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Nozaki T, Weiner B, Kleckner N. Rapid homologue juxtaposition during meiotic chromosome pairing. Nature 2024:10.1038/s41586-024-07999-5. [PMID: 39358508 DOI: 10.1038/s41586-024-07999-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/28/2024] [Indexed: 10/04/2024]
Abstract
A central feature of meiosis is the pairing of homologous maternal and paternal chromosomes ('homologues') along their lengths1-3. Recognition between homologues and their juxtaposition in space is mediated by axis-associated recombination complexes. Also, pairing must occur without entanglements among unrelated chromosomes. Here we examine homologue juxtaposition in real time by four-dimensional fluorescence imaging of tagged chromosomal loci at high spatio-temporal resolution in budding yeast. We discover that corresponding loci come together from a substantial distance (1.8 µm) and complete pairing in a very short time, about 6 min (thus, rapid homologue juxtaposition or RHJ). Homologue loci first move rapidly together (in 30 s, at speeds of roughly 60 nm s-1) into an intermediate stage corresponding to canonical 400 nm axis coalignment. After a short pause, crossover/non-crossover differentiation (crossover interference) mediates a second short, rapid transition that ultimately gives close pairing of axes at 100 nm by means of synaptonemal complex formation. Furthermore, RHJ (1) occurs after chromosomes acquire prophase chromosome organization, (2) is nearly synchronous over thirds of chromosome lengths, but (3) is asynchronous throughout the genome. Finally, cytoskeleton-mediated movement is important for the timing and distance of RHJ onset and for ensuring its normal progression. General implications for local and global aspects of pairing are discussed.
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Affiliation(s)
- Tadasu Nozaki
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Beth Weiner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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2
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Nozaki T, Weiner B, Kleckner N. Rapid Homolog Juxtaposition During Meiotic Chromosome Pairing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.23.586418. [PMID: 38586034 PMCID: PMC10996542 DOI: 10.1101/2024.03.23.586418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A central basic feature of meiosis is pairing of homologous maternal and paternal chromosomes ("homologs") intimately along their lengths. Recognition between homologs and their juxtaposition in space are mediated by axis-associated DNA recombination complexes. Additional effects ensure that pairing occurs without ultimately giving entanglements among unrelated chromosomes. Here we examine the process of homolog juxtaposition in real time by 4D fluorescence imaging of tagged chromosomal loci at high spatio-temporal resolution in budding yeast. We discover that corresponding loci start coming together from a quite large distance (∼1.8 µm) and progress to completion of pairing in a very short time, usually less than six minutes (thus, "rapid homolog juxtaposition" or "RHJ"). Juxtaposition initiates by motion-mediated extension of a nascent interhomolog DNA linkage, raising the possibility of a tension-mediated trigger. In a first transition, homolog loci move rapidly together (in ∼30 sec, at speeds of up to ∼60 nm/sec) into a discrete intermediate state corresponding to canonical ∼400 nm axis distance coalignment. Then, after a short pause, crossover/noncrossover differentiation (crossover interference) mediates a second short, rapid transition that brings homologs even closer together. If synaptonemal complex (SC) component Zip1 is present, this transition concomitantly gives final close pairing by axis juxtaposition at ∼100 nm, the "SC distance". We also find that: (i) RHJ occurs after chromosomes acquire their prophase chromosome organization; (ii) is nearly synchronously over thirds (or more) of chromosome lengths; but (iii) is asynchronous throughout the genome. Furthermore, cytoskeleton-mediated movement is important for the timing and distance of RHJ onset and also for ensuring normal progression. Potential implications for local and global aspects of pairing are discussed.
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Legrand S, Saifudeen A, Bordelet H, Vernerey J, Guille A, Bignaud A, Thierry A, Acquaviva L, Gaudin M, Sanchez A, Johnson D, Friedrich A, Schacherer J, Neale MJ, Borde V, Koszul R, Llorente B. Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri. Proc Natl Acad Sci U S A 2024; 121:e2312820121. [PMID: 38478689 PMCID: PMC10962940 DOI: 10.1073/pnas.2312820121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/24/2024] [Indexed: 03/27/2024] Open
Abstract
Meiotic recombination shows broad variations across species and along chromosomes and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here, we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence of recruitment of the two chromosome axis proteins Red1 and Hop1, essential for proper Spo11-DSBs formation. Furthermore, cytological observation of spread pachytene meiotic chromosomes reveals that Lakl0C-left does not undergo synapsis. However, we show that the behavior of Lakl0C-left is independent of its particularly early replication timing and is not accompanied by any peculiar chromosome structure as detectable by Hi-C in this yet poorly studied yeast. Finally, we observed an accumulation of heterozygous mutations on Lakl0C-left and a sexual dimorphism of the haploid meiotic offspring, supporting a direct effect of this absence of meiotic recombination on L. kluyveri genome evolution and fitness. Because suppression of meiotic recombination on sex chromosomes is widely observed across eukaryotes, the mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.
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Affiliation(s)
- Sylvain Legrand
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Asma Saifudeen
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Hélène Bordelet
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Julien Vernerey
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Arnaud Guille
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Laurent Acquaviva
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Maxime Gaudin
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
| | - Aurore Sanchez
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Anne Friedrich
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, Génétique moléculaire, génomique, microbiologie UMR 7156, Strasbourg67000, France
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BrightonBN1 9RH, United Kingdom
| | - Valérie Borde
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris75005, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris75015, France
| | - Bertrand Llorente
- Centre de recherche en cancérologie de Marseille, CNRS UMR 7258, INSERM, Aix Marseille Université, Institut Paoli Calmettes, Marseille13009, France
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López Ruiz LM, Johnson D, Gittens WH, Brown GGB, Allison RM, Neale MJ. Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference. PLoS Genet 2024; 20:e1011140. [PMID: 38427688 PMCID: PMC10936813 DOI: 10.1371/journal.pgen.1011140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 03/13/2024] [Accepted: 01/17/2024] [Indexed: 03/03/2024] Open
Abstract
During meiosis, genetic recombination is initiated by the formation of many DNA double-strand breaks (DSBs) catalysed by the evolutionarily conserved topoisomerase-like enzyme, Spo11, in preferred genomic sites known as hotspots. DSB formation activates the Tel1/ATM DNA damage responsive (DDR) kinase, locally inhibiting Spo11 activity in adjacent hotspots via a process known as DSB interference. Intriguingly, in S. cerevisiae, over short genomic distances (<15 kb), Spo11 activity displays characteristics of concerted activity or clustering, wherein the frequency of DSB formation in adjacent hotspots is greater than expected by chance. We have proposed that clustering is caused by a limited number of sub-chromosomal domains becoming primed for DSB formation. Here, we provide evidence that DSB clustering is abolished when meiotic prophase timing is extended via deletion of the NDT80 transcription factor. We propose that extension of meiotic prophase enables most cells, and therefore most chromosomal domains within them, to reach an equilibrium state of similar Spo11-DSB potential, reducing the impact that priming has on estimates of coincident DSB formation. Consistent with this view, when Tel1 is absent but Ndt80 is present and thus cells are able to rapidly exit meiotic prophase, genome-wide maps of Spo11-DSB formation are skewed towards pericentromeric regions and regions that load pro-DSB factors early-revealing regions of preferential priming-but this effect is abolished when NDT80 is deleted. Our work highlights how the stochastic nature of Spo11-DSB formation in individual cells within the limited temporal window of meiotic prophase can cause localised DSB clustering-a phenomenon that is exacerbated in tel1Δ cells due to the dual roles that Tel1 has in DSB interference and meiotic prophase checkpoint control.
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Affiliation(s)
- Luz María López Ruiz
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - William H. Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - George G. B. Brown
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rachal M. Allison
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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5
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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6
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Börner GV, Hochwagen A, MacQueen AJ. Meiosis in budding yeast. Genetics 2023; 225:iyad125. [PMID: 37616582 PMCID: PMC10550323 DOI: 10.1093/genetics/iyad125] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/13/2023] [Indexed: 08/26/2023] Open
Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
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Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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Liu C, Xu W, Wang L, Yang Z, Li K, Hu J, Chen Y, Zhang R, Xiao S, Liu W, Wei H, Chen JY, Sun Q, Li W. Dual roles of R-loops in the formation and processing of programmed DNA double-strand breaks during meiosis. Cell Biosci 2023; 13:82. [PMID: 37170281 PMCID: PMC10173651 DOI: 10.1186/s13578-023-01026-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Meiotic recombination is initiated by Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions called hotspots; however, the factor(s) that specify the positions of meiotic DSB hotspots remain unclear. RESULTS Here, we examined the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, during budding yeast meiosis and found that the R-loops were changed dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage and found that these R-loops were associated with meiotic recombination during yeast meiosis. We show that transcription-replication head-on collisions could promote R-loop formation during meiotic DNA replication, and these R-loops are associated with Spo11. Furthermore, meiotic recombination hotspots can be eliminated by reversing the direction of transcription or replication, and reversing both of these directions can reconstitute the hotspots. CONCLUSIONS Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.
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Affiliation(s)
- Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liying Wang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yinghong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruidan Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sai Xiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenwen Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huafang Wei
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Abstract
KEY MESSAGE Chromatin state, and dynamic loading of pro-crossover protein HEI10 at recombination intermediates shape meiotic chromosome patterning in plants. Meiosis is the basis of sexual reproduction, and its basic progression is conserved across eukaryote kingdoms. A key feature of meiosis is the formation of crossovers which result in the reciprocal exchange of segments of maternal and paternal chromosomes. This exchange generates chromosomes with new combinations of alleles, increasing the efficiency of both natural and artificial selection. Crossovers also form a physical link between homologous chromosomes at metaphase I which is critical for accurate chromosome segregation and fertility. The patterning of crossovers along the length of chromosomes is a highly regulated process, and our current understanding of its regulation forms the focus of this review. At the global scale, crossover patterning in plants is largely governed by the classically observed phenomena of crossover interference, crossover homeostasis and the obligatory crossover which regulate the total number of crossovers and their relative spacing. The molecular actors behind these phenomena have long remained obscure, but recent studies in plants implicate HEI10 and ZYP1 as key players in their coordination. In addition to these broad forces, a wealth of recent studies has highlighted how genomic and epigenomic features shape crossover formation at both chromosomal and local scales, revealing that crossovers are primarily located in open chromatin associated with gene promoters and terminators with low nucleosome occupancy.
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Affiliation(s)
- Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK.
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Ziesel A, Weng Q, Ahuja JS, Bhattacharya A, Dutta R, Cheng E, Börner GV, Lichten M, Hollingsworth NM. Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase. PLoS Genet 2022; 18:e1010407. [PMID: 36508468 PMCID: PMC9779700 DOI: 10.1371/journal.pgen.1010407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/22/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
During meiosis, recombination between homologous chromosomes (homologs) generates crossovers that promote proper segregation at the first meiotic division. Recombination is initiated by Spo11-catalyzed DNA double strand breaks (DSBs). 5' end resection of the DSBs creates 3' single strand tails that two recombinases, Rad51 and Dmc1, bind to form presynaptic filaments that search for homology, mediate strand invasion and generate displacement loops (D-loops). D-loop processing then forms crossover and non-crossover recombinants. Meiotic recombination occurs in two temporally distinct phases. During Phase 1, Rad51 is inhibited and Dmc1 mediates the interhomolog recombination that promotes homolog synapsis. In Phase 2, Rad51 becomes active and functions with Rad54 to repair residual DSBs, making increasing use of sister chromatids. The transition from Phase 1 to Phase 2 is controlled by the meiotic recombination checkpoint through the meiosis-specific effector kinase Mek1. This work shows that constitutive activation of Rad51 in Phase 1 results in a subset of DSBs being repaired by a Rad51-mediated interhomolog recombination pathway that is distinct from that of Dmc1. Strand invasion intermediates generated by Rad51 require more time to be processed into recombinants, resulting in a meiotic recombination checkpoint delay in prophase I. Without the checkpoint, Rad51-generated intermediates are more likely to involve a sister chromatid, thereby increasing Meiosis I chromosome nondisjunction. This Rad51 interhomolog recombination pathway is specifically promoted by the conserved 5'-3' helicase PIF1 and its paralog, RRM3 and requires Pif1 helicase activity and its interaction with PCNA. This work demonstrates that (1) inhibition of Rad51 during Phase 1 is important to prevent competition with Dmc1 for DSB repair, (2) Rad51-mediated meiotic recombination intermediates are initially processed differently than those made by Dmc1, and (3) the meiotic recombination checkpoint provides time during prophase 1 for processing of Rad51-generated recombination intermediates.
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Affiliation(s)
- Andrew Ziesel
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Qixuan Weng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Jasvinder S. Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Abhishek Bhattacharya
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Raunak Dutta
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Evan Cheng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - G. Valentin Börner
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nancy M. Hollingsworth
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
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10
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Palacios-Blanco I, Martín-Castellanos C. Cyclins and CDKs in the regulation of meiosis-specific events. Front Cell Dev Biol 2022; 10:1069064. [PMID: 36523509 PMCID: PMC9745066 DOI: 10.3389/fcell.2022.1069064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 07/13/2024] Open
Abstract
How eukaryotic cells control their duplication is a fascinating example of how a biological system self-organizes specific activities to temporally order cellular events. During cell cycle progression, the cellular level of CDK (Cyclin-Dependent Kinase) activity temporally orders the different cell cycle phases, ensuring that DNA replication occurs prior to segregation into two daughter cells. CDK activity requires the binding of a regulatory subunit (cyclin) to the core kinase, and both CDKs and cyclins are well conserved throughout evolution from yeast to humans. As key regulators, they coordinate cell cycle progression with metabolism, DNA damage, and cell differentiation. In meiosis, the special cell division that ensures the transmission of genetic information from one generation to the next, cyclins and CDKs have acquired novel functions to coordinate meiosis-specific events such as chromosome architecture, recombination, and synapsis. Interestingly, meiosis-specific cyclins and CDKs are common in evolution, some cyclins seem to have evolved to acquire CDK-independent functions, and even some CDKs associate with a non-cyclin partner. We will review the functions of these key regulators in meiosis where variation has specially flourished.
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11
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Brinkmeier J, Coelho S, de Massy B, Bourbon HM. Evolution and Diversity of the TopoVI and TopoVI-like Subunits With Extensive Divergence of the TOPOVIBL subunit. Mol Biol Evol 2022; 39:msac227. [PMID: 36256608 PMCID: PMC9665070 DOI: 10.1093/molbev/msac227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Type II DNA topoisomerases regulate topology by double-stranded DNA cleavage and ligation. The TopoVI family of DNA topoisomerase, first identified and biochemically characterized in Archaea, represents, with TopoVIII and mini-A, the type IIB family. TopoVI has several intriguing features in terms of function and evolution. TopoVI has been identified in some eukaryotes, and a global view is lacking to understand its evolutionary pattern. In addition, in eukaryotes, the two TopoVI subunits (TopoVIA and TopoVIB) have been duplicated and have evolved to give rise to Spo11 and TopoVIBL, forming TopoVI-like (TopoVIL), a complex essential for generating DNA breaks that initiate homologous recombination during meiosis. TopoVIL is essential for sexual reproduction. How the TopoVI subunits have evolved to ensure this meiotic function is unclear. Here, we investigated the phylogenetic conservation of TopoVI and TopoVIL. We demonstrate that BIN4 and RHL1, potentially interacting with TopoVIB, have co-evolved with TopoVI. Based on model structures, this observation supports the hypothesis for a role of TopoVI in decatenation of replicated chromatids and predicts that in eukaryotes the TopoVI catalytic complex includes BIN4 and RHL1. For TopoVIL, the phylogenetic analysis of Spo11, which is highly conserved among Eukarya, highlighted a eukaryal-specific N-terminal domain that may be important for its regulation. Conversely, TopoVIBL was poorly conserved, giving rise to ATP hydrolysis-mutated or -truncated protein variants, or was undetected in some species. This remarkable plasticity of TopoVIBL provides important information for the activity and function of TopoVIL during meiosis.
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Affiliation(s)
- Julia Brinkmeier
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Susana Coelho
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Henri-Marc Bourbon
- Centre de Biologie Intégrative, CNRS, Université de Toulouse, Toulouse 31400, France
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12
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Guan Y, Lin H, Leu NA, Ruthel G, Fuchs SY, Busino L, Luo M, Wang PJ. SCF ubiquitin E3 ligase regulates DNA double-strand breaks in early meiotic recombination. Nucleic Acids Res 2022; 50:5129-5144. [PMID: 35489071 PMCID: PMC9122608 DOI: 10.1093/nar/gkac304] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
Homeostasis of meiotic DNA double strand breaks (DSB) is critical for germline genome integrity and homologous recombination. Here we demonstrate an essential role for SKP1, a constitutive subunit of the SCF (SKP1-Cullin-F-box) ubiquitin E3 ligase, in early meiotic processes. SKP1 restrains accumulation of HORMAD1 and the pre-DSB complex (IHO1-REC114-MEI4) on the chromosome axis in meiotic germ cells. Loss of SKP1 prior to meiosis leads to aberrant localization of DSB repair proteins and a failure in synapsis initiation in meiosis of both males and females. Furthermore, SKP1 is crucial for sister chromatid cohesion during the pre-meiotic S-phase. Mechanistically, FBXO47, a meiosis-specific F-box protein, interacts with SKP1 and HORMAD1 and targets HORMAD1 for polyubiquitination and degradation in HEK293T cells. Our results support a model wherein the SCF ubiquitin E3 ligase prevents hyperactive DSB formation through proteasome-mediated degradation of HORMAD1 and subsequent modulation of the pre-DSB complex during meiosis.
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Affiliation(s)
- Yongjuan Guan
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Huijuan Lin
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
- Department of Tissue and Embryology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei Province, China
| | - N Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Gordon Ruthel
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Serge Y Fuchs
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mengcheng Luo
- Department of Tissue and Embryology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei Province, China
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
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13
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Trainor BM, Ciccaglione K, Czymek M, Law MJ. Distinct requirements for the COMPASS core subunits Set1, Swd1, and Swd3 during meiosis in the budding yeast Saccharomyces cerevisiae. G3 GENES|GENOMES|GENETICS 2021; 11:6342418. [PMID: 34849786 PMCID: PMC8527496 DOI: 10.1093/g3journal/jkab283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 11/21/2022]
Abstract
Meiosis-specific chromatin structures, guided by histone modifications, are critical mediators of a meiotic transient transcription program and progression through prophase I. Histone H3K4 can be methylated up to three times by the Set1-containing COMPASS complex and each methylation mark corresponds to a different chromatin conformation. The level of H3K4 modification is directed by the activity of additional COMPASS components. In this study, we characterized the role of the COMPASS subunits during meiosis in Saccharomyces cerevisiae. In vegetative cells, previous studies revealed a role for subunits Swd2, Sdc1, and Bre2 for H3K4me2 while Spp1 supported trimethylation. However, we found that Bre2 and Sdc1 are required for H3K4me3 as yeast prepare to enter meiosis while Spp1 is not. Interestingly, we identified distinct meiotic functions for the core COMPASS complex members that required for all H3K4me, Set1, Swd1, and Swd3. While Set1 and Swd1 are required for progression through early meiosis, Swd3 is critical for late meiosis and spore morphogenesis. Furthermore, the meiotic requirement for Set1 is independent of H3K4 methylation, suggesting the presence of nonhistone substrates. Finally, checkpoint suppression analyses indicate that Set1 and Swd1 are required for both homologous recombination and chromosome segregation. These data suggest that COMPASS has important new roles for meiosis that are independent of its well-characterized functions during mitotic divisions.
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Affiliation(s)
- Brandon M Trainor
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University-School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Kerri Ciccaglione
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University-School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Miranda Czymek
- Biochemistry and Molecular Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, NJ 08205, USA
| | - Michael J Law
- Biochemistry and Molecular Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, NJ 08205, USA
- Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, NJ 08205, USA
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14
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Halliwell JA, Hoffmann ER. First come, first served: Mammalian recombination is timed to replication. Cell 2021; 184:4112-4114. [PMID: 34358467 DOI: 10.1016/j.cell.2021.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Meiotic recombination drives the formation of new chromosomes in germ cells and is essential for fertility in mammals. In this issue of Cell, Pratto et al. have developed a method to map replication origins directly in mammalian tissue for the first time, revealing evolutionary conservation between replication timing and meiotic recombination in males.
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Affiliation(s)
- Jason A Halliwell
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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15
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Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 2021; 184:4251-4267.e20. [PMID: 34260899 DOI: 10.1016/j.cell.2021.06.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/02/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Genetic recombination generates novel trait combinations, and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots; however, megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns; therefore, we devised an approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis, and a distinctive replication pattern in human males underlies the subtelomeric increase in recombination. We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.
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16
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Kar FM, Hochwagen A. Phospho-Regulation of Meiotic Prophase. Front Cell Dev Biol 2021; 9:667073. [PMID: 33928091 PMCID: PMC8076904 DOI: 10.3389/fcell.2021.667073] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Germ cells undergoing meiosis rely on an intricate network of surveillance mechanisms that govern the production of euploid gametes for successful sexual reproduction. These surveillance mechanisms are particularly crucial during meiotic prophase, when cells execute a highly orchestrated program of chromosome morphogenesis and recombination, which must be integrated with the meiotic cell division machinery to ensure the safe execution of meiosis. Dynamic protein phosphorylation, controlled by kinases and phosphatases, has emerged as one of the main signaling routes for providing readout and regulation of chromosomal and cellular behavior throughout meiotic prophase. In this review, we discuss common principles and provide detailed examples of how these phosphorylation events are employed to ensure faithful passage of chromosomes from one generation to the next.
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Affiliation(s)
- Funda M Kar
- Department of Biology, New York University, New York, NY, United States
| | - Andreas Hochwagen
- Department of Biology, New York University, New York, NY, United States
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17
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Yadav VK, Claeys Bouuaert C. Mechanism and Control of Meiotic DNA Double-Strand Break Formation in S. cerevisiae. Front Cell Dev Biol 2021; 9:642737. [PMID: 33748134 PMCID: PMC7968521 DOI: 10.3389/fcell.2021.642737] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Developmentally programmed formation of DNA double-strand breaks (DSBs) by Spo11 initiates a recombination mechanism that promotes synapsis and the subsequent segregation of homologous chromosomes during meiosis. Although DSBs are induced to high levels in meiosis, their formation and repair are tightly regulated to minimize potentially dangerous consequences for genomic integrity. In S. cerevisiae, nine proteins participate with Spo11 in DSB formation, but their molecular functions have been challenging to define. Here, we describe our current view of the mechanism of meiotic DSB formation based on recent advances in the characterization of the structure and function of DSB proteins and discuss regulatory pathways in the light of recent models.
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Affiliation(s)
| | - Corentin Claeys Bouuaert
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
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18
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Poot M, Hochstenbach R. Prevalence and Phenotypic Impact of Robertsonian Translocations. Mol Syndromol 2021; 12:1-11. [PMID: 33776621 PMCID: PMC7983559 DOI: 10.1159/000512676] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Robertsonian translocations (RTs) result from fusion of 2 acrocentric chromosomes (e.g., 13, 14, 15, 21, 22) and consequential losses of segments of the p arms containing 47S rDNA clusters and transcription factor binding sites. Depending on the position of the breakpoints, the size of these losses vary considerably between types of RTs. The prevalence of RTs in the general population is estimated to be around 1 per 800 individuals, making RTs the most common chromosomal rearrangement in healthy individuals. Based on their prevalence, RTs are classified as "common," rob(13;14) and rob(14;21), or "rare" (the 8 remaining nonhomologous combinations). Carriers of RTs are at an increased risk for offspring with chromosomal imbalances or with uniparental disomy. RTs are generally regarded as phenotypically neutral, although, due to RTs formation, 2 of the 10 ribosomal rDNA gene clusters, several long noncoding RNAs, and in the case of RTs involving chromosome 21, several mRNA encoding genes are lost. Nevertheless, recent evidence indicates that RTs may have a significant phenotypic impact. In particular, rob(13;14) carriers have a significantly elevated risk for breast cancer. While RTs are easily spotted by routine karyotyping, they may go unnoticed if only array-CGH and NextGen sequencing methods are applied. This review first discusses possible molecular mechanisms underlying the particularly high rates of RT formation and their incidence in the general population, and second, likely causes for the elevated cancer risk of some RTs will be examined.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Ron Hochstenbach
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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19
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Mu X, Murakami H, Mohibullah N, Keeney S. Chromosome-autonomous feedback down-regulates meiotic DNA break competence upon synaptonemal complex formation. Genes Dev 2020; 34:1605-1618. [PMID: 33184224 PMCID: PMC7706706 DOI: 10.1101/gad.342873.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/29/2020] [Indexed: 01/20/2023]
Abstract
The number of DNA double-strand breaks (DSBs) initiating meiotic recombination is elevated in Saccharomyces cerevisiae mutants that are globally defective in forming crossovers and synaptonemal complex (SC), a protein scaffold juxtaposing homologous chromosomes. These mutants thus appear to lack a negative feedback loop that inhibits DSB formation when homologs engage one another. This feedback is predicted to be chromosome autonomous, but this has not been tested. Moreover, what chromosomal process is recognized as "homolog engagement" remains unclear. To address these questions, we evaluated effects of homolog engagement defects restricted to small portions of the genome using karyotypically abnormal yeast strains with a homeologous chromosome V pair, monosomic V, or trisomy XV. We found that homolog engagement-defective chromosomes incurred more DSBs, concomitant with prolonged retention of the DSB-promoting protein Rec114, while the rest of the genome remained unaffected. SC-deficient, crossover-proficient mutants ecm11 and gmc2 experienced increased DSB numbers diagnostic of homolog engagement defects. These findings support the hypothesis that SC formation provokes DSB protein dissociation, leading in turn to loss of a DSB competent state. Our findings show that DSB number is regulated in a chromosome-autonomous fashion and provide insight into how homeostatic DSB controls respond to aneuploidy during meiosis.
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Affiliation(s)
- Xiaojing Mu
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10021, USA
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Neeman Mohibullah
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Scott Keeney
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10021, USA
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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20
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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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21
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Murakami H, Lam I, Huang PC, Song J, van Overbeek M, Keeney S. Multilayered mechanisms ensure that short chromosomes recombine in meiosis. Nature 2020; 582:124-128. [PMID: 32494071 PMCID: PMC7298877 DOI: 10.1038/s41586-020-2248-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/12/2020] [Indexed: 12/17/2022]
Abstract
In most species, homologous chromosomes must recombine in order to segregate accurately during meiosis1. Because small chromosomes would be at risk of missegregation if recombination were randomly distributed, the double-strand breaks (DSBs) that initiate recombination are not located arbitrarily2. How the nonrandomness of DSB distributions is controlled is not understood, although several pathways are known to regulate the timing, location and number of DSBs. Meiotic DSBs are generated by Spo11 and accessory DSB proteins, including Rec114 and Mer2, which assemble on chromosomes3-7 and are nearly universal in eukaryotes8-11. Here we demonstrate how Saccharomyces cerevisiae integrates multiple temporally distinct pathways to regulate the binding of Rec114 and Mer2 to chromosomes, thereby controlling the duration of a DSB-competent state. The engagement of homologous chromosomes with each other regulates the dissociation of Rec114 and Mer2 later in prophase I, whereas the timing of replication and the proximity to centromeres or telomeres influence the accumulation of Rec114 and Mer2 early in prophase I. Another early mechanism enhances the binding of Rec114 and Mer2 specifically on the shortest chromosomes, and is subject to selection pressure to maintain the hyperrecombinogenic properties of these chromosomes. Thus, the karyotype of an organism and its risk of meiotic missegregation influence the shape and evolution of its recombination landscape. Our results provide a cohesive view of a multifaceted and evolutionarily constrained system that allocates DSBs to all pairs of homologous chromosomes.
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Affiliation(s)
- Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Isabel Lam
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pei-Ching Huang
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Jacquelyn Song
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Megan van Overbeek
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Caribou Biosciences, Inc., Berkeley, CA, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Graduate School of Medical Sciences, Cornell University, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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22
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Ku JC, Ronceret A, Golubovskaya I, Lee DH, Wang C, Timofejeva L, Kao YH, Gomez Angoa AK, Kremling K, Williams-Carrier R, Meeley R, Barkan A, Cande WZ, Wang CJR. Dynamic localization of SPO11-1 and conformational changes of meiotic axial elements during recombination initiation of maize meiosis. PLoS Genet 2020; 16:e1007881. [PMID: 32310948 PMCID: PMC7192515 DOI: 10.1371/journal.pgen.1007881] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 04/30/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Meiotic double-strand breaks (DSBs) are generated by the evolutionarily conserved SPO11 complex in the context of chromatin loops that are organized along axial elements (AEs) of chromosomes. However, how DSBs are formed with respect to chromosome axes and the SPO11 complex remains unclear in plants. Here, we confirm that DSB and bivalent formation are defective in maize spo11-1 mutants. Super-resolution microscopy demonstrates dynamic localization of SPO11-1 during recombination initiation, with variable numbers of SPO11-1 foci being distributed in nuclei but similar numbers of SPO11-1 foci being found on AEs. Notably, cytological analysis of spo11-1 meiocytes revealed an aberrant AE structure. At leptotene, AEs of wild-type and spo11-1 meiocytes were similarly curly and discontinuous. However, during early zygotene, wild-type AEs become uniform and exhibit shortened axes, whereas the elongated and curly AEs persisted in spo11-1 mutants, suggesting that loss of SPO11-1 compromised AE structural maturation. Our results reveal an interesting relationship between SPO11-1 loading onto AEs and the conformational remodeling of AEs during recombination initiation. Meiosis is essential during sexual reproduction to produce haploid gametes. Recombination is the most crucial step during meiotic prophase I. It enables pairing of homologous chromosomes prior to their reductional division and generates new combinations of genetic alleles for transmission to the next generation. Meiotic recombination is initiated by generating DNA double-strand breaks (DSBs) via SPO11, a topoisomerase-related enzyme. The activity, timing and location of this DSB machinery must be controlled precisely, but how this is achieved remains obscure. Here, we show dynamic localization of SPO11-1 on chromatin during meiotic initiation in maize, yet a similar number of SPO11-1 is able to load onto axial elements (AEs), which accompanies a structural change of the AEs of wild-type meiotic chromosomes. Interestingly, loss of SPO11-1 not only affects DSB formation but also impairs structural alterations of AEs, resulting in abnormally long and curly AEs during early meiosis. Our study provides new insights into SPO11-1 localization during recombination initiation and suggests an intimate relationship between DSB formation and AE structural changes.
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Affiliation(s)
- Jia-Chi Ku
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Arnaud Ronceret
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
- Instituto de Biotecnología / UNAM Cuernavaca, Morelos Mexico
| | - Inna Golubovskaya
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
- N.I. Vavilov Institute of Plant Industry, St. Petersburg, Russia
| | - Ding Hua Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chiting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ljudmilla Timofejeva
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Yu-Hsin Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | | - Karl Kremling
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | | | - Robert Meeley
- Corteva Agriscience, Johnston, Iowa, United States of America
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America
| | - W. Zacheus Cande
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Chung-Ju Rachel Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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23
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Genetic Interactions of Histone Modification Machinery Set1 and PAF1C with the Recombination Complex Rec114-Mer2-Mei4 in the Formation of Meiotic DNA Double-Strand Breaks. Int J Mol Sci 2020; 21:ijms21082679. [PMID: 32290544 PMCID: PMC7215556 DOI: 10.3390/ijms21082679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 11/19/2022] Open
Abstract
Homologous recombination is essential for chromosome segregation during meiosis I. Meiotic recombination is initiated by the introduction of double-strand breaks (DSBs) at specific genomic locations called hotspots, which are catalyzed by Spo11 and its partners. DSB hotspots during meiosis are marked with Set1-mediated histone H3K4 methylation. The Spo11 partner complex, Rec114-Mer2-Mei4, essential for the DSB formation, localizes to the chromosome axes. For efficient DSB formation, a hotspot with histone H3K4 methylation on the chromatin loops is tethered to the chromosome axis through the H3K4 methylation reader protein, Spp1, on the axes, which interacts with Mer2. In this study, we found genetic interaction of mutants in a histone modification protein complex called PAF1C with the REC114 and MER2 in the DSB formation in budding yeast Saccharomyces cerevisiae. Namely, the paf1c mutations rtf1 and cdc73 showed synthetic defects in meiotic DSB formation only when combined with a wild-type-like tagged allele of either the REC114 or MER2. The synthetic defect of the tagged REC114 allele in the DSB formation was seen also with the set1, but not with spp1 deletion. These results suggest a novel role of histone modification machinery in DSB formation during meiosis, which is independent of Spp1-mediated loop-axis tethering.
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24
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Arbel‐Eden A, Simchen G. Elevated Mutagenicity in Meiosis and Its Mechanism. Bioessays 2019; 41:e1800235. [DOI: 10.1002/bies.201800235] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/31/2019] [Indexed: 12/25/2022]
Affiliation(s)
| | - Giora Simchen
- Department of GeneticsThe Hebrew University of JerusalemJerusalem 91904 Israel
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25
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CDK contribution to DSB formation and recombination in fission yeast meiosis. PLoS Genet 2019; 15:e1007876. [PMID: 30640914 PMCID: PMC6331086 DOI: 10.1371/journal.pgen.1007876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
CDKs (cyclin-dependent kinases) associate with different cyclins to form different CDK-complexes that are fundamental for an ordered cell cycle progression, and the coordination of this progression with different aspects of the cellular physiology. During meiosis programmed DNA double-strand breaks (DSBs) initiate recombination that in addition to generating genetic variability are essential for the reductional chromosome segregation during the first meiotic division, and therefore for genome stability and viability of the gametes. However, how meiotic progression and DSB formation are coordinated, and the role CDKs have in the process, is not well understood. We have used single and double cyclin deletion mutants, and chemical inhibition of global CDK activity using the cdc2-asM17 allele, to address the requirement of CDK activity for DSB formation and recombination in fission yeast. We report that several cyclins (Cig1, Cig2, and the meiosis-specific Crs1) control DSB formation and recombination, with a major contribution of Crs1. Moreover, complementation analysis indicates specificity at least for this cyclin, suggesting that different CDK complexes might act in different pathways to promote recombination. Down-regulation of CDK activity impinges on the formation of linear elements (LinEs, protein complexes required for break formation at most DSB hotspot sites). This defect correlates with a reduction in the capability of one structural component (Rec25) to bind chromatin, suggesting a molecular mechanism by which CDK controls break formation. However, reduction in DSB formation in cyclin deletion mutants does not always correspondingly correlate with a proportional reduction in meiotic recombination (crossovers), suggesting that specific CDK complexes might also control downstream events balancing repair pathways. Therefore, our work points to CDK regulation of DSB formation as a key conserved feature in the initiation of meiotic recombination, in addition to provide a view of possible roles CDK might have in other steps of the recombination process. Meiotic division is a cell division process where a single round of DNA replication is followed by two sequential chromosome segregations, the first reductional (homologous chromosomes separate) and the second equational (sister chromatids segregate). As a consequence diploid organisms halve ploidy, producing haploid gametes that after fertilization generate a new diploid organism with a complete chromosome complement. At early stages of meiosis physical exchange between homologous chromosomes ensures the accurate following reductional segregation. Physical exchange is provided by recombination that initiates with highly-controlled self-inflicted DNA damage (DSBs, double strand breaks). We have found that the conserved CDK (cyclin-dependent kinase) activity controls DSB formation in fission yeast. Available data were uncertain about the conservation of CDK in the process, and thus our work points to a broad evolutionary conservation of this regulation. Regulation is exerted at least by controlling chromatin-binding of one structural component of linear elements, a protein complex related to the synaptonemal complex and required for high levels of DSBs. Correspondingly, depletion of CDK activity impairs formation of these structures. In addition, CDK might control homeostatic mechanisms, critical to maintain efficient levels of recombination across the genome and, therefore, high rates of genetic exchange between parental chromosomes.
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26
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Singh B, Wu PYJ. Regulation of the program of DNA replication by CDK: new findings and perspectives. Curr Genet 2018; 65:79-85. [PMID: 29926159 DOI: 10.1007/s00294-018-0860-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
Abstract
Progression through the cell cycle is driven by the activities of the cyclin-dependent kinase (CDK) family of enzymes, which establish an ordered passage through the cell cycle phases. CDK activity is crucial for the cellular transitions from G1 to S and G2 to M, which are highly controlled to promote the faithful duplication of the genetic material and the transmission of the genome into daughter cells, respectively. While oscillations in CDK activity are essential for cell division, how its specific dynamics may shape cellular processes remains an open question. Recently, we have investigated the potential role of CDK in establishing the profile of replication initiation along the chromosomes, also referred to as the replication program. Our results demonstrated that the timing and level of CDK activity at G1/S provide two critical and independent inputs that modulate the pattern of origin usage. In this review, we will present the conclusions of our study and discuss the implications of our findings for cellular function and physiology.
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Affiliation(s)
- Balveer Singh
- CNRS, Institute of Genetics and Development of Rennes, University of Rennes, UMR 6290, 2 avenue du Pr. Léon Bernard, 35043, Rennes, France
| | - Pei-Yun Jenny Wu
- CNRS, Institute of Genetics and Development of Rennes, University of Rennes, UMR 6290, 2 avenue du Pr. Léon Bernard, 35043, Rennes, France.
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27
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Gaysinskaya V, Miller BF, De Luca C, van der Heijden GW, Hansen KD, Bortvin A. Transient reduction of DNA methylation at the onset of meiosis in male mice. Epigenetics Chromatin 2018; 11:15. [PMID: 29618374 PMCID: PMC5883305 DOI: 10.1186/s13072-018-0186-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 01/12/2023] Open
Abstract
Background Meiosis is a specialized germ cell cycle that generates haploid gametes. In the initial stage of meiosis, meiotic prophase I (MPI), homologous chromosomes pair and recombine. Extensive changes in chromatin in MPI raise an important question concerning the contribution of epigenetic mechanisms such as DNA methylation to meiosis. Interestingly, previous studies concluded that in male mice, genome-wide DNA methylation patters are set in place prior to meiosis and remain constant subsequently. However, no prior studies examined DNA methylation during MPI in a systematic manner necessitating its further investigation. Results In this study, we used genome-wide bisulfite sequencing to determine DNA methylation of adult mouse spermatocytes at all MPI substages, spermatogonia and haploid sperm. This analysis uncovered transient reduction of DNA methylation (TRDM) of spermatocyte genomes. The genome-wide scope of TRDM, its onset in the meiotic S phase and presence of hemimethylated DNA in MPI are all consistent with a DNA replication-dependent DNA demethylation. Following DNA replication, spermatocytes regain DNA methylation gradually but unevenly, suggesting that key MPI events occur in the context of hemimethylated genome. TRDM also uncovers the prior deficit of DNA methylation of LINE-1 retrotransposons in spermatogonia resulting in their full demethylation during TRDM and likely contributing to the observed mRNA and protein expression of some LINE-1 elements in early MPI. Conclusions Our results suggest that contrary to the prevailing view, chromosomes exhibit dynamic changes in DNA methylation in MPI. We propose that TRDM facilitates meiotic prophase processes and gamete quality control. Electronic supplementary material The online version of this article (10.1186/s13072-018-0186-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valeriya Gaysinskaya
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Brendan F Miller
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chiara De Luca
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Godfried W van der Heijden
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA.
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28
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Adam C, Guérois R, Citarella A, Verardi L, Adolphe F, Béneut C, Sommermeyer V, Ramus C, Govin J, Couté Y, Borde V. The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes. PLoS Genet 2018; 14:e1007223. [PMID: 29444071 PMCID: PMC5828529 DOI: 10.1371/journal.pgen.1007223] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 02/27/2018] [Accepted: 01/25/2018] [Indexed: 11/18/2022] Open
Abstract
Histone H3K4 methylation is a feature of meiotic recombination hotspots shared by many organisms including plants and mammals. Meiotic recombination is initiated by programmed double-strand break (DSB) formation that in budding yeast takes place in gene promoters and is promoted by histone H3K4 di/trimethylation. This histone modification is recognized by Spp1, a PHD finger containing protein that belongs to the conserved histone H3K4 methyltransferase Set1 complex. During meiosis, Spp1 binds H3K4me3 and interacts with a DSB protein, Mer2, to promote DSB formation close to gene promoters. How Set1 complex- and Mer2- related functions of Spp1 are connected is not clear. Here, combining genome-wide localization analyses, biochemical approaches and the use of separation of function mutants, we show that Spp1 is present within two distinct complexes in meiotic cells, the Set1 and the Mer2 complexes. Disrupting the Spp1-Set1 interaction mildly decreases H3K4me3 levels and does not affect meiotic recombination initiation. Conversely, the Spp1-Mer2 interaction is required for normal meiotic recombination initiation, but dispensable for Set1 complex-mediated histone H3K4 methylation. Finally, we provide evidence that Spp1 preserves normal H3K4me3 levels independently of the Set1 complex. We propose a model where Spp1 works in three ways to promote recombination initiation: first by depositing histone H3K4 methylation (Set1 complex), next by “reading” and protecting histone H3K4 methylation, and finally by making the link with the chromosome axis (Mer2-Spp1 complex). This work deciphers the precise roles of Spp1 in meiotic recombination and opens perspectives to study its functions in other organisms where H3K4me3 is also present at recombination hotspots. Meiotic recombination is a conserved pathway of sexual reproduction that is required to faithfully segregate homologous chromosomes and produce viable gametes. Recombination events between homologous chromosomes are triggered by the programmed formation of DNA breaks, which occur preferentially at places called hotspots. In many organisms, these hotspots are located close to a particular chromatin modification, the methylation of lysine 4 of histone H3 (H3K4me3). It was previously shown in the budding yeast model that one protein, Spp1, plays an important function in this process. We further explored the functional link between Spp1 and its interacting partners, and show that Spp1 shows genetically separable functions, by depositing the H3K4me3 mark on the chromatin, “reading” and protecting it, and linking it to the recombination proteins. We provide evidence that Spp1 is in distinct complexes to perform these functions. This work opens perspectives for understanding the process in other eukaryotes such as mammals, where most of the proteins involved are conserved.
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Affiliation(s)
- Céline Adam
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Anna Citarella
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Laura Verardi
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Florine Adolphe
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Claire Béneut
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Vérane Sommermeyer
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Claire Ramus
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Jérôme Govin
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Valérie Borde
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
- * E-mail:
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29
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Lam I, Mohibullah N, Keeney S. Sequencing Spo11 Oligonucleotides for Mapping Meiotic DNA Double-Strand Breaks in Yeast. Methods Mol Biol 2018; 1471:51-98. [PMID: 28349390 DOI: 10.1007/978-1-4939-6340-9_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Meiosis is a specialized form of cell division resulting in reproductive cells with a reduced, usually haploid, genome complement. A key step after premeiotic DNA replication is the occurrence of homologous recombination at multiple places throughout the genome, initiated with the formation of DNA double-strand breaks (DSBs) catalyzed by the topoisomerase-like protein Spo11. DSBs are distributed non-randomly in genomes, and understanding the mechanisms that shape this distribution is important for understanding how meiotic recombination influences heredity and genome evolution. Several methods exist for mapping where Spo11 acts. Of these, sequencing of Spo11-associated oligonucleotides (Spo11 oligos) is the most precise, specifying the locations of DNA breaks to the base pair. In this chapter we detail the steps involved in Spo11-oligo mapping in the SK1 strain of budding yeast Saccharomyces cerevisiae, from harvesting cells of highly synchronous meiotic cultures, through preparation of sequencing libraries, to the mapping pipeline used for processing the data.
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Affiliation(s)
- Isabel Lam
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Neeman Mohibullah
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Scott Keeney
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. .,Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. .,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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30
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Khan FA, Ali SO. Physiological Roles of DNA Double-Strand Breaks. J Nucleic Acids 2017; 2017:6439169. [PMID: 29181194 PMCID: PMC5664317 DOI: 10.1155/2017/6439169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/24/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic integrity is constantly threatened by sources of DNA damage, internal and external alike. Among the most cytotoxic lesions is the DNA double-strand break (DSB) which arises from the cleavage of both strands of the double helix. Cells boast a considerable set of defences to both prevent and repair these breaks and drugs which derail these processes represent an important category of anticancer therapeutics. And yet, bizarrely, cells deploy this very machinery for the intentional and calculated disruption of genomic integrity, harnessing potentially destructive DSBs in delicate genetic transactions. Under tight spatiotemporal regulation, DSBs serve as a tool for genetic modification, widely used across cellular biology to generate diverse functionalities, ranging from the fundamental upkeep of DNA replication, transcription, and the chromatin landscape to the diversification of immunity and the germline. Growing evidence points to a role of aberrant DSB physiology in human disease and an understanding of these processes may both inform the design of new therapeutic strategies and reduce off-target effects of existing drugs. Here, we review the wide-ranging roles of physiological DSBs and the emerging network of their multilateral regulation to consider how the cell is able to harness DNA breaks as a critical biochemical tool.
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Affiliation(s)
- Farhaan A. Khan
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
| | - Syed O. Ali
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
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31
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Abstract
Microsatellite repeat DNA is best known for its length mutability, which is implicated in several neurological diseases and cancers, and often exploited as a genetic marker. Less well-known is the body of work exploring the widespread and surprisingly diverse functional roles of microsatellites. Recently, emerging evidence includes the finding that normal microsatellite polymorphism contributes substantially to the heritability of human gene expression on a genome-wide scale, calling attention to the task of elucidating the mechanisms involved. At present, these are underexplored, but several themes have emerged. I review evidence demonstrating roles for microsatellites in modulation of transcription factor binding, spacing between promoter elements, enhancers, cytosine methylation, alternative splicing, mRNA stability, selection of transcription start and termination sites, unusual structural conformations, nucleosome positioning and modification, higher order chromatin structure, noncoding RNA, and meiotic recombination hot spots.
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32
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Escorcia W, Forsburg SL. Destabilization of the replication fork protection complex disrupts meiotic chromosome segregation. Mol Biol Cell 2017; 28:2978-2997. [PMID: 28855376 PMCID: PMC5662257 DOI: 10.1091/mbc.e17-02-0101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 08/21/2017] [Accepted: 08/23/2017] [Indexed: 12/17/2022] Open
Abstract
The replication fork protection complex (FPC) coordinates multiple processes that are crucial for unimpeded passage of the replisome through various barriers and difficult to replicate areas of the genome. We examine the function of Swi1 and Swi3, fission yeast's primary FPC components, to elucidate how replication fork stability contributes to DNA integrity in meiosis. We report that destabilization of the FPC results in reduced spore viability, delayed replication, changes in recombination, and chromosome missegregation in meiosis I and meiosis II. These phenotypes are linked to accumulation and persistence of DNA damage markers in meiosis and to problems with cohesion stability at the centromere. These findings reveal an important connection between meiotic replication fork stability and chromosome segregation, two processes with major implications to human reproductive health.
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Affiliation(s)
- Wilber Escorcia
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910
| | - Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910
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33
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Correlation of Meiotic DSB Formation and Transcription Initiation Around Fission Yeast Recombination Hotspots. Genetics 2017; 206:801-809. [PMID: 28396503 DOI: 10.1534/genetics.116.197954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/31/2017] [Indexed: 11/18/2022] Open
Abstract
Meiotic homologous recombination, a critical event for ensuring faithful chromosome segregation and creating genetic diversity, is initiated by programmed DNA double-strand breaks (DSBs) formed at recombination hotspots. Meiotic DSB formation is likely to be influenced by other DNA-templated processes including transcription, but how DSB formation and transcription interact with each other has not been understood well. In this study, we used fission yeast to investigate a possible interplay of these two events. A group of hotspots in fission yeast are associated with sequences similar to the cyclic AMP response element and activated by the ATF/CREB family transcription factor dimer Atf1-Pcr1. We first focused on one of those hotspots, ade6-3049, and Atf1. Our results showed that multiple transcripts, shorter than the ade6 full-length messenger RNA, emanate from a region surrounding the ade6-3049 hotspot. Interestingly, we found that the previously known recombination-activation region of Atf1 is also a transactivation domain, whose deletion affected DSB formation and short transcript production at ade6-3049 These results point to a possibility that the two events may be related to each other at ade6-3049 In fact, comparison of published maps of meiotic transcripts and hotspots suggested that hotspots are very often located close to meiotically transcribed regions. These observations therefore propose that meiotic DSB formation in fission yeast may be connected to transcription of surrounding regions.
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34
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Martín AC, Rey MD, Shaw P, Moore G. Dual effect of the wheat Ph1 locus on chromosome synapsis and crossover. Chromosoma 2017; 126:669-680. [PMID: 28365783 PMCID: PMC5688220 DOI: 10.1007/s00412-017-0630-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 11/28/2022]
Abstract
Allopolyploids must possess a mechanism for facilitating synapsis and crossover (CO) between homologues, in preference to homoeologues (related chromosomes), to ensure successful meiosis. In hexaploid wheat, the Ph1 locus has a major effect on the control of these processes. Studying a wheat mutant lacking Ph1 provides an opportunity to explore the underlying mechanisms. Recently, it was proposed that Ph1 stabilises wheat during meiosis, both by promoting homologue synapsis during early meiosis and preventing MLH1 sites on synapsed homoeologues from becoming COs later in meiosis. Here, we explore these two effects and demonstrate firstly that whether or not Ph1 is present, synapsis between homoeologues does not take place during the telomere bouquet stage, with only homologous synapsis taking place during this stage. Furthermore, in wheat lacking Ph1, overall synapsis is delayed with respect to the telomere bouquet, with more synapsis occurring after the bouquet stage, when homoeologous synapsis is also possible. Secondly, we show that in the absence of Ph1, we can increase the number of MLH1 sites progressing to COs by altering environmental growing conditions; we show that higher nutrient levels in the soil or lower temperatures increase the level of both homologue and homoeologue COs. These observations suggest opportunities to improve the exploitation of the Ph1 wheat mutant in breeding programmes.
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Affiliation(s)
| | | | - Peter Shaw
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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35
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Roles of CDK and DDK in Genome Duplication and Maintenance: Meiotic Singularities. Genes (Basel) 2017; 8:genes8030105. [PMID: 28335524 PMCID: PMC5368709 DOI: 10.3390/genes8030105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 12/16/2022] Open
Abstract
Cells reproduce using two types of divisions: mitosis, which generates two daughter cells each with the same genomic content as the mother cell, and meiosis, which reduces the number of chromosomes of the parent cell by half and gives rise to four gametes. The mechanisms that promote the proper progression of the mitotic and meiotic cycles are highly conserved and controlled. They require the activities of two types of serine-threonine kinases, the cyclin-dependent kinases (CDKs) and the Dbf4-dependent kinase (DDK). CDK and DDK are essential for genome duplication and maintenance in both mitotic and meiotic divisions. In this review, we aim to highlight how these kinases cooperate to orchestrate diverse processes during cellular reproduction, focusing on meiosis-specific adaptions of their regulation and functions in DNA metabolism.
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36
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Abstract
Meiosis, the mechanism of creating haploid gametes, is a complex cellular process observed across sexually reproducing organisms. Fundamental to meiosis is the process of homologous recombination, whereby DNA double-strand breaks are introduced into the genome and are subsequently repaired to generate either noncrossovers or crossovers. Although homologous recombination is essential for chromosome pairing during prophase I, the resulting crossovers are critical for maintaining homolog interactions and enabling accurate segregation at the first meiotic division. Thus, the placement, timing, and frequency of crossover formation must be exquisitely controlled. In this review, we discuss the proteins involved in crossover formation, the process of their formation and designation, and the rules governing crossovers, all within the context of the important landmarks of prophase I. We draw together crossover designation data across organisms, analyze their evolutionary divergence, and propose a universal model for crossover regulation.
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Affiliation(s)
- Stephen Gray
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, New York 14853; ,
| | - Paula E Cohen
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, New York 14853; ,
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37
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Yan X, Zeng X, Wang S, Li K, Yuan R, Gao H, Luo J, Liu F, Wu Y, Li Y, Zhu L, Wu G. Aberrant Meiotic Prophase I Leads to Genic Male Sterility in the Novel TE5A Mutant of Brassica napus. Sci Rep 2016; 6:33955. [PMID: 27670217 PMCID: PMC5037387 DOI: 10.1038/srep33955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/05/2016] [Indexed: 12/15/2022] Open
Abstract
Genic male sterility (GMS) has already been extensively utilized for hybrid rapeseed production. TE5A is a novel thermo-sensitive dominant GMS line in Brassica napus, however, its mechanisms of GMS remain largely unclear. Histological and Transmission electron microscopy (TEM) analyses of anthers showed that the male gamete development of TE5A was arrested at meiosis prophase I. EdU uptake of S-phase meiocytes revealed that the TE5A mutant could accomplish DNA replication, however, chromosomal and fluorescence in situ hybridization (FISH) analyses of TE5A showed that homologous chromosomes could not pair, synapse, condense and form bivalents. We then analyzed the transcriptome differences between young floral buds of sterile plants and its near-isogenic fertile plants through RNA-Seq. A total of 3,841 differentially expressed genes (DEGs) were obtained, some of which were associated with homologous chromosome behavior and cell cycle control during meiosis. Dynamic expression changes of selected candidate DEGs were then analyzed at different anther developmental stages. The present study not only demonstrated that the TE5A mutant had defects in meiotic prophase I via detailed cytological analysis, but also provided a global insight into GMS-associated DEGs and elucidated the mechanisms of GMS in TE5A through RNA-Seq.
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Affiliation(s)
- Xiaohong Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Xinhua Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Shasha Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Rong Yuan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Hongfei Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Junling Luo
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Fang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Yuhua Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Yunjing Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Li Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Gang Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
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38
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Yelina NE, Lambing C, Hardcastle TJ, Zhao X, Santos B, Henderson IR. DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis. Genes Dev 2016; 29:2183-202. [PMID: 26494791 PMCID: PMC4617981 DOI: 10.1101/gad.270876.115] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Yelina et al. show that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. This work demonstrates that DNA methylation plays a key role in establishing domains of meiotic recombination along chromosomes. During meiosis, homologous chromosomes undergo crossover recombination, which is typically concentrated in narrow hot spots that are controlled by genetic and epigenetic information. Arabidopsis chromosomes are highly DNA methylated in the repetitive centromeres, which are also crossover-suppressed. Here we demonstrate that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. However, loss of CG DNA methylation maintenance in met1 triggers epigenetic crossover remodeling at the chromosome scale, with pericentromeric decreases and euchromatic increases in recombination. We used recombination mutants that alter interfering and noninterfering crossover repair pathways (fancm and zip4) to demonstrate that remodeling primarily involves redistribution of interfering crossovers. Using whole-genome bisulfite sequencing, we show that crossover remodeling is driven by loss of CG methylation within the centromeric regions. Using cytogenetics, we profiled meiotic DNA double-strand break (DSB) foci in met1 and found them unchanged relative to wild type. We propose that met1 chromosome structure is altered, causing centromere-proximal DSBs to be inhibited from maturation into interfering crossovers. These data demonstrate that DNA methylation is sufficient to silence crossover hot spots and plays a key role in establishing domains of meiotic recombination along chromosomes.
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Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Bruno Santos
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Abstract
The study of homologous recombination has its historical roots in meiosis. In this context, recombination occurs as a programmed event that culminates in the formation of crossovers, which are essential for accurate chromosome segregation and create new combinations of parental alleles. Thus, meiotic recombination underlies both the independent assortment of parental chromosomes and genetic linkage. This review highlights the features of meiotic recombination that distinguish it from recombinational repair in somatic cells, and how the molecular processes of meiotic recombination are embedded and interdependent with the chromosome structures that characterize meiotic prophase. A more in-depth review presents our understanding of how crossover and noncrossover pathways of meiotic recombination are differentiated and regulated. The final section of this review summarizes the studies that have defined defective recombination as a leading cause of pregnancy loss and congenital disease in humans.
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Affiliation(s)
- Neil Hunter
- Howard Hughes Medical Institute, Department of Microbiology & Molecular Genetics, Department of Molecular & Cellular Biology, Department of Cell Biology & Human Anatomy, University of California Davis, Davis, California 95616
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High-Resolution Global Analysis of the Influences of Bas1 and Ino4 Transcription Factors on Meiotic DNA Break Distributions in Saccharomyces cerevisiae. Genetics 2015; 201:525-42. [PMID: 26245832 DOI: 10.1534/genetics.115.178293] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 08/02/2015] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination initiates with DNA double-strand breaks (DSBs) made by Spo11. In Saccharomyces cerevisiae, many DSBs occur in "hotspots" coinciding with nucleosome-depleted gene promoters. Transcription factors (TFs) stimulate DSB formation in some hotspots, but TF roles are complex and variable between locations. Until now, available data for TF effects on global DSB patterns were of low spatial resolution and confined to a single TF. Here, we examine at high resolution the contributions of two TFs to genome-wide DSB distributions: Bas1, which was known to regulate DSB activity at some loci, and Ino4, for which some binding sites were known to be within strong DSB hotspots. We examined fine-scale DSB distributions in TF mutant strains by deep sequencing oligonucleotides that remain covalently bound to Spo11 as a byproduct of DSB formation, mapped Bas1 and Ino4 binding sites in meiotic cells, evaluated chromatin structure around DSB hotspots, and measured changes in global messenger RNA levels. Our findings show that binding of these TFs has essentially no predictive power for DSB hotspot activity and definitively support the hypothesis that TF control of DSB numbers is context dependent and frequently indirect. TFs often affected the fine-scale distributions of DSBs within hotspots, and when seen, these effects paralleled effects on local chromatin structure. In contrast, changes in DSB frequencies in hotspots did not correlate with quantitative measures of chromatin accessibility, histone H3 lysine 4 trimethylation, or transcript levels. We also ruled out hotspot competition as a major source of indirect TF effects on DSB distributions. Thus, counter to prevailing models, roles of these TFs on DSB hotspot strength cannot be simply explained via chromatin "openness," histone modification, or compensatory interactions between adjacent hotspots.
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42
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Keeney S, Lange J, Mohibullah N. Self-organization of meiotic recombination initiation: general principles and molecular pathways. Annu Rev Genet 2015; 48:187-214. [PMID: 25421598 DOI: 10.1146/annurev-genet-120213-092304] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recombination in meiosis is a fascinating case study for the coordination of chromosomal duplication, repair, and segregation with each other and with progression through a cell-division cycle. Meiotic recombination initiates with formation of developmentally programmed DNA double-strand breaks (DSBs) at many places across the genome. DSBs are important for successful meiosis but are also dangerous lesions that can mutate or kill, so cells ensure that DSBs are made only at the right times, places, and amounts. This review examines the complex web of pathways that accomplish this control. We explore how chromosome breakage is integrated with meiotic progression and how feedback mechanisms spatially pattern DSB formation and make it homeostatic, robust, and error correcting. Common regulatory themes recur in different organisms or in different contexts in the same organism. We review this evolutionary and mechanistic conservation but also highlight where control modules have diverged. The framework that emerges helps explain how meiotic chromosomes behave as a self-organizing system.
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Affiliation(s)
- Scott Keeney
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
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43
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Joshi N, Brown MS, Bishop DK, Börner GV. Gradual implementation of the meiotic recombination program via checkpoint pathways controlled by global DSB levels. Mol Cell 2015; 57:797-811. [PMID: 25661491 DOI: 10.1016/j.molcel.2014.12.027] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 09/03/2014] [Accepted: 12/16/2014] [Indexed: 11/16/2022]
Abstract
During meiosis, Spo11-induced double-strand breaks (DSBs) are processed into crossovers, ensuring segregation of homologous chromosomes (homologs). Meiotic DSB processing entails 5' end resection and preferred strand exchange with the homolog rather than the sister chromatid (homolog bias). In many organisms, DSBs appear gradually along the genome. Here we report unexpected effects of global DSB levels on local recombination events. Early-occurring, low-abundance "scout" DSBs lack homolog bias. Their resection and interhomolog processing are controlled by the conserved checkpoint proteins Tel1(ATM) kinase and Pch2(TRIP13) ATPase. Processing pathways controlled by Mec1(ATR) kinase take over these functions only above a distinct DSB threshold, resulting in progressive strengthening of the homolog bias. We conclude that Tel1(ATM)/Pch2 and Mec1(ATR) DNA damage response pathways are sequentially activated during wild-type meiosis because of their distinct sensitivities to global DSB levels. Moreover, relative DSB order controls the DSB repair pathway choice and, ultimately, recombination outcome.
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Affiliation(s)
- Neeraj Joshi
- Center for Gene Regulation in Health and Disease and Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - M Scott Brown
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, IL 60637, USA; Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Douglas K Bishop
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, IL 60637, USA; Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA; Committee on Genetics, University of Chicago, Chicago, IL 60637, USA
| | - G Valentin Börner
- Center for Gene Regulation in Health and Disease and Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA; Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.
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44
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Abstract
Initiation of meiotic recombination by DNA double-strand break formation is temporally coordinated with replication. Murakami and Keeney show that this coordination requires recruitment of the Dbf4-dependent kinase to the replication fork by the conserved TIM-TIPIN complex. The same mechanism may regulate other important replication-associated processes.
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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: 297] [Impact Index Per Article: 29.7] [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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46
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Increased meiotic crossovers and reduced genome stability in absence of Schizosaccharomyces pombe Rad16 (XPF). Genetics 2014; 198:1457-72. [PMID: 25293972 DOI: 10.1534/genetics.114.171355] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Schizosaccharomyces pombe Rad16 is the ortholog of the XPF structure-specific endonuclease, which is required for nucleotide excision repair and implicated in the single strand annealing mechanism of recombination. We show that Rad16 is important for proper completion of meiosis. In its absence, cells suffer reduced spore viability and abnormal chromosome segregation with evidence for fragmentation. Recombination between homologous chromosomes is increased, while recombination within sister chromatids is reduced, suggesting that Rad16 is not required for typical homolog crossovers but influences the balance of recombination between the homolog and the sister. In vegetative cells, rad16 mutants show evidence for genome instability. Similar phenotypes are associated with mutants affecting Rhp14(XPA) but are independent of other nucleotide excision repair proteins such as Rad13(XPG). Thus, the XPF/XPA module of the nucleotide excision repair pathway is incorporated into multiple aspects of genome maintenance even in the absence of external DNA damage.
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Zaghloul L, Drillon G, Boulos RE, Argoul F, Thermes C, Arneodo A, Audit B. Large replication skew domains delimit GC-poor gene deserts in human. Comput Biol Chem 2014; 53 Pt A:153-65. [PMID: 25224847 DOI: 10.1016/j.compbiolchem.2014.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 01/25/2023]
Abstract
Besides their large-scale organization in isochores, mammalian genomes display megabase-sized regions, spanning both genes and intergenes, where the strand nucleotide composition asymmetry decreases linearly, possibly due to replication activity. These so-called skew-N domains cover about a third of the human genome and are bordered by two skew upward jumps that were hypothesized to compose a subset of "master" replication origins active in the germline. Skew-N domains were shown to exhibit a particular gene organization. Genes with CpG-rich promoters likely expressed in the germline are over represented near the master replication origins, with large genes being co-oriented with replication fork progression, which suggests some coordination of replication and transcription. In this study, we describe another skew structure that covers ∼13% of the human genome and that is bordered by putative master replication origins similar to the ones flanking skew-N domains. These skew-split-N domains have a shape reminiscent of a N, but split in half, leaving in the center a region of null skew whose length increases with domain size. These central regions (median size ∼860 kb) have a homogeneous composition, i.e. both a null and constant skew and a constant and low GC content. They correspond to heterochromatin gene deserts found in low-GC isochores with an average gene density of 0.81 promoters/Mb as compared to 7.73 promoters/Mb genome wide. The analysis of epigenetic marks and replication timing data confirms that, in these late replicating heterochomatic regions, the initiation of replication is likely to be random. This contrasts with the transcriptionally active euchromatin state found around the bordering well positioned master replication origins. Altogether skew-N domains and skew-split-N domains cover about 50% of the human genome.
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Affiliation(s)
- Lamia Zaghloul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Guénola Drillon
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Rasha E Boulos
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Françoise Argoul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Claude Thermes
- Centre de Génétique Moléculaire, CNRS UPR 3404, Gif-sur-Yvette, France
| | - Alain Arneodo
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Benjamin Audit
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.
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48
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Murakami H, Keeney S. Temporospatial coordination of meiotic DNA replication and recombination via DDK recruitment to replisomes. Cell 2014; 158:861-873. [PMID: 25126790 PMCID: PMC4141489 DOI: 10.1016/j.cell.2014.06.028] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 05/06/2014] [Accepted: 06/11/2014] [Indexed: 12/15/2022]
Abstract
It has been long appreciated that, during meiosis, DNA replication is coordinated with the subsequent formation of the double-strand breaks (DSBs) that initiate recombination, but a mechanistic understanding of this process was elusive. We now show that, in yeast, the replisome-associated components Tof1 and Csm3 physically associate with the Dbf4-dependent Cdc7 kinase (DDK) and recruit it to the replisome, where it phosphorylates the DSB-promoting factor Mer2 in the wake of the replication fork, synchronizing replication with an early prerequisite for DSB formation. Recruiting regulatory kinases to replisomes may be a general mechanism to ensure spatial and temporal coordination of replication with other chromosomal processes.
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Affiliation(s)
- Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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Cooper TJ, Wardell K, Garcia V, Neale MJ. Homeostatic regulation of meiotic DSB formation by ATM/ATR. Exp Cell Res 2014; 329:124-31. [PMID: 25116420 DOI: 10.1016/j.yexcr.2014.07.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/14/2014] [Indexed: 12/30/2022]
Abstract
Ataxia-telangiectasia mutated (ATM) and RAD3-related (ATR) are widely known as being central players in the mitotic DNA damage response (DDR), mounting responses to DNA double-strand breaks (DSBs) and single-stranded DNA (ssDNA) respectively. The DDR signalling cascade couples cell cycle control to damage-sensing and repair processes in order to prevent untimely cell cycle progression while damage still persists [1]. Both ATM/ATR are, however, also emerging as essential factors in the process of meiosis; a specialised cell cycle programme responsible for the formation of haploid gametes via two sequential nuclear divisions. Central to achieving accurate meiotic chromosome segregation is the introduction of numerous DSBs spread across the genome by the evolutionarily conserved enzyme, Spo11. This review seeks to explore and address how cells utilise ATM/ATR pathways to regulate Spo11-DSB formation, establish DSB homeostasis and ensure meiosis is completed unperturbed.
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Affiliation(s)
- Tim J Cooper
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Kayleigh Wardell
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Valerie Garcia
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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50
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de Massy B. Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. Annu Rev Genet 2014; 47:563-99. [PMID: 24050176 DOI: 10.1146/annurev-genet-110711-155423] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Meiotic recombination is essential for fertility in most sexually reproducing species. This process also creates new combinations of alleles and has important consequences for genome evolution. Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs), which are repaired by homologous recombination. DSBs are catalyzed by the evolutionarily conserved SPO11 protein, assisted by several other factors. Some of them are absolutely required, whereas others are needed only for full levels of DSB formation and may participate in the regulation of DSB timing and frequency as well as the coordination between DSB formation and repair. The sites where DSBs occur are not randomly distributed in the genome, and remarkably distinct strategies have emerged to control their localization in different species. Here, I review the recent advances in the components required for DSB formation and localization in the various model organisms in which these studies have been performed.
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Affiliation(s)
- Bernard de Massy
- Institute of Human Genetics, Centre National de la Recherché Scientifique, UPR1142, 34396 Montpellier, France;
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