1, with RAD51 playing a supporting role. PLoS Genet 2013; 9:e1003787. [PMID: 24086145 PMCID: PMC3784562 DOI: 10.1371/journal.pgen.1003787] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 07/26/2013] [Indexed: 11/29/2022] Open
Abstract
Recombination establishes the chiasmata that physically link pairs of homologous chromosomes in meiosis, ensuring their balanced segregation at the first meiotic division and generating genetic variation. The visible manifestation of genetic crossing-overs, chiasmata are the result of an intricate and tightly regulated process involving induction of DNA double-strand breaks and their repair through invasion of a homologous template DNA duplex, catalysed by RAD51 and DMC1 in most eukaryotes. We describe here a RAD51-GFP fusion protein that retains the ability to assemble at DNA breaks but has lost its DNA break repair capacity. This protein fully complements the meiotic chromosomal fragmentation and sterility of Arabidopsis rad51, but not rad51 dmc1 mutants. Even though DMC1 is the only active meiotic strand transfer protein in the absence of RAD51 catalytic activity, no effect on genetic map distance was observed in complemented rad51 plants. The presence of inactive RAD51 nucleofilaments is thus able to fully support meiotic DSB repair and normal levels of crossing-over by DMC1. Our data demonstrate that RAD51 plays a supporting role for DMC1 in meiotic recombination in the flowering plant, Arabidopsis. Recombination ensures coordinated disjunction of pairs of homologous chromosomes and generates genetic exchanges in meiosis and, with some exceptions, involves the co-operation of the RAD51 and DMC1 strand-exchange proteins. We describe here a RAD51-GFP fusion protein that has lost its DNA break repair capacity but retains the ability to assemble at DNA breaks in the plant, Arabidopsis - fully complementing the meiotic chromosomal fragmentation and sterility of rad51 mutants, and this depends upon DMC1. No effect on genetic map distance was observed in complemented rad51 plants even though DMC1 is the only active strand transfer protein. The inactive RAD51 nucleofilaments are thus able to fully support meiotic DSB repair and normal levels of crossing-over by DMC1 in Arabidopsis. The RAD51-GFP protein confers a dominant-negative inhibition of RAD51-dependent mitotic recombination, while remaining fully fertile - a novel and valuable tool for research in this domain. These phenotypes are equivalent to those of the recently reported yeast rad51-II3A mutant, (Cloud et al. 2012), carrying the implication of their probable generality in other eukaryotes and extending them to a species with a very different relation between numbers of meiotic DNA double-strand breaks and crossing-overs (∼2 DSB/CO in yeast; ∼25–30 DSB/CO in Arabidopsis; ∼15 DSB/CO in mice).
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37
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Da Ines O, Degroote F, Amiard S, Goubely C, Gallego ME, White CI. Effects of XRCC2 and RAD51B mutations on somatic and meiotic recombination in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:959-70. [PMID: 23521529 DOI: 10.1111/tpj.12182] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/11/2013] [Accepted: 03/15/2013] [Indexed: 05/12/2023]
Abstract
Homologous recombination is key to the maintenance of genome integrity and the creation of genetic diversity. At the mechanistic level, recombination involves the invasion of a homologous DNA template by broken DNA ends, repair of the break and exchange of genetic information between the two DNA molecules. Invasion of the template in eukaryotic cells is catalysed by the RAD51 and DMC1 recombinases, assisted by a number of accessory proteins, including the RAD51 paralogues. Eukaryotic genomes encode a variable number of RAD51 paralogues, ranging from two in yeast to five in animals and plants. The RAD51 paralogues form at least two distinct protein complexes, believed to play roles in the assembly and stabilization of the RAD51-DNA nucleofilament. Somatic recombination assays and immunocytology confirm that the three 'non-meiotic' paralogues of Arabidopsis, RAD51B, RAD51D and XRCC2, are involved in somatic homologous recombination, and that they are not required for the formation of radioinduced RAD51 foci. Given the presence of all five proteins in meiotic cells, the apparent absence of a meiotic role for RAD51B, RAD51D and XRCC2 is surprising, and perhaps simply the result of a more subtle meiotic phenotype in the mutants. Analysis of meiotic recombination confirms this, showing that the absence of XRCC2, and to a lesser extent RAD51B, but not RAD51D, increases rates of meiotic crossing over. The roles of RAD51B and XRCC2 in recombination are thus not limited to mitotic cells.
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Affiliation(s)
- Olivier Da Ines
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63171, Aubière, France
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38
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Currall BB, Chiang C, Talkowski ME, Morton CC. Mechanisms for Structural Variation in the Human Genome. CURRENT GENETIC MEDICINE REPORTS 2013; 1:81-90. [PMID: 23730541 DOI: 10.1007/s40142-013-0012-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It has been known for several decades that genetic variation involving changes to chromosomal structure (i.e., structural variants) can contribute to disease; however this relationship has been brought into acute focus in recent years largely based on innovative new genomics approaches and technology. Structural variants (SVs) arise from improperly repaired DNA double-strand breaks (DSB). DSBs are a frequent occurrence in all cells and two major pathways are involved in their repair: homologous recombination and non-homologous end joining. Errors during these repair mechanisms can result in SVs that involve losses, gains and rearrangements ranging from a few nucleotides to entire chromosomal arms. Factors such as rearrangements, hotspots and induced DSBs are implicated in the formation of SVs. While de novo SVs are often associated with disease, some SVs are conserved within human subpopulations and may have had a meaningful influence on primate evolution. As the ability to sequence the whole human genome rapidly evolves, the diversity of SVs is illuminated, including very complex rearrangements involving multiple DSBs in a process recently designated as "chromothripsis". Elucidating mechanisms involved in the etiology of SVs informs disease pathogenesis as well as the dynamic function associated with the biology and evolution of human genomes.
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Affiliation(s)
- Benjamin B Currall
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, New Research Building, Room 160D, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Harvard Medical School, Boston, MA, USA
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39
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de Vries M, Ramos L, de Boer P. Immunofluorescent characterization of meiotic recombination in human males with variable spermatogenesis. Andrology 2012; 1:262-73. [DOI: 10.1111/j.2047-2927.2012.00039.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 11/30/2022]
Affiliation(s)
- M. de Vries
- Department of Obstetrics and Gynaecology; Radboud University Nijmegen Medical Centre; Nijmegen; 6500 HB; The Netherlands
| | - L. Ramos
- Department of Obstetrics and Gynaecology; Radboud University Nijmegen Medical Centre; Nijmegen; 6500 HB; The Netherlands
| | - P. de Boer
- Department of Obstetrics and Gynaecology; Radboud University Nijmegen Medical Centre; Nijmegen; 6500 HB; The Netherlands
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