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Balboni M, Yang C, Komaki S, Brun J, Schnittger A. COMET Functions as a PCH2 Cofactor in Regulating the HORMA Domain Protein ASY1. Curr Biol 2020; 30:4113-4127.e6. [DOI: 10.1016/j.cub.2020.07.089] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022]
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52
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Blackwell AR, Dluzewska J, Szymanska-Lejman M, Desjardins S, Tock AJ, Kbiri N, Lambing C, Lawrence EJ, Bieluszewski T, Rowan B, Higgins JD, Ziolkowski PA, Henderson IR. MSH2 shapes the meiotic crossover landscape in relation to interhomolog polymorphism in Arabidopsis. EMBO J 2020; 39:e104858. [PMID: 32935357 PMCID: PMC7604573 DOI: 10.15252/embj.2020104858] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 11/09/2022] Open
Abstract
During meiosis, DNA double-strand breaks undergo interhomolog repair to yield crossovers between homologous chromosomes. To investigate how interhomolog sequence polymorphism affects crossovers, we sequenced multiple recombinant populations of the model plant Arabidopsis thaliana. Crossovers were elevated in the diverse pericentromeric regions, showing a local preference for polymorphic regions. We provide evidence that crossover association with elevated diversity is mediated via the Class I crossover formation pathway, although very high levels of diversity suppress crossovers. Interhomolog polymorphism causes mismatches in recombining molecules, which can be detected by MutS homolog (MSH) mismatch repair protein heterodimers. Therefore, we mapped crossovers in a msh2 mutant, defective in mismatch recognition, using multiple hybrid backgrounds. Although total crossover numbers were unchanged in msh2 mutants, recombination was remodelled from the diverse pericentromeres towards the less-polymorphic sub-telomeric regions. Juxtaposition of megabase heterozygous and homozygous regions causes crossover remodelling towards the heterozygous regions in wild type Arabidopsis, but not in msh2 mutants. Immunostaining showed that MSH2 protein accumulates on meiotic chromosomes during prophase I, consistent with MSH2 regulating meiotic recombination. Our results reveal a pro-crossover role for MSH2 in regions of higher sequence diversity in A. thaliana.
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Affiliation(s)
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Stuart Desjardins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | | | - Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Tomasz Bieluszewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Beth Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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Benyahya F, Nadaud I, Da Ines O, Rimbert H, White C, Sourdille P. SPO11.2 is essential for programmed double-strand break formation during meiosis in bread wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:30-43. [PMID: 32603485 DOI: 10.1111/tpj.14903] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 05/20/2023]
Abstract
Meiotic recombination is initiated by formation of DNA double-strand breaks (DSBs). This involves a protein complex that includes in plants the two similar proteins, SPO11-1 and SPO11-2. We analysed the sequences of SPO11-2 in hexaploid bread wheat (Triticum aestivum), as well as in its diploid and tetraploid progenitors. We investigated its role during meiosis using single, double and triple mutants. The three homoeologous SPO11-2 copies of hexaploid wheat exhibit high nucleotide and amino acid similarities with those of the diploids, tetraploids and Arabidopsis. Interestingly, however, two nucleotides deleted in exon-2 of the A copy lead to a premature stop codon and suggest that it encodes a non-functional protein. Remarkably, the mutation was absent from the diploid A-relative Triticum urartu, but present in the tetraploid Triticum dicoccoides and in different wheat cultivars indicating that the mutation occurred after the first polyploidy event and has since been conserved. We further show that triple mutants with all three copies (A, B, D) inactivated are sterile. Cytological analyses of these mutants show synapsis defects, accompanied by severe reductions in bivalent formation and numbers of DMC1 foci, thus confirming the essential role of TaSPO11-2 in meiotic recombination in wheat. In accordance with its 2-nucleotide deletion in exon-2, double mutants for which only the A copy remained are also sterile. Notwithstanding, some DMC1 foci remain visible in this mutant, suggesting a residual activity of the A copy, albeit not sufficient to restore fertility.
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Affiliation(s)
- Fatiha Benyahya
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Isabelle Nadaud
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, UMR CNRS 6293 - Université Clermont Auvergne - INSERM U1103, Clermont-Ferrand, 63001, France
| | - Hélène Rimbert
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Charles White
- Génétique, Reproduction et Développement, UMR CNRS 6293 - Université Clermont Auvergne - INSERM U1103, Clermont-Ferrand, 63001, France
| | - Pierre Sourdille
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
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Abstract
Meiosis is the basis of the generative reproduction of eukaryotes. The crucial first step is homologous chromosome pairing. In higher eukaryotes, micrometer-scale chromosomes, micrometer distances apart, are brought together by nanometer DNA sequences, at least a factor of 1000 size difference. Models of homology search, homologue movement, and pairing at the DNA level in higher eukaryotes are primarily based on studies with yeast where the emphasis is on the induction and repair of DNA double-strand breaks (DSB). For such a model, the very large nuclei of most plants and animals present serious problems. Homology search without DSBs cannot be explained by models based on DSB repair. The movement of homologues to meet each other and make contact at the molecular level is not understood. These problems are discussed and the conclusion is that at present practically nothing is known of meiotic homologue pairing in higher eukaryotes up to the formation of the synaptonemal complex, and that new, necessarily speculative models must be developed. Arguments are given that RNA plays a central role in homology search and a tentative model involving RNA in homology search is presented. A role of actin in homologue movement is proposed. The primary role of DSBs in higher eukaryotes is concluded to not be in paring but in the preparation of Holliday junctions, ultimately leading to chromatid exchange.
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Affiliation(s)
- J Sybenga
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands.,Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands
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55
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Sepsi A, Schwarzacher T. Chromosome-nuclear envelope tethering - a process that orchestrates homologue pairing during plant meiosis? J Cell Sci 2020; 133:jcs243667. [PMID: 32788229 PMCID: PMC7438012 DOI: 10.1242/jcs.243667] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During prophase I of meiosis, homologous chromosomes pair, synapse and exchange their genetic material through reciprocal homologous recombination, a phenomenon essential for faithful chromosome segregation. Partial sequence identity between non-homologous and heterologous chromosomes can also lead to recombination (ectopic recombination), a highly deleterious process that rapidly compromises genome integrity. To avoid ectopic exchange, homology recognition must be extended from the narrow position of a crossover-competent double-strand break to the entire chromosome. Here, we review advances on chromosome behaviour during meiotic prophase I in higher plants, by integrating centromere- and telomere dynamics driven by cytoskeletal motor proteins, into the processes of homologue pairing, synapsis and recombination. Centromere-centromere associations and the gathering of telomeres at the onset of meiosis at opposite nuclear poles create a spatially organised and restricted nuclear state in which homologous DNA interactions are favoured but ectopic interactions also occur. The release and dispersion of centromeres from the nuclear periphery increases the motility of chromosome arms, allowing meiosis-specific movements that disrupt ectopic interactions. Subsequent expansion of interstitial synapsis from numerous homologous interactions further corrects ectopic interactions. Movement and organisation of chromosomes, thus, evolved to facilitate the pairing process, and can be modulated by distinct stages of chromatin associations at the nuclear envelope and their collective release.
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Affiliation(s)
- Adél Sepsi
- Department of Plant Cell Biology, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- BME Budapest University of Technology and Economics, Department of Applied Biotechnology and Food Science (ABÉT), 1111, Budapest, Mu˝ egyetem rkp. 3-9., Hungary
| | - Trude Schwarzacher
- University of Leicester, Department of Genetics and Genome Biology, University Road, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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56
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PCH-2 collaborates with CMT-1 to proofread meiotic homolog interactions. PLoS Genet 2020; 16:e1008904. [PMID: 32730253 PMCID: PMC7433886 DOI: 10.1371/journal.pgen.1008904] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 08/18/2020] [Accepted: 06/01/2020] [Indexed: 11/19/2022] Open
Abstract
The conserved ATPase, PCH-2/TRIP13, is required during both the spindle checkpoint and meiotic prophase. However, its specific role in regulating meiotic homolog pairing, synapsis and recombination has been enigmatic. Here, we report that this enzyme is required to proofread meiotic homolog interactions. We generated a mutant version of PCH-2 in C. elegans that binds ATP but cannot hydrolyze it: pch-2E253Q. In vitro, this mutant can bind a known substrate but is unable to remodel it. This mutation results in some non-homologous synapsis and impaired crossover assurance. Surprisingly, worms with a null mutation in PCH-2's adapter protein, CMT-1, the ortholog of p31comet, localize PCH-2 to meiotic chromosomes, exhibit non-homologous synapsis and lose crossover assurance. The similarity in phenotypes between cmt-1 and pch-2E253Q mutants suggest that PCH-2 can bind its meiotic substrates in the absence of CMT-1, in contrast to its role during the spindle checkpoint, but requires its adapter to hydrolyze ATP and remodel them.
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57
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Seear PJ, France MG, Gregory CL, Heavens D, Schmickl R, Yant L, Higgins JD. A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata. PLoS Genet 2020; 16:e1008900. [PMID: 32667955 PMCID: PMC7392332 DOI: 10.1371/journal.pgen.1008900] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 07/30/2020] [Accepted: 06/01/2020] [Indexed: 01/09/2023] Open
Abstract
In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20-100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.
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Affiliation(s)
- Paul J. Seear
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martin G. France
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Catherine L. Gregory
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Darren Heavens
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, United Kingdom
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Levi Yant
- Future Food Beacon of Excellence and the School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- * E-mail: (LY); (JDH)
| | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- * E-mail: (LY); (JDH)
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58
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Yao Y, Li X, Chen W, Liu H, Mi L, Ren D, Mo A, Lu P. ATM Promotes RAD51-Mediated Meiotic DSB Repair by Inter-Sister-Chromatid Recombination in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:839. [PMID: 32670319 PMCID: PMC7329986 DOI: 10.3389/fpls.2020.00839] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/26/2020] [Indexed: 05/17/2023]
Abstract
Meiotic recombination ensures accurate homologous chromosome segregation during meiosis and generates novel allelic combinations among gametes. During meiosis, DNA double strand breaks (DSBs) are generated to facilitate recombination. To maintain genome integrity, meiotic DSBs must be repaired using appropriate DNA templates. Although the DNA damage response protein kinase Ataxia-telangiectasia mutated (ATM) has been shown to be involved in meiotic recombination in Arabidopsis, its mechanistic role is still unclear. In this study, we performed cytological analysis in Arabidopsis atm mutant, we show that there are fewer γH2AX foci, but more RAD51 and DMC1 foci on atm meiotic chromosomes. Furthermore, we observed an increase in meiotic Type I crossovers (COs) in atm. Our genetic analysis shows that the meiotic phenotype of atm rad51 double mutants is similar to the rad51 single mutant. Whereas, the atm dmc1 double mutant has a more severe chromosome fragmentation phenotype compared to both single mutants, suggesting that ATM functions in concert with RAD51, but in parallel to DMC1. Lastly, we show that atm asy1 double mutants also have more severe meiotic recombination defects. These data lead us to propose a model wherein ATM promotes RAD51-mediated meiotic DSB repair by inter-sister-chromatid (IS) recombination in Arabidopsis.
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Affiliation(s)
- Yuan Yao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaojing Li
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wanli Chen
- School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Liu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Limin Mi
- School of Life Sciences, Fudan University, Shanghai, China
| | - Ding Ren
- School of Life Sciences, Fudan University, Shanghai, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai, China
| | - Pingli Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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59
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Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum. Heredity (Edinb) 2020; 125:212-226. [PMID: 32523055 PMCID: PMC7490355 DOI: 10.1038/s41437-020-0328-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 02/05/2023] Open
Abstract
Naturally occurring autopolyploid species, such as the autotetraploid potato Solanum tuberosum, face a variety of challenges during meiosis. These include proper pairing, recombination and correct segregation of multiple homologous chromosomes, which can form complex multivalent configurations at metaphase I, and in turn alter allelic segregation ratios through double reduction. Here, we present a reference map of meiotic stages in diploid and tetraploid S. tuberosum using fluorescence in situ hybridisation (FISH) to differentiate individual meiotic chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving bivalent configurations was predominant in all three tetraploid varieties. The crossover frequency per bivalent was significantly reduced in the tetraploids compared with a diploid variety, which likely indicates meiotic adaptation to the autotetraploid state. Nevertheless, bivalents were accompanied by a substantial frequency of multivalents, which varied by variety and by chromosome (7-48%). We identified possible sites of synaptic partner switching, leading to multivalent formation, and found potential defects in the polymerisation and/or maintenance of the synaptonemal complex in tetraploids. These findings demonstrate the rise of S. tuberosum as a model for autotetraploid meiotic recombination research and highlight constraints on meiotic chromosome configurations and chiasma frequencies as an important feature of an evolved autotetraploid meiosis.
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60
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ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis. Proc Natl Acad Sci U S A 2020; 117:13647-13658. [PMID: 32499315 PMCID: PMC7306779 DOI: 10.1073/pnas.1921055117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During meiosis, interhomolog recombination produces crossovers and noncrossovers to create genetic diversity. Meiotic recombination frequency varies at multiple scales, with high subtelomeric recombination and suppressed centromeric recombination typical in many eukaryotes. During recombination, sister chromatids are tethered as loops to a polymerized chromosome axis, which, in plants, includes the ASY1 HORMA domain protein and REC8-cohesin complexes. Using chromatin immunoprecipitation, we show an ascending telomere-to-centromere gradient of ASY1 enrichment, which correlates strongly with REC8-cohesin ChIP-seq data. We mapped crossovers genome-wide in the absence of ASY1 and observe that telomere-led recombination becomes dominant. Surprisingly, asy1/+ heterozygotes also remodel crossovers toward subtelomeric regions at the expense of the pericentromeres. Telomeric recombination increases in asy1/+ occur in distal regions where ASY1 and REC8 ChIP enrichment are lowest in wild type. In wild type, the majority of crossovers show interference, meaning that they are more widely spaced along the chromosomes than expected by chance. To measure interference, we analyzed double crossover distances, MLH1 foci, and fluorescent pollen tetrads. Interestingly, while crossover interference is normal in asy1/+, it is undetectable in asy1 mutants, indicating that ASY1 is required to mediate crossover interference. Together, this is consistent with ASY1 antagonizing telomere-led recombination and promoting spaced crossover formation along the chromosomes via interference. These findings provide insight into the role of the meiotic axis in patterning recombination frequency within plant genomes.
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61
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Lei X, Ning Y, Eid Elesawi I, Yang K, Chen C, Wang C, Liu B. Heat stress interferes with chromosome segregation and cytokinesis during male meiosis in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2020; 15:1746985. [PMID: 32275182 PMCID: PMC7238882 DOI: 10.1080/15592324.2020.1746985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In higher plants, male meiosis is a key process of microsporogenesis and is crucial for plant fertility. Male meiosis programs are prone to be influenced by altered temperature conditions. Studies have reported that an increased temperature (28°C) within a fertile threshold can affect the frequency of meiotic recombination in Arabidopsis. However, not much has been known how male meiosis responses to an extremely high temperature beyond the fertile threshold. To understand the impact of extremely high temperature on male meiosis in Arabidopsis, we treated flowering Arabidopsis plants with 36-38°C and found that the high-temperature condition significantly reduced pollen shed and plant fertility, and led to formation of pollen grains with varied sizes. The heat stress-induced unbalanced tetrads, polyad and meiotic restitution, suggesting that male meiosis was interfered. Fluorescence in situ hybridization (FISH) assay confirmed that both homologous chromosome separation and sister chromatids cohesion were influenced. Aniline blue staining of tetrad-stage pollen mother cells (PMCs) revealed that meiotic cytokinesis was severely disrupted by the heat stress. Supportively, immunolocalization of ɑ-tubulin showed that the construction of spindle and phragmoplast at both meiosis I and II were interfered. Overall, our findings demonstrate that an extremely high-temperature stress over the fertile threshold affects both chromosome segregation and cytokinesis during male meiosis by disturbing microtubular cytoskeleton in Arabidopsis.
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Affiliation(s)
- Xiaoning Lei
- Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, China
| | - Yingjie Ning
- College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Ibrahim Eid Elesawi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
- Department of Agricultural Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ke Yang
- College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Chong Wang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Science, Shanghai Normal University, Shanghai, China
- Chong Wang Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Science, Shanghai Normal University, Shanghai, China
| | - Bing Liu
- College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- CONTACT Bing Liu College of Life Sciences, South-Central University for Nationalities, Wuhan China
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62
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Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa. Proc Natl Acad Sci U S A 2020; 117:8980-8988. [PMID: 32273390 PMCID: PMC7183234 DOI: 10.1073/pnas.1919459117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genome duplication is an important factor in the evolution of eukaryotic lineages, but it poses challenges for the regular segregation of chromosomes in meiosis and thus fertility. To survive, polyploid lineages must evolve to overcome initial challenges that accompany doubling the chromosome complement. Understanding how evolution can solve the challenge of segregating multiple homologous chromosomes promises fundamental insights into the mechanisms of genome maintenance and could open polyploidy as a crop improvement tool. We previously identified candidate genes for meiotic stabilization of Arabidopsis arenosa, which has natural diploid and tetraploid variants. Here we test the role that derived alleles of two genes under selection in tetraploid A. arenosa might have in meiotic stabilization in tetraploids. Polyploidy, which results from whole genome duplication (WGD), has shaped the long-term evolution of eukaryotic genomes in all kingdoms. Polyploidy is also implicated in adaptation, domestication, and speciation. Yet when WGD newly occurs, the resulting neopolyploids face numerous challenges. A particularly pernicious problem is the segregation of multiple chromosome copies in meiosis. Evolution can overcome this challenge, likely through modification of chromosome pairing and recombination to prevent deleterious multivalent chromosome associations, but the molecular basis of this remains mysterious. We study mechanisms underlying evolutionary stabilization of polyploid meiosis using Arabidopsis arenosa, a relative of A. thaliana with natural diploid and meiotically stable autotetraploid populations. Here we investigate the effects of ancestral (diploid) versus derived (tetraploid) alleles of two genes, ASY1 and ASY3, that were among several meiosis genes under selection in the tetraploid lineage. These genes encode interacting proteins critical for formation of meiotic chromosome axes, long linear multiprotein structures that form along sister chromatids in meiosis and are essential for recombination, chromosome segregation, and fertility. We show that derived alleles of both genes are associated with changes in meiosis, including reduced formation of multichromosome associations, reduced axis length, and a tendency to more rod-shaped bivalents in metaphase I. Thus, we conclude that ASY1 and ASY3 are components of a larger multigenic solution to polyploid meiosis in which individual genes have subtle effects. Our results are relevant for understanding polyploid evolution and more generally for understanding how meiotic traits can evolve when faced with challenges.
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63
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Lambing C, Tock AJ, Topp SD, Choi K, Kuo PC, Zhao X, Osman K, Higgins JD, Franklin FCH, Henderson IR. Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis. THE PLANT CELL 2020; 32:1218-1239. [PMID: 32024691 PMCID: PMC7145502 DOI: 10.1105/tpc.19.00866] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/03/2020] [Accepted: 02/03/2020] [Indexed: 05/20/2023]
Abstract
Meiosis recombines genetic variation and influences eukaryote genome evolution. During meiosis, DNA double-strand breaks (DSBs) enter interhomolog repair to yield crossovers and noncrossovers. DSB repair occurs as replicated sister chromatids are connected to a polymerized axis. Cohesin rings containing the REC8 kleisin subunit bind sister chromatids and anchor chromosomes to the axis. Here, we report the genomic landscape of REC8 using chromatin immunoprecipitation sequencing (ChIP-seq) in Arabidopsis (Arabidopsis thaliana). REC8 associates with regions of high nucleosome occupancy in multiple chromatin states, including histone methylation at H3K4 (expressed genes), H3K27 (silent genes), and H3K9 (silent transposons). REC8 enrichment is associated with suppression of meiotic DSBs and crossovers at the chromosome and fine scales. As REC8 enrichment is greatest in transposon-dense heterochromatin, we repeated ChIP-seq in kyp suvh5 suvh6 H3K9me2 mutants. Surprisingly, REC8 enrichment is maintained in kyp suvh5 suvh6 heterochromatin and no defects in centromeric cohesion were observed. REC8 occupancy within genes anti-correlates with transcription and is reduced in COPIA transposons that reactivate expression in kyp suvh5 suvh6 Abnormal axis structures form in rec8 that recruit DSB-associated protein foci and undergo synapsis, which is followed by chromosome fragmentation. Therefore, REC8 occupancy correlates with multiple chromatin states and is required to organize meiotic chromosome architecture and interhomolog recombination.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Stephanie D Topp
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Pallas C Kuo
- 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
| | - Kim Osman
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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64
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Lee MS, Joo JW, Choi H, Kang HA, Kim K. Mec1 Modulates Interhomolog Crossover and Interplays with Tel1 at Post Double-Strand Break Stages. J Microbiol Biotechnol 2020; 30:469-475. [PMID: 31847509 PMCID: PMC9728206 DOI: 10.4014/jmb.1909.09020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 12/15/2022]
Abstract
During meiosis I, programmed DNA double-strand breaks (DSBs) occur to promote chromosome pairing and recombination between homologs. In Saccharomyces cerevisiae, Mec1 and Tel1, the orthologs of human ATR and ATM, respectively, regulate events upstream of the cell cycle checkpoint to initiate DNA repair. Tel1ATM and Mec1ATR are required for phosphorylating various meiotic proteins during recombination. This study aimed to investigate the role of Tel1ATM and Mec1ATR in meiotic prophase via physical analysis of recombination. Tel1ATM cooperated with Mec1ATR to mediate DSB-to-single end invasion transition, but negatively regulated DSB formation. Furthermore, Mec1ATR was required for the formation of interhomolog joint molecules from early prophase, thus establishing a recombination partner choice. Moreover, Mec1ATR specifically promoted crossover-fated DSB repair. Together, these results suggest that Tel1ATM and Mec1ATR function redundantly or independently in all post-DSB stages.
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Affiliation(s)
- Min-Su Lee
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jung Whan Joo
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyungseok Choi
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ah Kang
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Keunpil Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
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65
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Li X, Shahid MQ, Wen M, Chen S, Yu H, Jiao Y, Lu Z, Li Y, Liu X. Global identification and analysis revealed differentially expressed lncRNAs associated with meiosis and low fertility in autotetraploid rice. BMC PLANT BIOLOGY 2020; 20:82. [PMID: 32075588 PMCID: PMC7032005 DOI: 10.1186/s12870-020-2290-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/13/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Autotetraploid rice is a useful germplasm for polyploid rice breeding. Our previous research showed that non-coding RNAs might be associated with low fertility in autotetraploid rice. However, little information is available on long non-coding RNAs (lncRNAs) involved in the low fertility of autotetraploid rice. In the present study, RNA-seq was employed to detect the differentially expressed meiosis-related lncRNAs in autotetraploid rice, and gene overexpression and knock out experiments were used to validate the potential function of candidate lncRNA. RESULTS A total of 444 differentially expressed lncRNAs (DEL) were detected during anther and ovary meiosis in autotetraploid rice. Of these, 328 DEL were associated with the transposable elements, which displayed low expression levels during meiosis in autotetraploid rice. We used rapid amplification of cDNA ends (RACE) assay to validate 10 DEL and found that the lncRNAs were not assembly artifacts, and six of them were conserved in tetraploid rice. Moreover, 237 and 20 lncRNAs were associated with pollen mother cell (PMC) and embryo sac mother cell (EMC) meiosis in autotetraploid rice, respectively. The differential expressions of some meiosis-related targets and its DEL regulator, including MEL1 regulated by TCONS_00068868, LOC_Os12g41350 (meiotic asynaptic mutant 1) by TCONS_00057811 in PMC, and LOC_Os12g39420 by TCONS_00144592 in EMC, were confirmed by qRT-PCR. TCONS_00057811, TCONS_00055980 and TCONS_00130461 showed anther specific expression patterns and were found to be highly expressed during meiosis. CRISPR/Cas9 editing of lncRNA57811 displayed similar morphology compared to wild type. The overexpression of lncRNA57811 resulted in low pollen fertility (29.70%) and seed setting (33%) in rice. CONCLUSION The differential expression levels of lncRNAs, associated with transposable elements and meiosis-regulated targets, might be endogenous noncoding regulators of pollen/embryo sac development that cause low fertility in autotetraploid rice. The results enhance our understanding about rice lncRNAs, and facilitate functional research in autotetraploid rice.
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Affiliation(s)
- Xiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Minsi Wen
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Shuling Chen
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Yamin Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Yajing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642 China
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66
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Lambing C, Choi K, Blackwell AR, Henderson IR. Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol 2020; 2061:219-236. [PMID: 31583663 DOI: 10.1007/978-1-4939-9818-0_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During meiosis recombination occurs between homologous chromosomes which can result in reciprocal exchanges of genetic information, called crossovers. Crossover rate is heterogeneous within the genome, with local regions having a significantly higher recombination rate relative to the genome average. These regions are termed hotspots and typically occur with widths of kilobases. Therefore, there is a need to profile recombination factors at a similar resolution during meiosis via techniques such as chromatin immunoprecipitation (ChIP). Here we describe a ChIP protocol, combined with high throughput sequencing (ChIP-seq) optimised for analysis of meiotically expressed proteins in Arabidopsis thaliana flowers. We provide methods to (1) isolate nuclei and prepare the chromatin for shearing, (2) immunoprecipitate DNA molecules cross-linked to a protein of interest, (3) to size-select and purify immunoprecipitated DNA molecules, and (4) to prepare DNA sequencing libraries suitable for high-throughput sequencing. Together, these methods allow the detection of binding sites for meiotic proteins in the Arabidopsis genome at high resolution, which will provide insights into relationships between meiotic chromosome organization, chromatin and recombination.
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Affiliation(s)
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.,Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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67
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Prusicki MA, Hamamura Y, Schnittger A. A Practical Guide to Live-Cell Imaging of Meiosis in Arabidopsis. Methods Mol Biol 2020; 2061:3-12. [PMID: 31583648 DOI: 10.1007/978-1-4939-9818-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Plants are powerful model systems to study meiosis. Our knowledge about the cytology of plant meiosis is mainly based on the analysis of fixed material. Although highly informative, this approach is limited in understanding the dynamics of meiosis. Here, we present a step-by-step instruction for a newly developed method to follow meiosis in male meiocytes of Arabidopsis in real time by confocal laser scanning microscopy. We envision that this method can be easily translated to other plant species and especially crops (e.g., Brassica, maize, and potato).
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Affiliation(s)
- Maria Ada Prusicki
- Department of Developmental Biology, University of Hamburg, Hamburg, Germany
| | - Yuki Hamamura
- Department of Developmental Biology, University of Hamburg, Hamburg, Germany
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Hamburg, Germany.
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68
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Kariyazono R, Oda A, Yamada T, Ohta K. Conserved HORMA domain-containing protein Hop1 stabilizes interaction between proteins of meiotic DNA break hotspots and chromosome axis. Nucleic Acids Res 2019; 47:10166-10180. [PMID: 31665745 PMCID: PMC6821256 DOI: 10.1093/nar/gkz754] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/16/2019] [Accepted: 09/02/2019] [Indexed: 11/14/2022] Open
Abstract
HORMA domain-containing proteins such as Hop1 play crucial regulatory roles in various chromosomal functions. Here, we investigated roles of the fission yeast Hop1 in the formation of recombination-initiating meiotic DNA double strand breaks (DSBs). Meiotic DSB formation in fission yeast relies on multiple protein-protein interactions such as the one between the chromosome axial protein Rec10 and the DSB-forming complex subunit Rec15. Chromatin immunoprecipitation sequencing demonstrated that Hop1 is colocalized with both Rec10 and Rec15, and we observed physical interactions of Hop1 to Rec15 and Rec10. These results suggest that Hop1 promotes DSB formation by interacting with both axis components and the DSB-forming complex. We also show that Hop1 binding to DSB hotspots requires Rec15 and Rec10, while Hop1 axis binding requires Rec10 only, suggesting that Hop1 is recruited to the axis via Rec10, and to hotspots by hotspot-bound Rec15. Furthermore, we introduced separation-of-function Rec10 mutations, deficient for interaction with either Rec15 or Hop1. These single mutations and hop1Δ conferred only partial defects in meiotic recombination, while the combining the Rec15-binding-deficient rec10 mutation with hop1Δ synergistically reduced meiotic recombination, at least at a model hotspot. Taken together, Hop1 likely functions as a stabilizer for Rec15–Rec10 interaction to promote DSB formation.
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Affiliation(s)
- Ryo Kariyazono
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Arisa Oda
- Department of Life Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Takatomi Yamada
- Department of Life Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Kunihiro Ohta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.,Department of Life Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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69
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Rowan BA, Heavens D, Feuerborn TR, Tock AJ, Henderson IR, Weigel D. An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features. Genetics 2019; 213:771-787. [PMID: 31527048 PMCID: PMC6827372 DOI: 10.1534/genetics.119.302406] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/28/2019] [Indexed: 11/18/2022] Open
Abstract
Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of >17,000 COs between the Col-0 and Ler-0 accessions of Arabidopsis thaliana COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large- and small-scale SVs, representing an influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.
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Affiliation(s)
- Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Tatiana R Feuerborn
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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70
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Kim J, Choi K. Signaling-mediated meiotic recombination in plants. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:44-50. [PMID: 31048232 DOI: 10.1016/j.pbi.2019.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/21/2019] [Accepted: 04/01/2019] [Indexed: 05/21/2023]
Abstract
Meiotic recombination provides genetic diversity in populations and ensures accurate homologous chromosome segregation for genome integrity. During meiosis, recombination processes, from DNA double strand breaks (DSBs) to crossover formation are tightly linked to higher order chromosome structure, including chromatid cohesion, axial element formation, homolog pairing and synapsis. The extensive studies on plant meiosis have revealed the important conserved roles for meiotic proteins in homologous recombination. Recent works have focused on elucidating the mechanistic basis of how meiotic proteins regulate recombination events via protein complex formation and modifications such as phosphorylation, ubiquitination, and SUMOylation. Here, we highlight recent advances on the signaling and modifications of meiotic proteins that mediate the formation of DSBs and crossovers in plants.
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Affiliation(s)
- Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea.
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71
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Sims J, Copenhaver GP, Schlögelhofer P. Meiotic DNA Repair in the Nucleolus Employs a Nonhomologous End-Joining Mechanism. THE PLANT CELL 2019; 31:2259-2275. [PMID: 31266898 PMCID: PMC6751124 DOI: 10.1105/tpc.19.00367] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/12/2019] [Accepted: 06/28/2019] [Indexed: 05/03/2023]
Abstract
Ribosomal RNA genes are arranged in large arrays with hundreds of rDNA units in tandem. These highly repetitive DNA elements pose a risk to genome stability since they can undergo nonallelic exchanges. During meiosis, DNA double-strand breaks (DSBs) are induced as part of the regular program to generate gametes. Meiotic DSBs initiate homologous recombination (HR), which subsequently ensures genetic exchange and chromosome disjunction. In Arabidopsis (Arabidopsis thaliana), we demonstrate that all 45S rDNA arrays become transcriptionally active and are recruited into the nucleolus early in meiosis. This shields the rDNA from acquiring canonical meiotic chromatin modifications and meiotic cohesin and allows only very limited meiosis-specific DSB formation. DNA lesions within the rDNA arrays are repaired in an RAD51-independent but LIG4-dependent manner, establishing that nonhomologous end-joining maintains rDNA integrity during meiosis. Utilizing ectopically integrated rDNA repeats, we validate our findings and demonstrate that the rDNA constitutes an HR-refractory genome environment.
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Affiliation(s)
- Jason Sims
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
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72
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Prusicki MA, Keizer EM, van Rosmalen RP, Komaki S, Seifert F, Müller K, Wijnker E, Fleck C, Schnittger A. Live cell imaging of meiosis in Arabidopsis thaliana. eLife 2019; 8:e42834. [PMID: 31107238 PMCID: PMC6559805 DOI: 10.7554/elife.42834] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
To follow the dynamics of meiosis in the model plant Arabidopsis, we have established a live cell imaging setup to observe male meiocytes. Our method is based on the concomitant visualization of microtubules (MTs) and a meiotic cohesin subunit that allows following five cellular parameters: cell shape, MT array, nucleus position, nucleolus position, and chromatin condensation. We find that the states of these parameters are not randomly associated and identify 11 cellular states, referred to as landmarks, which occur much more frequently than closely related ones, indicating that they are convergence points during meiotic progression. As a first application of our system, we revisited a previously identified mutant in the meiotic A-type cyclin TARDY ASYNCHRONOUS MEIOSIS (TAM). Our imaging system enabled us to reveal both qualitatively and quantitatively altered landmarks in tam, foremost the formation of previously not recognized ectopic spindle- or phragmoplast-like structures that arise without attachment to chromosomes.
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Affiliation(s)
- Maria A Prusicki
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
| | - Emma M Keizer
- Department of Agrotechnology and Food SciencesWageningen UniversityWageningenThe Netherlands
| | - Rik P van Rosmalen
- Department of Agrotechnology and Food SciencesWageningen UniversityWageningenThe Netherlands
| | - Shinichiro Komaki
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
| | - Felix Seifert
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
| | - Katja Müller
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
| | - Erik Wijnker
- Department of Plant Science, Laboratory of GeneticsWageningen University and ResearchWageningenThe Netherlands
| | - Christian Fleck
- Department of Agrotechnology and Food SciencesWageningen UniversityWageningenThe Netherlands
| | - Arp Schnittger
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
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73
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Transition from a meiotic to a somatic-like DNA damage response during the pachytene stage in mouse meiosis. PLoS Genet 2019; 15:e1007439. [PMID: 30668564 PMCID: PMC6358097 DOI: 10.1371/journal.pgen.1007439] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 02/01/2019] [Accepted: 11/28/2018] [Indexed: 11/24/2022] Open
Abstract
Homologous recombination (HR) is the principal mechanism of DNA repair acting during meiosis and is fundamental for the segregation of chromosomes and the increase of genetic diversity. Nevertheless, non-homologous end joining (NHEJ) mechanisms can also act during meiosis, mainly in response to exogenously-induced DNA damage in late stages of first meiotic prophase. In order to better understand the relationship between these two repair pathways, we studied the response to DNA damage during male mouse meiosis after gamma radiation. We clearly discerned two types of responses immediately after treatment. From leptotene to early pachytene, exogenous damage triggered the massive presence of γH2AX throughout the nucleus, which was associated with DNA repair mediated by HR components (DMC1 and RAD51). This early pathway finished with the sequential removal of DMC1 and RAD51 and was no longer inducible at mid pachytene. However, from mid-pachytene to diplotene, γH2AX appeared as large discrete foci. This late repair pattern was mediated initially by NHEJ, involving Ku70 and XRCC4, which were constitutively present, and 53BP1, which appeared at sites of damage soon after irradiation. Nevertheless, 24 hours after irradiation, a HR pathway involving RAD51 but not DMC1 mostly replaced NHEJ. Additionally, we observed the occurrence of synaptonemal complex bridges between bivalents, most likely representing chromosome translocation events that may involve DMC1, RAD51 or 53BP1. Our results reinforce the idea that the early “meiotic” repair pathway that acts by default at the beginning of meiosis is replaced from mid-pachytene onwards by a “somatic-like” repair pattern. This shift might be important to resolve DNA damage (either endogenous or exogenous) that could not be repaired by the early meiotic mechanisms, for instance those in the sex chromosomes, which lack a homologous chromosome to repair with. This transition represents another layer of functional changes that occur in meiotic cells during mid pachytene, in addition to epigenetic reprograming, reactivation of transcription, changes in the gene expression profile and acquisition of competence to proceed to metaphase. DNA repair is critical for both somatic and meiotic cells. During meiosis, hundreds of DNA double strand breaks (DSBs) are introduced endogenously. To repair this damage, meiotic cells use a specialized version of the homologous recombination (HR) pathway that uses specific meiotic recombinases, such as DMC1, to promote repair with the homologous chromosome instead of the sister chromatid. This process is important to ensure chromosome segregation during meiosis and, as a side consequence, increases the genetic diversity of offspring. Nevertheless, under specific circumstances, meiotic cells can use other DNA repair mechanisms such as non-homologous end joining (NHEJ), which is error-prone. We investigated the response of mouse spermatocytes to increased DNA damage caused by gamma radiation, which is commonly used in cancer therapy. We found that the excess of DSBs produced by irradiation is processed by the meiotic HR recombination pathway in spermatocytes at the early stages of first meiotic prophase. However, this response is not inducible from the mid-pachytene stage onwards. From this point on, spermatocytes rely on a response that shares many features with that of somatic cells. In this response, the NHEJ pathway is first used to repair DNA damage but is subsequently replaced by a HR mechanism that does not use DMC1. Instead, it relies only on RAD51, which is known to function in both somatic and meiosis cells and, contrary to DMC1, has a preference for the sister chromatid. This switch from a meiotic to a somatic-like response is accompanied by a conspicuous change in the epigenetic response to DNA damage, reinforcing the idea that a functional transition occurs in meiotic cells during the mid-pachytene stage.
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74
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Xue M, Wang J, Jiang L, Wang M, Wolfe S, Pawlowski WP, Wang Y, He Y. The Number of Meiotic Double-Strand Breaks Influences Crossover Distribution in Arabidopsis. THE PLANT CELL 2018; 30:2628-2638. [PMID: 30282794 PMCID: PMC6241269 DOI: 10.1105/tpc.18.00531] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/17/2018] [Accepted: 09/30/2018] [Indexed: 05/06/2023]
Abstract
Meiotic recombination generates genetic diversity and ensures proper chromosome segregation. Recombination is initiated by the programmed formation of double-strand breaks (DSBs) in chromosomal DNA by DNA Topoisomerase VI-A Subunit (SPO11), a topoisomerase-like enzyme. Repair of some DSBs leads to the formation of crossovers (COs). In most organisms, including plants, the number of DSBs greatly exceeds the number of COs and which DSBs become CO sites is tightly controlled. The CO landscape is affected by DNA sequence and epigenome features of chromosomes as well as by global mechanisms controlling recombination dynamics. The latter are poorly understood and their effects on CO distribution are not well elucidated. To study how recombination dynamics affects CO distribution, we engineered Arabidopsis thaliana plants to carry hypomorphic alleles of SPO11-1 Two independent transgenic lines showed ∼30% and 40% reductions in DSB numbers, which were commensurate with the dosage of the SPO11-1 transcript. The reduction in DSB number resulted in proportional, although smaller, reductions of the number of COs. Most interestingly, CO distribution along the chromosomes was dramatically altered, with substantially fewer COs forming in pericentromeric chromosome regions. These results indicate that SPO11 activity, and the resulting DSB numbers are major factors shaping the CO landscape.
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Affiliation(s)
- Ming Xue
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Jun Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Luguang Jiang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Minghui Wang
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
- Bioinformatics Facility, Cornell University, Ithaca, New York 14853
| | - Sarah Wolfe
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | | | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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75
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Chambon A, West A, Vezon D, Horlow C, De Muyt A, Chelysheva L, Ronceret A, Darbyshire A, Osman K, Heckmann S, Franklin FCH, Grelon M. Identification of ASYNAPTIC4, a Component of the Meiotic Chromosome Axis. PLANT PHYSIOLOGY 2018; 178:233-246. [PMID: 30002256 PMCID: PMC6130017 DOI: 10.1104/pp.17.01725] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/27/2018] [Indexed: 05/20/2023]
Abstract
During the leptotene stage of prophase I of meiosis, chromatids become organized into a linear looped array via a protein axis that forms along the loop bases. Establishment of the axis is essential for the subsequent synapsis of the homologous chromosome pairs and the progression of recombination to form genetic crossovers. Here, we describe ASYNAPTIC4 (ASY4), a meiotic axis protein in Arabidopsis (Arabidopsis thaliana). ASY4 is a small coiled-coil protein that exhibits limited sequence similarity with the carboxyl-terminal region of the axis protein ASY3. We used enhanced yellow fluorescent protein-tagged ASY4 to show that ASY4 localizes to the chromosome axis throughout prophase I. Bimolecular fluorescence complementation revealed that ASY4 interacts with ASY1 and ASY3, and yeast two-hybrid analysis confirmed a direct interaction between ASY4 and ASY3. Mutants lacking full-length ASY4 exhibited defective axis formation and were unable to complete synapsis. Although the initiation of recombination appeared to be unaffected in the asy4 mutant, the number of crossovers was reduced significantly, and crossovers tended to group in the distal parts of the chromosomes. We conclude that ASY4 is required for normal axis and crossover formation. Furthermore, our data suggest that ASY3/ASY4 are the functional homologs of the mammalian SYCP2/SYCP3 axial components.
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Affiliation(s)
- Aurélie Chambon
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, 78026 Versailles cedex, France
| | - Allan West
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Daniel Vezon
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, 78026 Versailles cedex, France
| | - Christine Horlow
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, 78026 Versailles cedex, France
| | - Arnaud De Muyt
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, 78026 Versailles cedex, France
| | - Liudmila Chelysheva
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, 78026 Versailles cedex, France
| | - Arnaud Ronceret
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, 78026 Versailles cedex, France
| | - Alice Darbyshire
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Stefan Heckmann
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, RD10, 78026 Versailles cedex, France
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76
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Morgan CH, Zhang H, Bomblies K. Are the effects of elevated temperature on meiotic recombination and thermotolerance linked via the axis and synaptonemal complex? Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0470. [PMID: 29109229 PMCID: PMC5698628 DOI: 10.1098/rstb.2016.0470] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2017] [Indexed: 12/23/2022] Open
Abstract
Meiosis is unusual among cell divisions in shuffling genetic material by crossovers among homologous chromosomes and partitioning the genome into haploid gametes. Crossovers are critical for chromosome segregation in most eukaryotes, but are also an important factor in evolution, as they generate novel genetic combinations. The molecular mechanisms that underpin meiotic recombination and chromosome segregation are well conserved across kingdoms, but are also sensitive to perturbation by environment, especially temperature. Even subtle shifts in temperature can alter the number and placement of crossovers, while at greater extremes, structural failures can occur in the linear axis and synaptonemal complex structures which are essential for recombination and chromosome segregation. Understanding the effects of temperature on these processes is important for its implications in evolution and breeding, especially in the context of global warming. In this review, we first summarize the process of meiotic recombination and its reliance on axis and synaptonemal complex structures, and then discuss effects of temperature on these processes and structures. We hypothesize that some consistent effects of temperature on recombination and meiotic thermotolerance may commonly be two sides of the same coin, driven by effects of temperature on the folding or interaction of key meiotic proteins. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
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Affiliation(s)
| | - Huakun Zhang
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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77
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Modliszewski JL, Wang H, Albright AR, Lewis SM, Bennett AR, Huang J, Ma H, Wang Y, Copenhaver GP. Elevated temperature increases meiotic crossover frequency via the interfering (Type I) pathway in Arabidopsis thaliana. PLoS Genet 2018; 14:e1007384. [PMID: 29771908 PMCID: PMC5976207 DOI: 10.1371/journal.pgen.1007384] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/30/2018] [Accepted: 04/27/2018] [Indexed: 11/29/2022] Open
Abstract
For most eukaryotes, sexual reproduction is a fundamental process that requires meiosis. In turn, meiosis typically depends on a reciprocal exchange of DNA between each pair of homologous chromosomes, known as a crossover (CO), to ensure proper chromosome segregation. The frequency and distribution of COs are regulated by intrinsic and extrinsic environmental factors, but much more is known about the molecular mechanisms governing the former compared to the latter. Here we show that elevated temperature induces meiotic hyper-recombination in Arabidopsis thaliana and we use genetic analysis with mutants in different recombination pathways to demonstrate that the extra COs are derived from the major Type I interference sensitive pathway. We also show that heat-induced COs are not the result of an increase in DNA double-strand breaks and that the hyper-recombinant phenotype is likely specific to thermal stress rather than a more generalized stress response. Taken together, these findings provide initial mechanistic insight into how environmental cues modulate plant meiotic recombination and may also offer practical applications. Meiosis is the cell division used by sexually reproducing species to produce sperm and egg cells. During meiosis, programmed Double Strand Breaks (DSBs) occur on each chromosome, which allows DNA to be exchanged between chromosome pairs, resulting in crossovers (COs). COs are necessary to ensure faithful chromosome segregation during meiosis, and thus fertility, but are also an important source of genetic variation. As such, CO formation is tightly regulated. Despite this, CO frequency can be altered by external factors, such as temperature. In Arabidopsis thaliana, COs are formed through two pathways: interference-sensitive (Type I) and interference-insensitive (Type II). An increase in temperature results in an increase in CO frequency. Using a pollen based assay, we show that COs are formed in the Type I pathway, which accounts for approximately 85% of the COs in Arabidopsis. To investigate whether temperature-dependent COs are the result of additional DSBs, we used immunological staining to examine protein foci, which mark the sites of DSBs. We discovered that temperature likely increases CO frequency by shifting alternative repair outcomes, called non-crossovers, to favor additional COs, rather than by increasing DSBs. Lastly, we found that temperature is not a general stress response, as plants subject to salt stress did not exhibit an increase in CO frequency. Our results may prove valuable in aiding plant breeding by enhancing our ability to rapidly introgress suites of elite traits from wild-plants into their crop relatives, a method that is particularly attractive as it does not require genetic modifications.
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Affiliation(s)
- Jennifer L. Modliszewski
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hongkuan Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ashley R. Albright
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Scott M. Lewis
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alexander R. Bennett
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jiyue Huang
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
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78
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Choi K, Zhao X, Tock AJ, Lambing C, Underwood CJ, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR. Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res 2018; 28:532-546. [PMID: 29530928 PMCID: PMC5880243 DOI: 10.1101/gr.225599.117] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 02/08/2018] [Indexed: 02/02/2023]
Abstract
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access. A positive relationship was observed between SPO11-1-oligos and crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream from DSB formation. Although H3K4me3 is enriched in proximity to SPO11-1-oligo hotspots at gene 5' ends, H3K4me3 levels do not correlate with DSBs. Repetitive transposons are thought to be recombination silenced during meiosis, to prevent nonallelic interactions and genome instability. Unexpectedly, we found high SPO11-1-oligo levels in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin in SPO11-1-oligo distributions. Epigenetic activation of meiotic DSBs in proximity to centromeres and transposons occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription, and H3K4me3. Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant genomes.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom;,Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Andrew J. Tock
- 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
| | - Charles J. Underwood
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom;,Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas J. Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Piotr A. Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Nataliya E. Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Robert A. Martienssen
- Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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79
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Underwood CJ, Choi K, Lambing C, Zhao X, Serra H, Borges F, Simorowski J, Ernst E, Jacob Y, Henderson IR, Martienssen RA. Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Res 2018; 28:519-531. [PMID: 29530927 PMCID: PMC5880242 DOI: 10.1101/gr.227116.117] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/15/2018] [Indexed: 02/02/2023]
Abstract
Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant centromeres are surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced by histone 3 lysine 9 dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation pathways, for example, via mutation of the H3K9 methyltransferase genes KYP/SUVH4 SUVH5 SUVH6, or the CHG DNA methyltransferase gene CMT3, increases meiotic recombination in proximity to the centromeres. Using immunocytological detection of MLH1 foci and genotyping by sequencing of recombinant plants, we observe that H3K9me2 and non-CG DNA methylation pathway mutants show increased pericentromeric crossovers. Increased pericentromeric recombination in H3K9me2/non-CG mutants occurs in hybrid and inbred backgrounds and likely involves contributions from both the interfering and noninterfering crossover repair pathways. We also show that meiotic DNA double-strand breaks (DSBs) increase in H3K9me2/non-CG mutants within the pericentromeres, via purification and sequencing of SPO11-1-oligonucleotides. Therefore, H3K9me2 and non-CG DNA methylation exert a repressive effect on both meiotic DSB and crossover formation in plant pericentromeric heterochromatin. Our results may account for selection of enhancer trap Dissociation (Ds) transposons into the CMT3 gene by recombination with proximal transposon launch-pads.
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Affiliation(s)
- Charles J. Underwood
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;,Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Kyuha Choi
- 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
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Filipe Borges
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joe Simorowski
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yannick Jacob
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R. Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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80
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Choi K, Zhao X, Tock AJ, Lambing C, Underwood CJ, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR. Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res 2018. [PMID: 29530928 DOI: 10.1101/gr.225599.117.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access. A positive relationship was observed between SPO11-1-oligos and crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream from DSB formation. Although H3K4me3 is enriched in proximity to SPO11-1-oligo hotspots at gene 5' ends, H3K4me3 levels do not correlate with DSBs. Repetitive transposons are thought to be recombination silenced during meiosis, to prevent nonallelic interactions and genome instability. Unexpectedly, we found high SPO11-1-oligo levels in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin in SPO11-1-oligo distributions. Epigenetic activation of meiotic DSBs in proximity to centromeres and transposons occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription, and H3K4me3. Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant genomes.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Andrew J Tock
- 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
| | - Charles J Underwood
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Piotr A Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Robert A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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81
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Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants in Schizosaccharomyces pombe. Curr Genet 2018; 64:1089-1104. [PMID: 29550859 PMCID: PMC6153652 DOI: 10.1007/s00294-018-0827-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 11/28/2022]
Abstract
Hop1 is a component of the meiosis-specific chromosome axis and belongs to the evolutionarily conserved family of HORMA domain proteins. Hop1 and its orthologs in higher eukaryotes are a major factor in promoting double-strand DNA break formation and inter-homolog recombination. In budding yeast and mammals, they are also involved in a meiotic checkpoint kinase cascade monitoring the completion of double-strand DNA break repair. We used the fission yeast, Schizosaccharomyces pombe, which lacks a canonical synaptonemal complex to test whether Hop1 has a role beyond supporting the generation of double-strand DNA breaks and facilitating inter-homolog recombination events. We determined how mutants of homologous recombination factors genetically interact with hop1, studied the role(s) of the HORMA domain of Hop1, and characterized a bio-informatically predicted interactor of Hop1, Aho1 (SPAC688.03c). Our observations indicate that in fission yeast, Hop1 does require its HORMA domain to support wild-type levels of meiotic recombination and localization to meiotic chromatin. Furthermore, we show that hop1∆ only weakly interacts genetically with mutants of homologous recombination factors, and in fission yeast likely has no major role beyond break formation and promoting inter-homolog events. We speculate that after the evolutionary loss of the synaptonemal complex, Hop1 likely has become less important for modulating recombination outcome during meiosis in fission yeast, and that this led to a concurrent rewiring of genetic pathways controlling meiotic recombination.
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82
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Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis. Proc Natl Acad Sci U S A 2018; 115:2437-2442. [PMID: 29463699 DOI: 10.1073/pnas.1713071115] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
During meiosis, homologous chromosomes undergo reciprocal crossovers, which generate genetic diversity and underpin classical crop improvement. Meiotic recombination initiates from DNA double-strand breaks (DSBs), which are processed into single-stranded DNA that can invade a homologous chromosome. The resulting joint molecules can ultimately be resolved as crossovers. In Arabidopsis, competing pathways balance the repair of ∼100-200 meiotic DSBs into ∼10 crossovers per meiosis, with the excess DSBs repaired as noncrossovers. To bias DSB repair toward crossovers, we simultaneously increased dosage of the procrossover E3 ligase gene HEI10 and introduced mutations in the anticrossovers helicase genes RECQ4A and RECQ4B As HEI10 and recq4a recq4b increase interfering and noninterfering crossover pathways, respectively, they combine additively to yield a massive meiotic recombination increase. Interestingly, we also show that increased HEI10 dosage increases crossover coincidence, which indicates an effect on interference. We also show that patterns of interhomolog polymorphism and heterochromatin drive recombination increases distally towards the subtelomeres in both HEI10 and recq4a recq4b backgrounds, while the centromeres remain crossover suppressed. These results provide a genetic framework for engineering meiotic recombination landscapes in plant genomes.
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83
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Osman K, Yang J, Roitinger E, Lambing C, Heckmann S, Howell E, Cuacos M, Imre R, Dürnberger G, Mechtler K, Armstrong S, Franklin FCH. Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:17-33. [PMID: 29078019 PMCID: PMC5767750 DOI: 10.1111/tpj.13752] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 05/18/2023]
Abstract
During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functionally characterized. Our understanding of the physical and functional interactions between meiotic proteins is also limited. Here we use affinity proteomics to analyse the proteins that are associated with the meiotic chromosome axis protein, ASY1, in Brassica oleracea anthers and meiocytes. We show that during prophase I ASY1 and its interacting partner, ASY3, are extensively phosphorylated, and we precisely assign phosphorylation sites. We identify 589 proteins that co-immunoprecipitate with ASY1. These correspond to 492 Arabidopsis orthologues, over 90% of which form a coherent protein-protein interaction (PPI) network containing known and candidate meiotic proteins, including proteins more usually associated with other cellular processes such as DNA replication and proteolysis. Mutant analysis confirms that affinity proteomics is a viable strategy for revealing previously unknown meiotic proteins, and we show how the PPI network can be used to prioritise candidates for analysis. Finally, we identify another axis-associated protein with a role in meiotic recombination. Data are available via ProteomeXchange with identifier PXD006042.
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Affiliation(s)
- Kim Osman
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jianhua Yang
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Faculty of Engineering and ComputingCoventry UniversityCoventryCV1 5FBUK
| | | | - Christophe Lambing
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Stefan Heckmann
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | - Elaine Howell
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Maria Cuacos
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | | | - Gerhard Dürnberger
- IMP‐IMBA1030ViennaAustria
- Gregor Mendel Institute of Molecular Plant BiologyDr. Bohr‐Gasse 31030ViennaAustria
| | | | - Susan Armstrong
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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84
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Varas J, Pradillo M. Immunolabeling Protocols for Studying Meiosis in Plant Mutants Defective for Nuclear Envelope Components. Methods Mol Biol 2018; 1840:237-247. [PMID: 30141049 DOI: 10.1007/978-1-4939-8691-0_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The nuclear envelope (NE) is a dynamic boundary that allows the communication between nuclear and cytoplasmic components. It has essential roles in a variety of physiological processes including cell division. The linker of nucleoskeleton and cytoskeleton (LINC) complexes span the NE and are important during meiosis, the specialized cell division needed for sexual reproduction. During this division, the LINC complex proteins AtSUN1 and AtSUN2, located in the inner nuclear membrane (INM), are involved in tethering telomeres to the NE. This attachment promotes chromosome movements by the forces that are generated in the cytoplasmic face. In Arabidopsis, the double mutant Atsun1 Atsun2 exhibits a delayed prophase I meiotic progression, partial synapsis, and recombination defects that lead to the formation of unbalanced gametes and sterility. In meiocytes from these mutants, immunolabeling can be applied to analyze possible changes in the dynamics of different meiotic proteins. In addition, if the specific antibodies are available, this technique is an easy and useful tool to determine the spatial distribution of NE proteins.
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Affiliation(s)
- Javier Varas
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain.
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
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85
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Gao J, Colaiácovo MP. Zipping and Unzipping: Protein Modifications Regulating Synaptonemal Complex Dynamics. Trends Genet 2017; 34:232-245. [PMID: 29290403 DOI: 10.1016/j.tig.2017.12.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/23/2022]
Abstract
The proteinaceous zipper-like structure known as the synaptonemal complex (SC), which forms between pairs of homologous chromosomes during meiosis from yeast to humans, plays important roles in promoting interhomolog crossover formation, regulating cessation of DNA double-strand break (DSB) formation following crossover designation, and ensuring accurate meiotic chromosome segregation. Recent studies are starting to reveal critical roles for different protein modifications in regulating SC dynamics. Protein SUMOylation, N-terminal acetylation, and phosphorylation have been shown to be essential for the regulated assembly and disassembly of the SC. Moreover, phosphorylation of specific SC components has been found to link changes in SC dynamics with meiotic recombination. This review highlights the latest findings on how protein modifications regulate SC dynamics and functions.
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Affiliation(s)
- Jinmin Gao
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, Shandong, 250014, China; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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86
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Lawrence EJ, Griffin CH, Henderson IR. Modification of meiotic recombination by natural variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5471-5483. [PMID: 28992351 DOI: 10.1093/jxb/erx306] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is a specialized cell division that produces haploid gametes required for sexual reproduction. During the first meiotic division, homologous chromosomes pair and undergo reciprocal crossing over, which recombines linked sequence variation. Meiotic recombination frequency varies extensively both within and between species. In this review, we will examine the molecular basis of meiotic recombination rate variation, with an emphasis on plant genomes. We first consider cis modification caused by polymorphisms at the site of recombination, or elsewhere on the same chromosome. We review cis effects caused by mismatches within recombining joint molecules, the effect of structural hemizygosity, and the role of specific DNA sequence motifs. In contrast, trans modification of recombination is exerted by polymorphic loci encoding diffusible molecules, which are able to modulate recombination on the same and/or other chromosomes. We consider trans modifiers that act to change total recombination levels, hotspot locations, or interactions between homologous and homeologous chromosomes in polyploid species. Finally, we consider the significance of genetic variation that modifies meiotic recombination for adaptation and evolution of plant species.
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Affiliation(s)
- Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Catherine H Griffin
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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87
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Su Z, Zhao L, Zhao Y, Li S, Won S, Cai H, Wang L, Li Z, Chen P, Qin Y, Chen X. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr Biol 2017; 27:1597-1609.e2. [PMID: 28552357 DOI: 10.1016/j.cub.2017.05.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/12/2017] [Accepted: 05/05/2017] [Indexed: 12/21/2022]
Abstract
In most sexually reproducing plants, a single somatic, sub-epidermal cell in an ovule is selected to differentiate into a megaspore mother cell, which is committed to giving rise to the female germline. However, it remains unclear how intercellular signaling among somatic cells results in only one cell in the sub-epidermal layer differentiating into the megaspore mother cell. Here we uncovered a role of the THO complex in restricting the megaspore mother cell fate to a single cell. Mutations in TEX1, HPR1, and THO6, components of the THO/TREX complex, led to the formation of multiple megaspore mother cells, which were able to initiate gametogenesis. We demonstrated that TEX1 repressed the megaspore mother cell fate by promoting the biogenesis of TAS3-derived trans-acting small interfering RNA (ta-siRNA), which represses ARF3 expression. The TEX1 protein was present in epidermal cells, but not in the germline, and, through TAS3-derived ta-siRNA, restricted ARF3 expression to the medio domain of ovule primordia. Expansion of ARF3 expression into lateral epidermal cells in a TAS3 ta-siRNA-insensitive mutant led to the formation of supernumerary megaspore mother cells, suggesting that TEX1- and TAS3-mediated restriction of ARF3 expression limits excessive megaspore mother cell formation non-cell-autonomously. Our findings reveal the role of a small-RNA pathway in the regulation of female germline specification in Arabidopsis.
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Affiliation(s)
- Zhenxia Su
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Lihua Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - SoYoun Won
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Hanyang Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Zhenfang Li
- Crop Science College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Piaojuan Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA; Howard Hughes Medical Institute, Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA.
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88
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Pelé A, Falque M, Trotoux G, Eber F, Nègre S, Gilet M, Huteau V, Lodé M, Jousseaume T, Dechaumet S, Morice J, Poncet C, Coriton O, Martin OC, Rousseau-Gueutin M, Chèvre AM. Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas. PLoS Genet 2017; 13:e1006794. [PMID: 28493942 PMCID: PMC5444851 DOI: 10.1371/journal.pgen.1006794] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 05/25/2017] [Accepted: 05/02/2017] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs.
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Affiliation(s)
- Alexandre Pelé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Matthieu Falque
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Frédérique Eber
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Sylvie Nègre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Virginie Huteau
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Maryse Lodé
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Sylvain Dechaumet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | | | - Olivier Coriton
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Olivier C. Martin
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif sur Yvette, France
| | | | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
- * E-mail:
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89
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Modliszewski JL, Copenhaver GP. Meiotic recombination gets stressed out: CO frequency is plastic under pressure. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:95-102. [PMID: 28258986 DOI: 10.1016/j.pbi.2016.11.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/13/2016] [Indexed: 05/02/2023]
Abstract
Meiotic recombination ensures the fertility of gametes and creates novel genetic combinations. Although meiotic crossover (CO) frequency is under homeostatic control, CO frequency is also plastic in nature and can respond to environmental conditions. Most investigations have focused on temperature and recombination, but other external and internal stimuli also have important roles in modulating CO frequency. Even less is understood about the molecular mechanisms that underly these phenomenon, but recent work has begun to advance our knowledge in this field. In this review, we identify and explore potential mechanisms including changes in: the synaptonemal complex, chromatin state, DNA methylation, and RNA splicing.
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Affiliation(s)
- Jennifer L Modliszewski
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States.
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, United States
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90
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Nadarajan S, Lambert TJ, Altendorfer E, Gao J, Blower MD, Waters JC, Colaiácovo MP. Polo-like kinase-dependent phosphorylation of the synaptonemal complex protein SYP-4 regulates double-strand break formation through a negative feedback loop. eLife 2017; 6. [PMID: 28346135 PMCID: PMC5423773 DOI: 10.7554/elife.23437] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/23/2017] [Indexed: 12/22/2022] Open
Abstract
The synaptonemal complex (SC) is an ultrastructurally conserved proteinaceous structure that holds homologous chromosomes together and is required for the stabilization of pairing interactions and the completion of crossover (CO) formation between homologs during meiosis I. Here, we identify a novel role for a central region component of the SC, SYP-4, in negatively regulating formation of recombination-initiating double-strand breaks (DSBs) via a feedback loop triggered by crossover designation in C. elegans. We found that SYP-4 is phosphorylated dependent on Polo-like kinases PLK-1/2. SYP-4 phosphorylation depends on DSB formation and crossover designation, is required for stabilizing the SC in pachytene by switching the central region of the SC from a more dynamic to a less dynamic state, and negatively regulates DSB formation. We propose a model in which Polo-like kinases recognize crossover designation and phosphorylate SYP-4 thereby stabilizing the SC and making chromosomes less permissive for further DSB formation.
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Affiliation(s)
| | - Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | | | - Jinmin Gao
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Michael D Blower
- Department of Genetics, Harvard Medical School, Boston, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Jennifer C Waters
- Department of Cell Biology, Harvard Medical School, Boston, United States
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91
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Lambing C, Franklin FCH, Wang CJR. Understanding and Manipulating Meiotic Recombination in Plants. PLANT PHYSIOLOGY 2017; 173:1530-1542. [PMID: 28108697 PMCID: PMC5338670 DOI: 10.1104/pp.16.01530] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/18/2017] [Indexed: 05/18/2023]
Abstract
Meiosis is a specialized cell division, essential in most reproducing organisms to halve the number of chromosomes, thereby enabling the restoration of ploidy levels during fertilization. A key step of meiosis is homologous recombination, which promotes homologous pairing and generates crossovers (COs) to connect homologous chromosomes until their separation at anaphase I. These CO sites, seen cytologically as chiasmata, represent a reciprocal exchange of genetic information between two homologous nonsister chromatids. This gene reshuffling during meiosis has a significant influence on evolution and also plays an essential role in plant breeding, because a successful breeding program depends on the ability to bring the desired combinations of alleles on chromosomes. However, the number and distribution of COs during meiosis is highly constrained. There is at least one CO per chromosome pair to ensure accurate segregation of homologs, but in most organisms, the CO number rarely exceeds three regardless of chromosome size. Moreover, their positions are not random on chromosomes but exhibit regional preference. Thus, genes in recombination-poor regions tend to be inherited together, hindering the generation of novel allelic combinations that could be exploited by breeding programs. Recently, much progress has been made in understanding meiotic recombination. In particular, many genes involved in the process in Arabidopsis (Arabidopsis thaliana) have been identified and analyzed. With the coming challenges of food security and climate change, and our enhanced knowledge of how COs are formed, the interest and needs in manipulating CO formation are greater than ever before. In this review, we focus on advances in understanding meiotic recombination and then summarize the attempts to manipulate CO formation. Last, we pay special attention to the meiotic recombination in polyploidy, which is a common genomic feature for many crop plants.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
| | - F Chris H Franklin
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
| | - Chung-Ju Rachel Wang
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.);
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
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92
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Coordination of Double Strand Break Repair and Meiotic Progression in Yeast by a Mek1-Ndt80 Negative Feedback Loop. Genetics 2017; 206:497-512. [PMID: 28249986 DOI: 10.1534/genetics.117.199703] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/25/2017] [Indexed: 11/18/2022] Open
Abstract
During meiosis, homologous chromosomes are physically connected by crossovers and sister chromatid cohesion. Interhomolog crossovers are generated by the highly regulated repair of programmed double strand breaks (DSBs). The meiosis-specific kinase Mek1 is critical for this regulation. Mek1 downregulates the mitotic recombinase Rad51, indirectly promoting interhomolog strand invasion by the meiosis-specific recombinase Dmc1. Mek1 also promotes the formation of crossovers that are distributed throughout the genome by interference and is the effector kinase for a meiosis-specific checkpoint that delays entry into Meiosis I until DSBs have been repaired. The target of this checkpoint is a meiosis-specific transcription factor, Ndt80, which is necessary to express the polo-like kinase CDC5 and the cyclin CLB1 thereby allowing completion of recombination and meiotic progression. This work shows that Mek1 and Ndt80 negatively feedback on each other such that when DSB levels are high, Ndt80 is inactive due to high levels of Mek1 activity. As DSBs are repaired, chromosomes synapse and Mek1 activity is reduced below a threshold that allows activation of Ndt80. Ndt80 transcription of CDC5 results in degradation of Red1, a meiosis-specific protein required for Mek1 activation, thereby abolishing Mek1 activity completely. Elimination of Mek1 kinase activity allows Rad51-mediated repair of any remaining DSBs. In this way, cells do not enter Meiosis I until recombination is complete and all DSBs are repaired.
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93
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Ziolkowski PA, Underwood CJ, Lambing C, Martinez-Garcia M, Lawrence EJ, Ziolkowska L, Griffin C, Choi K, Franklin FCH, Martienssen RA, Henderson IR. Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination. Genes Dev 2017; 31:306-317. [PMID: 28223312 PMCID: PMC5358726 DOI: 10.1101/gad.295501.116] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/27/2017] [Indexed: 11/24/2022]
Abstract
During meiosis, homologous chromosomes undergo crossover recombination, which creates genetic diversity and balances homolog segregation. Despite these critical functions, crossover frequency varies extensively within and between species. Although natural crossover recombination modifier loci have been detected in plants, causal genes have remained elusive. Using natural Arabidopsis thaliana accessions, we identified two major recombination quantitative trait loci (rQTLs) that explain 56.9% of crossover variation in Col×Ler F2 populations. We mapped rQTL1 to semidominant polymorphisms in HEI10, which encodes a conserved ubiquitin E3 ligase that regulates crossovers. Null hei10 mutants are haploinsufficient, and, using genome-wide mapping and immunocytology, we show that transformation of additional HEI10 copies is sufficient to more than double euchromatic crossovers. However, heterochromatic centromeres remained recombination-suppressed. The strongest HEI10-mediated crossover increases occur in subtelomeric euchromatin, which is reminiscent of sex differences in Arabidopsis recombination. Our work reveals that HEI10 naturally limits Arabidopsis crossovers and has the potential to influence the response to selection.
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Affiliation(s)
- Piotr A Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
- Department of Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Charles J Underwood
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
- Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | | | - Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Liliana Ziolkowska
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Catherine Griffin
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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94
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Zeng X, Yan X, Yuan R, Li K, Wu Y, Liu F, Luo J, Li J, Wu G. Identification and Analysis of MS5d: A Gene That Affects Double-Strand Break (DSB) Repair during Meiosis I in Brassica napus Microsporocytes. FRONTIERS IN PLANT SCIENCE 2017; 7:1966. [PMID: 28101089 PMCID: PMC5209369 DOI: 10.3389/fpls.2016.01966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/12/2016] [Indexed: 05/13/2023]
Abstract
Here, we report the identification of the Brassica-specific gene MS5d, which is responsible for male sterility in Brassica napus. The MS5d gene is highly expressed in the microsporocyte and encodes a protein that localizes to the nucleus. Light microscopy analyses have demonstrated that the MS5d gene affects microsporocyte meiosis in the thermosensitive genic male sterility line TE5A. Sequence comparisons and genetic complementation revealed a C-to-T transition in MS5d, encoding a Leu-to-Phe (L281F) substitution and causing abnormal male meiosis in TE5A. These findings suggest arrested meiotic chromosome dynamics at pachytene. Furthermore, immunofluorescence analyses showed that double-strand break (DSB) formation and axial elements were normal but that DSB repair and spindle behavior were aberrant in TE5A meiocytes. Collectively, our results indicate that MS5d likely encodes a protein required for chromosomal DSB repair at early stages of meiosis in B. napus.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
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95
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Colas I, Darrier B, Arrieta M, Mittmann SU, Ramsay L, Sourdille P, Waugh R. Observation of Extensive Chromosome Axis Remodeling during the "Diffuse-Phase" of Meiosis in Large Genome Cereals. FRONTIERS IN PLANT SCIENCE 2017; 8:1235. [PMID: 28751906 PMCID: PMC5508023 DOI: 10.3389/fpls.2017.01235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/29/2017] [Indexed: 05/02/2023]
Abstract
The production of balanced fertile haploid gametes requires the faithful separation of paired (synapsed) chromosomes toward the end of meiotic prophase I (desynapsis). This involves the timely dissolution of the synaptonemal complex during the pachytene-diplotene transition, a stage traditionally referred to as the "diffuse stage." In species with large genomes such as, barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) we know most about the early stages of meiotic prophase I. There, synapsis initiates at the telomeric ends of chromosomes and progresses toward the centromeric regions through the ordered assembly of the synaptonemal complex (SC). Synapsis is impacted by recombination (crossing over, CO) which locally modifies the extent of chromatin compaction and extension. CO is uneven along the chromosomes, occurring mainly toward the telomeric regions resulting in a highly skewed distribution of recombination events. However, we know very little about the process of desynapsis which occurs during the "diffuse stage," where the synapsed and recombined chromosomes faithfully desynapse and separate into daughter cells. Here, using 3D-SIM super-resolution immuno-cytology combined with the use of antibodies directed against two crucial SC proteins, ASY1 and ZYP1, we followed the whole of meiosis I (i.e., both synapsis and desynapsis) in both barley and wheat. We showed that synapsis forms a characteristic tri-partite SC structure in zygotene (more clearly seen in barley). Toward the end of meiosis I, as the SC starts to disassemble, we show that extensive chromosome axis remodeling results in the formation of characteristic "tinsel-like" structures in both wheat and barley. By using a mutant (des10) that is severely compromised in polymerization of ZYP1during synapsis, we show that tinsel structure formation during SC dissolution is not dependant on full synapsis and may relate instead to changes in expansion stress. Our observations highlight a potentially new role for ASYNAPSIS1 (ASY1) in desynapsis, in addition to chromosome synapsis and cohesion.
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Affiliation(s)
- Isabelle Colas
- Cell and Molecular Sciences, The James Hutton InstituteDundee, United Kingdom
- *Correspondence: Isabelle Colas
| | - Benoit Darrier
- Institut National de la Recherche Agronomique UMR 1095, Génétique, Diversité & Ecophysiologie des CéréalesClermont-Ferrand, France
- Université Clermont Auvergne–UBPAubière, France
| | - Mikel Arrieta
- Cell and Molecular Sciences, The James Hutton InstituteDundee, United Kingdom
| | - Sybille U. Mittmann
- Cell and Molecular Sciences, The James Hutton InstituteDundee, United Kingdom
- Division of Plant Sciences, University of Dundee at The James Hutton InstituteDundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton InstituteDundee, United Kingdom
- Luke Ramsay
| | - Pierre Sourdille
- Institut National de la Recherche Agronomique UMR 1095, Génétique, Diversité & Ecophysiologie des CéréalesClermont-Ferrand, France
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton InstituteDundee, United Kingdom
- Division of Plant Sciences, University of Dundee at The James Hutton InstituteDundee, United Kingdom
- Robbie Waugh
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96
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Calvente A, Santos JL, Rufas JS. Do Exogenous DNA Double-Strand Breaks Change Incomplete Synapsis and Chiasma Localization in the Grasshopper Stethophyma grossum? PLoS One 2016; 11:e0168499. [PMID: 28005992 PMCID: PMC5179137 DOI: 10.1371/journal.pone.0168499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
Meiotic recombination occurs as a programmed event that initiates by the formation of DNA double-strand breaks (DSBs) that give rise to the formation of crossovers that are observed as chiasmata. Chiasmata are essential for the accurate chromosome segregation and the generation of new combinations of parental alleles. Some treatments that provoke exogenous DSBs also lead to alterations in the recombination pattern of some species in which full homologous synapsis is achieved at pachytene. We have carried out a similar approach in males of the grasshopper Stethophyma grossum, whose homologues show incomplete synapsis and proximal chiasma localization. After irradiating males with γ rays we have studied the distribution of both the histone variant γ-H2AX and the recombinase RAD51. These proteins are cytological markers of DSBs at early prophase I. We have inferred synaptonemal complex (SC) formation via identification of SMC3 and RAD 21 cohesin subunits. Whereas thick and thin SMC3 filaments would correspond to synapsed and unsynapsed regions, the presence of RAD21 is only restricted to synapsed regions. Results show that irradiated spermatocytes maintain restricted synapsis between homologues. However, the frequency and distribution of chiasmata in metaphase I bivalents is slightly changed and quadrivalents were also observed. These results could be related to the singular nuclear polarization displayed by the spermatocytes of this species.
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Affiliation(s)
- Adela Calvente
- Departamento de Biología, Edificio de Biológicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Luis Santos
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Julio S. Rufas
- Departamento de Biología, Edificio de Biológicas, Universidad Autónoma de Madrid, Madrid, Spain
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97
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Liu H, Nonomura KI. A wide reprogramming of histone H3 modifications during male meiosis I in rice is dependent on the Argonaute protein MEL1. J Cell Sci 2016; 129:3553-3561. [PMID: 27521428 DOI: 10.1242/jcs.184937] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 08/05/2016] [Indexed: 12/11/2022] Open
Abstract
The roles of epigenetic mechanisms, including small-RNA-mediated silencing, in plant meiosis largely remain unclear, despite their importance in plant reproduction. This study unveiled that rice chromosomes are reprogrammed during the premeiosis-to-meiosis transition in pollen mother cells (PMCs). This large-scale meiotic chromosome reprogramming (LMR) continued throughout meiosis I, during which time H3K9 dimethylation (H3K9me2) was increased, and H3K9 acetylation and H3S10 phosphorylation were broadly decreased, with an accompanying immunostaining pattern shift of RNA polymerase II. LMR was dependent on the rice Argonaute protein, MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1), which is specifically expressed in germ cells prior to meiosis, because LMR was severely diminished in mel1 mutant anthers. Pivotal meiotic events, such as pre-synaptic centromere association, DNA double-strand break initiation and synapsis of homologous chromosomes, were also disrupted in this mutant. Interestingly, and as opposed to the LMR loss in most chromosomal regions, aberrant meiotic protein loading and hypermethylation of H3K9 emerged on the nucleolar organizing region in the mel1 PMCs. These results suggest that MEL1 plays important roles in epigenetic LMR to promote faithful homologous recombination and synapsis during rice meiosis.
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Affiliation(s)
- Hua Liu
- Experimental Farm, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan Department of Life Science, Graduate University for Advanced Studies/SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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98
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Xin Q, Shen Y, Li X, Lu W, Wang X, Han X, Dong F, Wan L, Yang G, Hong D, Cheng Z. MS5 Mediates Early Meiotic Progression and Its Natural Variants May Have Applications for Hybrid Production in Brassica napus. THE PLANT CELL 2016; 28:1263-78. [PMID: 27194707 PMCID: PMC4944402 DOI: 10.1105/tpc.15.01018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/16/2016] [Indexed: 05/02/2023]
Abstract
During meiotic prophase I, chromatin undergoes dynamic changes to establish a structural basis for essential meiotic events. However, the mechanism that coordinates chromosome structure and meiotic progression remains poorly understood in plants. Here, we characterized a spontaneous sterile mutant MS5(b)MS5(b) in oilseed rape (Brassica napus) and found its meiotic chromosomes were arrested at leptotene. MS5 is preferentially expressed in reproductive organs and encodes a Brassica-specific protein carrying conserved coiled-coil and DUF626 domains with unknown function. MS5 is essential for pairing of homologs in meiosis, but not necessary for the initiation of DNA double-strand breaks. The distribution of the axis element-associated protein ASY1 occurs independently of MS5, but localization of the meiotic cohesion subunit SYN1 requires functional MS5. Furthermore, both the central element of the synaptonemal complex and the recombination element do not properly form in MS5(b)MS5(b) mutants. Our results demonstrate that MS5 participates in progression of meiosis during early prophase I and its allelic variants lead to differences in fertility, which may provide a promising strategy for pollination control for heterosis breeding.
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Affiliation(s)
- Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Lu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China College of Life Science, South-central University for Nationalities, Wuhan 430074, China
| | - Xiang Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue Han
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lili Wan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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99
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Wang H, Hu Q, Tang D, Liu X, Du G, Shen Y, Li Y, Cheng Z. OsDMC1 Is Not Required for Homologous Pairing in Rice Meiosis. PLANT PHYSIOLOGY 2016; 171:230-41. [PMID: 26960731 PMCID: PMC4854709 DOI: 10.1104/pp.16.00167] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 03/07/2016] [Indexed: 05/13/2023]
Abstract
Meiotic homologous recombination is pivotal to sexual reproduction. DMC1, a conserved recombinase, is involved in directing single-end invasion between interhomologs during meiotic recombination. In this study, we identified OsDMC1A and OsDMC1B, two closely related proteins in rice (Oryza sativa) with high sequence similarity to DMC1 proteins from other species. Analysis of Osdmc1a and Osdmc1b Tos17 insertion mutants indicated that these genes are functionally redundant. Immunolocalization analysis revealed OsDMC1 foci occurred at leptotene, which disappeared from late pachytene chromosomes in wild-type meiocytes. According to cytological analyses, homologous pairing is accomplished in the Osdmc1a Osdmc1b double mutant, but synapsis is seriously disrupted. The reduced number of bivalents and abnormal OsHEI10 foci in Osdmc1a Osdmc1b establishes an essential role for OsDMC1 in crossover formation. In the absence of OsDMC1, early recombination events probably occur normally, leading to normal localization of γH2AX, PAIR3, OsMRE11, OsCOM1, and OsRAD51C. Moreover, OsDMC1 was not detected in pairing-defective mutants, such as pair2, pair3, Oscom1, and Osrad51c, while it was loaded onto meiotic chromosomes in zep1, Osmer3, Oszip4, and Oshei10 Taken together, these results suggest that during meiosis, OsDMC1 is dispensable for homologous pairing in rice, which is quite different from the DMC1 homologs identified so far in other organisms.
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Affiliation(s)
- Hongjun Wang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Hu
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofei Liu
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guijie Du
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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100
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Melamed-Bessudo C, Shilo S, Levy AA. Meiotic recombination and genome evolution in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:82-7. [PMID: 26939088 DOI: 10.1016/j.pbi.2016.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/07/2016] [Accepted: 02/08/2016] [Indexed: 05/22/2023]
Abstract
Homologous recombination affects genome evolution through crossover, gene conversion and point mutations. Whole genome sequencing together with a detailed epigenome analysis have shed new light on our understanding of how meiotic recombination shapes plant genes and genome structure. Crossover events are associated with DNA sequence motifs, together with an open chromatin signature (hypomethylated CpGs, low nucleosome occupancy or specific histone modifications). The crossover landscape may differ between male and female meiocytes and between species. At the gene level, crossovers occur preferentially in promoter regions in Arabidopsis. In recent years, there is rising support suggesting that biased mismatch repair during meiotic recombination may increase GC content genome-wide and may be responsible for the GC content gradient found in many plant genes.
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Affiliation(s)
- Cathy Melamed-Bessudo
- Plant and Environmental Sciences Department, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shay Shilo
- Plant and Environmental Sciences Department, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avraham A Levy
- Plant and Environmental Sciences Department, The Weizmann Institute of Science, Rehovot 76100, Israel.
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