1
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Kim H, Kim J, Son N, Kuo P, Morgan C, Chambon A, Byun D, Park J, Lee Y, Park YM, Fozard JA, Guérin J, Hurel A, Lambing C, Howard M, Hwang I, Mercier R, Grelon M, Henderson IR, Choi K. Control of meiotic crossover interference by a proteolytic chaperone network. NATURE PLANTS 2024; 10:453-468. [PMID: 38379086 DOI: 10.1038/s41477-024-01633-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Meiosis is a specialized eukaryotic division that produces genetically diverse gametes for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal exchanges, called crossovers, which recombine genetic variation. Meiotic crossovers are stringently controlled with at least one obligate exchange forming per chromosome pair, while closely spaced crossovers are inhibited by interference. In Arabidopsis, crossover positions can be explained by a diffusion-mediated coarsening model, in which large, approximately evenly spaced foci of the pro-crossover E3 ligase HEI10 grow at the expense of smaller, closely spaced clusters. However, the mechanisms that control HEI10 dynamics during meiosis remain unclear. Here, through a forward genetic screen in Arabidopsis, we identified high crossover rate3 (hcr3), a dominant-negative mutant that reduces crossover interference and increases crossovers genome-wide. HCR3 encodes J3, a co-chaperone related to HSP40, which acts to target protein aggregates and biomolecular condensates to the disassembly chaperone HSP70, thereby promoting proteasomal degradation. Consistently, we show that a network of HCR3 and HSP70 chaperones facilitates proteolysis of HEI10, thereby regulating interference and the recombination landscape. These results reveal a new role for the HSP40/J3-HSP70 chaperones in regulating chromosome-wide dynamics of recombination via control of HEI10 proteolysis.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Namil Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Chris Morgan
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Aurélie Chambon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Dohwan Byun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jihye Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngkyung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yeong Mi Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - John A Fozard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Julie Guérin
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Aurélie Hurel
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
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2
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Chowdary KVSKA, Saini R, Singh AK. Epigenetic regulation during meiosis and crossover. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1945-1958. [PMID: 38222277 PMCID: PMC10784443 DOI: 10.1007/s12298-023-01390-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 01/16/2024]
Abstract
Meiosis is a distinctive type of cell division that reorganizes genetic material between generations. The initial stages of meiosis consist of several crucial steps which include double strand break, homologous chromosome pairing, break repair and crossover. Crossover frequency varies depending on the position on the chromosome, higher at euchromatin region and rare at heterochromatin, centromeres, telomeres and ribosomal DNA. Crossover positioning is dependent on various factors, especially epigenetic modifications. DNA methylation, histone post-translational modifications, histone variants and non-coding RNAs are most probably playing an important role in positioning of crossovers on a chromosomal level as well as hotspot level. DNA methylation negatively regulates crossover frequency and its effect is visible in centromeres, pericentromeres and heterochromatin regions. Pericentromeric chromatin and heterochromatin mark studies have been a centre of attraction in meiosis. Crossover hotspots are associated with euchromatin regions having specific chromatin modifications such as H3K4me3, H2A.Z. and H3 acetylation. This review will provide the current understanding of the epigenetic role in plants during meiotic recombination, chromosome synapsis, double strand break and hotspots with special attention to euchromatin and heterochromatin marks. Further, the role of epigenetic modifications in regulating meiosis and crossover in other organisms is also discussed.
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Affiliation(s)
- K. V. S. K. Arjun Chowdary
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Ramswaroop Saini
- Department of Biotechnology, Joy University, Vadakangulam, Tirunelveli, Tamil Nadu 627116 India
| | - Amit Kumar Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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3
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Dluzewska J, Dziegielewski W, Szymanska-Lejman M, Gazecka M, Henderson IR, Higgins JD, Ziolkowski PA. MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism. Nat Commun 2023; 14:6716. [PMID: 37872134 PMCID: PMC10593791 DOI: 10.1038/s41467-023-42511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism.
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Affiliation(s)
- Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Monika Gazecka
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
- Department of Molecular Virology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - 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, Poznań, Poland.
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4
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Huang J, Li X, Wang C, Wang Y. Evaluation of Crossover Number, Distribution, and Interference Using Cytological Assays in Arabidopsis. Curr Protoc 2022; 2:e599. [PMID: 36468904 DOI: 10.1002/cpz1.599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Meiosis involves the replication of nuclear chromosomes in a parent cell, followed by two successive nuclear divisions to produce haploid spores, which differentiate into the gametophyte generations that produce the egg and sperm in plants. Meiotic recombination or crossover (CO) is a hallmark of meiosis that allows shuffling of genetic information between homologous chromosomes (homologs), thereby giving rise to genetically diverse progeny cells and, ultimately, individuals in the progeny; this opens vast opportunities for genetic differentiation and hence speciation. Meiotic COs also ensure the formation of bivalents and fidelity of their equal segregation. Therefore, mechanisms that regulate meiotic recombination have been extensively studied in multiple species. Several approaches have been developed to observe or estimate the frequency of CO, in which CO can be visualized and analyzed cytologically by estimating the number of chiasma (plural chiasmata), a position where non-sister chromatids exchange genetic material between homologs. Furthermore, one CO event might influence the occurrence of another one nearby, along a chromosome; this is known as CO interference. Over the past decades, visualizing CO events and measuring CO interference have contributed greatly to our understanding of the regulatory mechanisms of meiotic recombination. Here, we describe protocols to estimate the number of chiasmata and CO interference in Arabidopsis using cytological methods involving chromosome spreads and immunostaining. Specifically, we describe how chromosome spreads can be used to estimate the number of chiasmata based on the conformations of metaphase I bivalents and provide a revised acid-based quick immunostaining assay that permits high-throughput and quantitative digital estimation of the relative distance between adjacent interference-sensitive CO foci at diakinesis. These methods can be easily established or modified, if necessary, for studying meiotic recombination in other plants and crops. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Estimation of the number of chiasmata per nucleus based on metaphase I bivalent conformations Basic Protocol 2: A chromosome spread-based immunostaining method for relative distance analysis of adjacent interference-sensitive CO foci at diakinesis in Arabidopsis meiocytes.
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Affiliation(s)
- Jiyue Huang
- College of Life Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Xiang Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, China
| | - Cong Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yingxiang Wang
- College of Life Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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5
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Poethig RS, Cullina WL, Doody E, Floyd T, Fouracre JP, Hu T, Xu M, Zhao J. Short-interval traffic lines: versatile tools for genetic analysis in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2022; 12:6677228. [PMID: 36018241 PMCID: PMC9526051 DOI: 10.1093/g3journal/jkac202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/17/2022] [Indexed: 12/30/2022]
Abstract
Traffic lines are transgenic stocks of Arabidopsis thaliana that contain a pair of linked seed-specific eGFP and DsRed markers. These stocks were originally developed for the purpose of studying recombination, but can also be used to follow the inheritance of unmarked chromosomes placed in trans to the marked chromosome. They are particularly useful for this latter purpose if the distance between markers is short, making double recombination within this interval relatively rare. We generated 163 traffic lines that cover the Arabidopsis genome in overlapping intervals of approximately 1.2 Mb (6.9 cM). These stocks make it possible to predict the genotype of a plant based on its seed fluorescence (or lack thereof) and facilitate many experiments in genetic analysis that are difficult, tedious, or expensive to perform using current techniques. Here, we show how these lines enable a phenotypic analysis of alleles with weak or variable phenotypes, genetic mapping of novel mutations, introducing transgenes into a lethal or sterile genetic background, and separating closely linked mutations.
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Affiliation(s)
- R Scott Poethig
- Corresponding author: Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA.
| | - William L Cullina
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Erin Doody
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Taré Floyd
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | | | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA,Department of Biological Sciences, University of South Carolina, Charlottesville, SC 29208, USA
| | - Jianfei Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19146, USA
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6
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Schreiber M, Chen YY, Ramsay L, Waugh R. Measuring the frequency and distribution of meiotic crossovers in homozygous barley inbred lines. FRONTIERS IN PLANT SCIENCE 2022; 13:965217. [PMID: 36035701 PMCID: PMC9403744 DOI: 10.3389/fpls.2022.965217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
We report a novel approach for establishing the number and position of CO events in individual homozygous inbred plants by combining low level EMS mutagenesis, speed breeding, whole genome shotgun sequencing and sliding window analysis of the induced molecular variant data. We demonstrate the approach by exploring CO frequency and distribution in self-fertilised progeny of the inbred barley cultivar Bowman and compare these observations to similar data obtained from a Bowman nearly isogenic line (BW230 Hvmlh3) containing a mutation in the DNA mismatch repair gene HvMLH3. We have previously shown that Hvmlh3 decreases both plant fertility and recombination by ~50%. We compare our results to those from previously published traditional genetic analysis of F3 families derived from multiple F2 lines containing WT or mutant alleles of HvMLH3, revealing a high level of correspondence between analyses. We discuss possible applications of the approach in streamlining the assessment of recombination in plant meiosis research.
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Affiliation(s)
- Miriam Schreiber
- Informational and Computational Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Yun-Yu Chen
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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7
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Kim J, Park J, Kim H, Son N, Kim E, Kim J, Byun D, Lee Y, Park YM, Nageswaran DC, Kuo P, Rose T, Dang TVT, Hwang I, Lambing C, Henderson IR, Choi K. Arabidopsis HEAT SHOCK FACTOR BINDING PROTEIN is required to limit meiotic crossovers and HEI10 transcription. EMBO J 2022; 41:e109958. [PMID: 35670129 PMCID: PMC9289711 DOI: 10.15252/embj.2021109958] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023] Open
Abstract
The number of meiotic crossovers is tightly controlled and most depend on pro-crossover ZMM proteins, such as the E3 ligase HEI10. Despite the importance of HEI10 dosage for crossover formation, how HEI10 transcription is controlled remains unexplored. In a forward genetic screen using a fluorescent crossover reporter in Arabidopsis thaliana, we identify heat shock factor binding protein (HSBP) as a repressor of HEI10 transcription and crossover numbers. Using genome-wide crossover mapping and cytogenetics, we show that hsbp mutations or meiotic HSBP knockdowns increase ZMM-dependent crossovers toward the telomeres, mirroring the effects of HEI10 overexpression. Through RNA sequencing, DNA methylome, and chromatin immunoprecipitation analysis, we reveal that HSBP is required to repress HEI10 transcription by binding with heat shock factors (HSFs) at the HEI10 promoter and maintaining DNA methylation over the HEI10 5' untranslated region. Our findings provide insights into how the temperature response regulator HSBP restricts meiotic HEI10 transcription and crossover number by attenuating HSF activity.
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Affiliation(s)
- Juhyun Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Jihye Park
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Heejin Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Namil Son
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Eun‐Jung Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Jaeil Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Dohwan Byun
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Youngkyung Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Yeong Mi Park
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | | | - Pallas Kuo
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Teresa Rose
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | - Tuong Vi T Dang
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Ildoo Hwang
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
| | - Christophe Lambing
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
- Department of Plant SciencesRothamsted ResearchHarpendenUK
| | - Ian R Henderson
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Kyuha Choi
- Department of Life SciencesPohang University of Science and TechnologyPohangKorea
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8
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Lian Q, Solier V, Walkemeier B, Durand S, Huettel B, Schneeberger K, Mercier R. The megabase-scale crossover landscape is largely independent of sequence divergence. Nat Commun 2022; 13:3828. [PMID: 35780220 PMCID: PMC9250513 DOI: 10.1038/s41467-022-31509-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
Meiotic recombination frequency varies along chromosomes and strongly correlates with sequence divergence. However, the causal relationship between recombination landscapes and polymorphisms is unclear. Here, we characterize the genome-wide recombination landscape in the quasi-absence of polymorphisms, using Arabidopsis thaliana homozygous inbred lines in which a few hundred genetic markers were introduced through mutagenesis. We find that megabase-scale recombination landscapes in inbred lines are strikingly similar to the recombination landscapes in hybrids, with the notable exception of heterozygous large rearrangements where recombination is prevented locally. In addition, the megabase-scale recombination landscape can be largely explained by chromatin features. Our results show that polymorphisms are not a major determinant of the shape of the megabase-scale recombination landscape but rather favour alternative models in which recombination and chromatin shape sequence divergence across the genome. The frequency of recombination varies along chromosomes and highly correlates with sequence divergence. Here, the authors show that polymorphisms are not a major determinant of the megabase-scale recombination landscape in Arabidopsis, which is rather determined by chromatin accessibility and DNA methylation.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Victor Solier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stéphanie Durand
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Bruno Huettel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany. .,Faculty of Biology, LMU Munich, 82152, Planegg-Martinsried, Germany.
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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9
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Calvo‐Baltanás V, De Jaeger‐Braet J, Cher WY, Schönbeck N, Chae E, Schnittger A, Wijnker E. Knock-down of gene expression throughout meiosis and pollen formation by virus-induced gene silencing in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:19-37. [PMID: 35340073 PMCID: PMC9543169 DOI: 10.1111/tpj.15733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Through the inactivation of genes that act during meiosis it is possible to direct the genetic make-up of plants in subsequent generations and optimize breeding schemes. Offspring may show higher recombination of parental alleles resulting from elevated crossover (CO) incidence, or by omission of meiotic divisions, offspring may become polyploid. However, stable mutations in genes essential for recombination, or for either one of the two meiotic divisions, can have pleiotropic effects on plant morphology and line stability, for instance by causing lower fertility. Therefore, it is often favorable to temporarily change gene expression during meiosis rather than relying on stable null mutants. It was previously shown that virus-induced gene silencing (VIGS) can be used to transiently reduce CO frequencies. We asked if VIGS could also be used to modify other processes throughout meiosis and during pollen formation in Arabidopsis thaliana. Here, we show that VIGS-mediated knock-down of FIGL1, RECQ4A/B, OSD1 and QRT2 can induce (i) an increase in chiasma numbers, (ii) unreduced gametes and (iii) pollen tetrads. We further show that VIGS can target both sexes and different genetic backgrounds and can simultaneously silence different gene copies. The successful knock-down of these genes in A. thaliana suggests that VIGS can be exploited to manipulate any process during or shortly after meiosis. Hence, the transient induction of changes in inheritance patterns can be used as a powerful tool for applied research and biotechnological applications.
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Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Joke De Jaeger‐Braet
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Wei Yuan Cher
- A*STAR, Institute of Molecular and Cell Biology (IMCB)61 Biopolis DriveProteos138673Singapore
| | - Nils Schönbeck
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- UKEMartinistrasse 5220251HamburgGermany
| | - Eunyoung Chae
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Arp Schnittger
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
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10
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Kim H, Choi K. Fast and Precise: How to Measure Meiotic Crossovers in Arabidopsis. Mol Cells 2022; 45:273-283. [PMID: 35444069 PMCID: PMC9095510 DOI: 10.14348/molcells.2022.2054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/21/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022] Open
Abstract
During meiosis, homologous chromosomes (homologs) pair and undergo genetic recombination via assembly and disassembly of the synaptonemal complex. Meiotic recombination is initiated by excess formation of DNA double-strand breaks (DSBs), among which a subset are repaired by reciprocal genetic exchange, called crossovers (COs). COs generate genetic variations across generations, profoundly affecting genetic diversity and breeding. At least one CO between homologs is essential for the first meiotic chromosome segregation, but generally only one and fewer than three inter-homolog COs occur in plants. CO frequency and distribution are biased along chromosomes, suppressed in centromeres, and controlled by pro-CO, anti-CO, and epigenetic factors. Accurate and high-throughput detection of COs is important for our understanding of CO formation and chromosome behavior. Here, we review advanced approaches that enable precise measurement of the location, frequency, and genomic landscapes of COs in plants, with a focus on Arabidopsis thaliana.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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11
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Histone demethylase IBM1-mediated meiocyte gene expression ensures meiotic chromosome synapsis and recombination. PLoS Genet 2022; 18:e1010041. [PMID: 35192603 PMCID: PMC8896719 DOI: 10.1371/journal.pgen.1010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/04/2022] [Accepted: 01/17/2022] [Indexed: 11/19/2022] Open
Abstract
Histone methylation and demethylation play important roles in plant growth and development, but the involvement of histone demethylation during meiosis is poorly understood. Here we show that disruption of Arabidopsis thaliana INCREASE IN BONSAI METHYLATION 1 (IBM1) causes incomplete synapsis, chromosome entanglement and reduction of recombination during meiosis, leading to sterility. Interestingly, these ibm1 meiotic defects are rescued by mutations in either SUVH4/KYP or CMT3. Using transcriptomic analyses we show that mutation of IBM1 down-regulates thousands of genes expressed in meiocytes, and that expression of about 38% of these genes are restored to wild type levels in ibm1 cmt3 double mutants. Changes in the expression of 437 of these, including the ARABIDOPSIS MEI2-LIKE AML3-5 genes, are correlated with a significant reduction of gene body CHG methylation. Consistently, the aml3 aml4 aml5 triple have defects in synapsis and chromosome entanglement similar to ibm1. Genetic analysis shows that aml3 aml4 aml5 ibm1 quadruple mutants resembles the ibm1 single mutant. Strikingly, over expression of AML5 in ibm1 can partially rescue the ibm1 meiotic defects. Taken together, our results demonstrate that histone demethylase IBM1 is required for meiosis likely via coordinated regulation of meiocyte gene expression during meiosis.
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Kbiri N, Dluzewska J, Henderson IR, Ziolkowski PA. Quantifying Meiotic Crossover Recombination in Arabidopsis Lines Expressing Fluorescent Reporters in Seeds Using SeedScoring Pipeline for CellProfiler. Methods Mol Biol 2022; 2484:121-134. [PMID: 35461449 DOI: 10.1007/978-1-0716-2253-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The number of crossovers during meiosis is relatively low, so multiple meioses need to be analyzed to accurately measure crossover frequency. In Arabidopsis, systems based on the segregation of fluorescent T-DNA reporters that are expressed in seeds (fluorescent-tagged lines, FTLs) allow for an accurate measurement of crossover frequency in specific chromosome regions. A major advantage of FTL-based experiments is the ability to analyze thousands of seeds for each biological replicate, which requires the use of automatic seed scoring. Here, we describe a protocol to computationally count the proportion of seeds that experienced a crossover event within the tested FTL interval and so measure the recombination frequency within that interval. We describe SeedScoring, a CellProfiler pipeline where the total time needed to measure crossover frequency in a single FTL line is approximately 5 min using a series of three images taken under a fluorescent stereomicroscope (3 min) and passing these images through the SeedScoring pipeline described in this protocol (2 min).
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Affiliation(s)
- Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Julia Dluzewska
- 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.
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
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13
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Byun D, Choi K. High-Throughput Fluorescent Pollen Tetrad Analysis Using DeepTetrad. Methods Mol Biol 2022; 2484:277-290. [PMID: 35461458 DOI: 10.1007/978-1-0716-2253-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Meiotic recombination initiates from ~100-200 s of programmed DNA double stranded breaks (DSBs) in plants. Meiotic DSBs can be repaired using homologous chromosomes to generate a crossover . Meiotic crossover is critical for chromosomal segregation and increasing genetic variation. The number of crossovers is limited to one and three per chromosome pair in most plant species. Genetic, epigenetic, and environmental factors control crossover frequency and distribution. Due to the limited number of crossovers it is challenging to measure crossover frequency along chromosomes. We adapted fluorescence-tagged lines (FTLs ) that contain quartet1 mutations and linked transgenes expressing dsRed, eYFP, and eCFP in pollen tetrads into the deep learning-based image analysis tool, DeepTetrad. DeepTetrad enables the measurement of crossover frequency and interference by classifying 12 types of tetrads from three-color FTLs in a high-throughput manner, using conventional microscope instruments and a Linux machine. Here, we provide detailed procedures for preparing tetrad samples, tetrad imaging, running DeepTetrad, and analysis of DeepTetrad outputs. DeepTetrad-based measurements of crossover frequency and interference ratio will accelerate the genetic dissection of meiotic crossover control.
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Affiliation(s)
- Dohwan Byun
- 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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14
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Li X, Zhang J, Huang J, Xu J, Chen Z, Copenhaver GP, Wang Y. Regulation of interference-sensitive crossover distribution ensures crossover assurance in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:e2107543118. [PMID: 34795056 PMCID: PMC8617516 DOI: 10.1073/pnas.2107543118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
During meiosis, crossovers (COs) are typically required to ensure faithful chromosomal segregation. Despite the requirement for at least one CO between each pair of chromosomes, closely spaced double COs are usually underrepresented due to a phenomenon called CO interference. Like Mus musculus and Saccharomyces cerevisiae, Arabidopsis thaliana has both interference-sensitive (Class I) and interference-insensitive (Class II) COs. However, the underlying mechanism controlling CO distribution remains largely elusive. Both AtMUS81 and AtFANCD2 promote the formation of Class II CO. Using both AtHEI10 and AtMLH1 immunostaining, two markers of Class I COs, we show that AtFANCD2 but not AtMUS81 is required for normal Class I CO distribution among chromosomes. Depleting AtFANCD2 leads to a CO distribution pattern that is intermediate between that of wild-type and a Poisson distribution. Moreover, in Atfancm, Atfigl1, and Atrmi1 mutants where increased Class II CO frequency has been reported previously, we observe Class I CO distribution patterns that are strikingly similar to Atfancd2. Surprisingly, we found that AtFANCD2 plays opposite roles in regulating CO frequency in Atfancm compared with either in Atfigl1 or Atrmi1. Together, these results reveal that although AtFANCD2, AtFANCM, AtFIGL1, and AtRMI1 regulate Class II CO frequency by distinct mechanisms, they have similar roles in controlling the distribution of Class I COs among chromosomes.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiyue Huang
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jing Xu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, 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, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China;
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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15
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Natural variation identifies SNI1, the SMC5/6 component, as a modifier of meiotic crossover in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021970118. [PMID: 34385313 PMCID: PMC8379953 DOI: 10.1073/pnas.2021970118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination plays a fundamental role in shaping genetic diversity in eukaryotes. Extensive variation in crossover rate exists between populations and species. The identity of modifier loci and their roles in genome evolution remain incompletely understood. We explored natural variation in Arabidopsis crossover and identified SNI1 as the causal gene underlying a major modifier locus. To date, SNI1 had no known role in crossover. SNI1 is a component of the SMC5/6 complex that is closely related to cohesin and condensin. Arabidopsis sni1 and other SMC5/6 mutants show similar effects on the interference-independent crossover pathway. Hence, our findings demonstrate that the SMC5/6 complex, which is known for its role in DNA damage repair, is also important for control of meiotic crossover. The frequency and distribution of meiotic crossovers are tightly controlled; however, variation in this process can be observed both within and between species. Using crosses of two natural Arabidopsis thaliana accessions, Col and Ler, we mapped a crossover modifier locus to semidominant polymorphisms in SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), which encodes a component of the SMC5/6 complex. The sni1 mutant exhibits a modified pattern of recombination across the genome with crossovers elevated in chromosome distal regions but reduced in pericentromeres. Mutations in SNI1 result in reduced crossover interference and can partially restore the fertility of a Class I crossover pathway mutant, which suggests that the protein affects noninterfering crossover repair. Therefore, we tested genetic interactions between SNI1 and both RECQ4 and FANCM DNA helicases, which showed that additional Class II crossovers observed in the sni1 mutant are FANCM independent. Furthermore, genetic analysis of other SMC5/6 mutants confirms the observations of crossover redistribution made for SNI1. The study reveals the importance of the SMC5/6 complex in ensuring the proper progress of meiotic recombination in plants.
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Kurzbauer MT, Janisiw MP, Paulin LF, Prusén Mota I, Tomanov K, Krsicka O, von Haeseler A, Schubert V, Schlögelhofer P. ATM controls meiotic DNA double-strand break formation and recombination and affects synaptonemal complex organization in plants. THE PLANT CELL 2021; 33:1633-1656. [PMID: 33659989 PMCID: PMC8254504 DOI: 10.1093/plcell/koab045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/29/2021] [Indexed: 05/04/2023]
Abstract
Meiosis is a specialized cell division that gives rise to genetically distinct gametic cells. Meiosis relies on the tightly controlled formation of DNA double-strand breaks (DSBs) and their repair via homologous recombination for correct chromosome segregation. Like all forms of DNA damage, meiotic DSBs are potentially harmful and their formation activates an elaborate response to inhibit excessive DNA break formation and ensure successful repair. Previous studies established the protein kinase ATM as a DSB sensor and meiotic regulator in several organisms. Here we show that Arabidopsis ATM acts at multiple steps during DSB formation and processing, as well as crossover (CO) formation and synaptonemal complex (SC) organization, all vital for the successful completion of meiosis. We developed a single-molecule approach to quantify meiotic breaks and determined that ATM is essential to limit the number of meiotic DSBs. Local and genome-wide recombination screens showed that ATM restricts the number of interference-insensitive COs, while super-resolution STED nanoscopy of meiotic chromosomes revealed that the kinase affects chromatin loop size and SC length and width. Our study extends our understanding of how ATM functions during plant meiosis and establishes it as an integral factor of the meiotic program.
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Affiliation(s)
- Marie-Therese Kurzbauer
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Michael Peter Janisiw
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Luis F Paulin
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Ignacio Prusén Mota
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Konstantin Tomanov
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Ondrej Krsicka
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
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17
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Ahn YJ, Fuchs J, Houben A, Heckmann S. High-throughput measuring of meiotic recombination rates in barley pollen nuclei using Crystal Digital PCR TM. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:649-661. [PMID: 33949030 DOI: 10.1111/tpj.15305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Breeding exploits novel allelic combinations assured by meiotic recombination. Barley (Hordeum vulgare) single pollen nucleus genotyping enables measurement of meiotic recombination rates in gametes before fertilization without the need for segregating populations. However, so far, established methods rely on whole-genome amplification of every single pollen nucleus due to their limited DNA content, thus restricting the number of analyzed samples. In this study, high-throughput measurements of meiotic recombination rates in barley pollen nuclei without whole-genome amplification were performed through a Crystal Digital PCRTM -based genotyping assay. Meiotic recombination rates within two centromeric and two distal chromosomal intervals were measured in hybrid plants by genotyping a total of >42 000 individual pollen nuclei (up to 4900 nuclei analyzed per plant). Determined recombination frequencies in pollen nuclei were similar to frequencies in segregating populations. We improved the efficiency of the genotyping by pretreating the pollen nuclei with a thermostable restriction enzyme. Additional opportunities for a higher sample throughput and a further increase of the genotyping efficiency are presented and discussed. Taken together, single barley pollen nucleus genotyping based on Crystal Digital PCRTM enables reliable, rapid and high-throughput meiotic recombination measurements within defined chromosomal intervals of intraspecific hybrid plants. The successful encapsulation of nuclei from a range of species with different nuclear and genome sizes suggests that the proposed method is broadly applicable to genotyping single nuclei.
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Affiliation(s)
- Yun-Jae Ahn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, Stadt Seeland, 06466, Germany
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18
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Hernandez Sanchez-Rebato M, Bouatta AM, Gallego ME, White CI, Da Ines O. RAD54 is essential for RAD51-mediated repair of meiotic DSB in Arabidopsis. PLoS Genet 2021; 17:e1008919. [PMID: 34003859 PMCID: PMC8162660 DOI: 10.1371/journal.pgen.1008919] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 05/28/2021] [Accepted: 05/03/2021] [Indexed: 12/17/2022] Open
Abstract
An essential component of the homologous recombination machinery in eukaryotes, the RAD54 protein is a member of the SWI2/SNF2 family of helicases with dsDNA-dependent ATPase, DNA translocase, DNA supercoiling and chromatin remodelling activities. It is a motor protein that translocates along dsDNA and performs multiple functions in homologous recombination. In particular, RAD54 is an essential cofactor for regulating RAD51 activity. It stabilizes the RAD51 nucleofilament, remodels nucleosomes, and stimulates the homology search and strand invasion activities of RAD51. Accordingly, deletion of RAD54 has dramatic consequences on DNA damage repair in mitotic cells. In contrast, its role in meiotic recombination is less clear. RAD54 is essential for meiotic recombination in Drosophila and C. elegans, but plays minor roles in yeast and mammals. We present here characterization of the roles of RAD54 in meiotic recombination in the model plant Arabidopsis thaliana. Absence of RAD54 has no detectable effect on meiotic recombination in otherwise wild-type plants but RAD54 becomes essential for meiotic DSB repair in absence of DMC1. In Arabidopsis, dmc1 mutants have an achiasmate meiosis, in which RAD51 repairs meiotic DSBs. Lack of RAD54 leads to meiotic chromosomal fragmentation in absence of DMC1. The action of RAD54 in meiotic RAD51 activity is thus mainly downstream of the role of RAD51 in supporting the activity of DMC1. Equivalent analyses show no effect on meiosis of combining dmc1 with the mutants of the RAD51-mediators RAD51B, RAD51D and XRCC2. RAD54 is thus required for repair of meiotic DSBs by RAD51 and the absence of meiotic phenotype in rad54 plants is a consequence of RAD51 playing a RAD54-independent supporting role to DMC1 in meiotic recombination. Homologous recombination is a universal pathway which repairs broken DNA molecules through the use of homologous DNA templates. It is both essential for maintenance of genome stability and for the generation of genetic diversity through sexual reproduction. A central step of the homologous recombination process is the search for and invasion of a homologous, intact DNA sequence that will be used as template. This key step is catalysed by the RAD51 recombinase in somatic cells and RAD51 and DMC1 in meiotic cells, assisted by a number of associated factors. Among these, the chromatin-remodelling protein RAD54 is a required cofactor for RAD51 in mitotic cells. Understanding of its role during meiotic recombination however remains elusive. We show here that RAD54 is required for repair of meiotic double strand breaks by RAD51 in the plant Arabidopsis thaliana, and this function is downstream of the meiotic role of RAD51 in supporting the activity of DMC1. These results provide new insights into the regulation of the central step of homologous recombination in plants and very probably also other multicellular eukaryotes.
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Affiliation(s)
- Miguel Hernandez Sanchez-Rebato
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Alida M Bouatta
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Maria E Gallego
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Charles I White
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
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19
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Cuacos M, Lambing C, Pachon-Penalba M, Osman K, Armstrong SJ, Henderson IR, Sanchez-Moran E, Franklin FCH, Heckmann S. Meiotic chromosome axis remodelling is critical for meiotic recombination in Brassica rapa. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3012-3027. [PMID: 33502451 PMCID: PMC8023211 DOI: 10.1093/jxb/erab035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/21/2021] [Indexed: 05/23/2023]
Abstract
Meiosis generates genetic variation through homologous recombination (HR) that is harnessed during breeding. HR occurs in the context of meiotic chromosome axes and the synaptonemal complex. To study the role of axis remodelling in crossover (CO) formation in a crop species, we characterized mutants of the axis-associated protein ASY1 and the axis-remodelling protein PCH2 in Brassica rapa. asy1 plants form meiotic chromosome axes that fail to synapse. CO formation is almost abolished, and residual chiasmata are proportionally enriched in terminal chromosome regions, particularly in the nucleolar organizing region (NOR)-carrying chromosome arm. pch2 plants show impaired ASY1 loading and remodelling, consequently achieving only partial synapsis, which leads to reduced CO formation and loss of the obligatory CO. PCH2-independent chiasmata are proportionally enriched towards distal chromosome regions. Similarly, in Arabidopsis pch2, COs are increased towards telomeric regions at the expense of (peri-) centromeric COs compared with the wild type. Taken together, in B. rapa, axis formation and remodelling are critical for meiotic fidelity including synapsis and CO formation, and in asy1 and pch2 CO distributions are altered. While asy1 plants are sterile, pch2 plants are semi-sterile and thus PCH2 could be an interesting target for breeding programmes.
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Affiliation(s)
- Maria Cuacos
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, D-06466 Seeland, Germany
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Susan J Armstrong
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | | | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, D-06466 Seeland, Germany
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20
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Nageswaran DC, Kim J, Lambing C, Kim J, Park J, Kim EJ, Cho HS, Kim H, Byun D, Park YM, Kuo P, Lee S, Tock AJ, Zhao X, Hwang I, Choi K, Henderson IR. HIGH CROSSOVER RATE1 encodes PROTEIN PHOSPHATASE X1 and restricts meiotic crossovers in Arabidopsis. NATURE PLANTS 2021; 7:452-467. [PMID: 33846593 PMCID: PMC7610654 DOI: 10.1038/s41477-021-00889-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/25/2021] [Indexed: 05/19/2023]
Abstract
Meiotic crossovers are tightly restricted in most eukaryotes, despite an excess of initiating DNA double-strand breaks. The majority of plant crossovers are dependent on class I interfering repair, with a minority formed via the class II pathway. Class II repair is limited by anti-recombination pathways; however, similar pathways repressing class I crossovers have not been identified. Here, we performed a forward genetic screen in Arabidopsis using fluorescent crossover reporters to identify mutants with increased or decreased recombination frequency. We identified HIGH CROSSOVER RATE1 (HCR1) as repressing crossovers and encoding PROTEIN PHOSPHATASE X1. Genome-wide analysis showed that hcr1 crossovers are increased in the distal chromosome arms. MLH1 foci significantly increase in hcr1 and crossover interference decreases, demonstrating an effect on class I repair. Consistently, yeast two-hybrid and in planta assays show interaction between HCR1 and class I proteins, including HEI10, PTD, MSH5 and MLH1. We propose that HCR1 plays a major role in opposition to pro-recombination kinases to restrict crossovers in Arabidopsis.
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Affiliation(s)
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | | | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jihye Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Eun-Jung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dohwan Byun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yeong Mi Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Seungchul Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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21
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ZYP1 is required for obligate cross-over formation and cross-over interference in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021671118. [PMID: 33782125 PMCID: PMC8040812 DOI: 10.1073/pnas.2021671118] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The synaptonemal complex (SC) is a meiosis-specific proteinaceous ultrastructure required to ensure cross-over (CO) formation in the majority of sexually reproducing eukaryotes. It is composed of two lateral elements adjoined by transverse filaments. Even though the general structure of the SC is conserved throughout kingdoms, phenotypic differences between mutants perpetuate the enigmatic role of the SC. Here, we have used genetic and cytogenetic approaches to show that the transverse filament protein, ZYP1, acts on multiple pathways of meiotic recombination in Arabidopsis. ZYP1 is required for CO assurance, thus ensuring that every chromosome pair receives at least one CO. ZYP1 limits the number of COs and mediates CO interference, the phenomenon that reduces the probability of multiple COs forming close together. The synaptonemal complex is a tripartite proteinaceous ultrastructure that forms between homologous chromosomes during prophase I of meiosis in the majority of eukaryotes. It is characterized by the coordinated installation of transverse filament proteins between two lateral elements and is required for wild-type levels of crossing over and meiotic progression. We have generated null mutants of the duplicated Arabidopsis transverse filament genes zyp1a and zyp1b using a combination of T-DNA insertional mutants and targeted CRISPR/Cas mutagenesis. Cytological and genetic analysis of the zyp1 null mutants reveals loss of the obligate chiasma, an increase in recombination map length by 1.3- to 1.7-fold and a virtual absence of cross-over (CO) interference, determined by a significant increase in the number of double COs. At diplotene, the numbers of HEI10 foci, a marker for Class I interference-sensitive COs, are twofold greater in the zyp1 mutant compared to wild type. The increase in recombination in zyp1 does not appear to be due to the Class II interference-insensitive COs as chiasmata were reduced by ∼52% in msh5/zyp1 compared to msh5. These data suggest that ZYP1 limits the formation of closely spaced Class I COs in Arabidopsis. Our data indicate that installation of ZYP1 occurs at ASY1-labeled axial bridges and that loss of the protein disrupts progressive coalignment of the chromosome axes.
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22
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Ferreira MTM, Glombik M, Perničková K, Duchoslav M, Scholten O, Karafiátová M, Techio VH, Doležel J, Lukaszewski AJ, Kopecký D. Direct evidence for crossover and chromatid interference in meiosis of two plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei). JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:254-267. [PMID: 33029645 PMCID: PMC7853598 DOI: 10.1093/jxb/eraa455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 05/02/2023]
Abstract
Crossing over, in addition to its strictly genetic role, also performs a critical mechanical function, by bonding homologues in meiosis. Hence, it is responsible for an orderly reduction of the chromosome number. As such, it is strictly controlled in frequency and distribution. The well-known crossover control is positive crossover interference which reduces the probability of a crossover in the vicinity of an already formed crossover. A poorly studied aspect of the control is chromatid interference. Such analyses are possible in very few organisms as they require observation of all four products of a single meiosis. Here, we provide direct evidence of chromatid interference. Using in situ probing in two interspecific plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei) during anaphase I, we demonstrate that the involvement of four chromatids in double crossovers is significantly more frequent than expected (64% versus 25%). We also provide a physical measure of the crossover interference distance, covering ~30-40% of the relative chromosome arm length, and show that the centromere acts as a barrier for crossover interference. The two arms of a chromosome appear to act as independent units in the process of crossing over. Chromatid interference has to be seriously addressed in genetic mapping approaches and further studies.
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Affiliation(s)
- Marco Tulio Mendes Ferreira
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Department of Biology, Federal University of Lavras, Lavras-MG, Brazil
| | - Marek Glombik
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska, Brno, Czech Republic
| | - Kateřina Perničková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska, Brno, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Olga Scholten
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Correspondence:
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Abstract
Visualization of meiotic chromatin from pollen mother cells has become an essential technique to study meiosis in the model plant Arabidopsis thaliana. Here we present an advanced cytogenetic method that combines improved immunocytology with chromosome painting, thereby generating a tool to quantitatively analyze localization of proteins to any given genomic region. Proteins involved in different processes such as DNA double-strand break formation and recombinational repair can be visualized on meiotic chromatin with the additional feature of assessing their abundance at specific chromosomal locations.
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Affiliation(s)
- Jason Sims
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota St. Paul, St. Paul, MN, USA
| | - Peter Schlögelhofer
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Marie-Therese Kurzbauer
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria.
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24
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Gratias A, Geffroy V. Deciphering the Impact of a Bacterial Infection on Meiotic Recombination in Arabidopsis with Fluorescence Tagged Lines. Genes (Basel) 2020; 11:genes11070832. [PMID: 32708324 PMCID: PMC7397157 DOI: 10.3390/genes11070832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
Plants are under strong evolutionary pressure to maintain surveillance against pathogens. One major disease resistance mechanism is based on NB-LRR (NLR) proteins that specifically recognize pathogen effectors. The cluster organization of the NLR gene family could favor sequence exchange between NLR genes via recombination, favoring their evolutionary dynamics. Increasing data, based on progeny analysis, suggest the existence of a link between the perception of biotic stress and the production of genetic diversity in the offspring. This could be driven by an increased rate of meiotic recombination in infected plants, but this has never been strictly demonstrated. In order to test if pathogen infection can increase DNA recombination in pollen meiotic cells, we infected Arabidopsis Fluorescent Tagged Lines (FTL) with the virulent bacteria Pseudomonas syringae. We measured the meiotic recombination rate in two regions of chromosome 5, containing or not an NLR gene cluster. In all tested intervals, no significant difference in genetic recombination frequency between infected and control plants was observed. Although it has been reported that pathogen exposure can sometimes increase the frequency of recombinant progeny in plants, our findings suggest that meiotic recombination rate in Arabidopsis may be resilient to at least some pathogen attack. Alternative mechanisms are discussed.
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Affiliation(s)
- Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, 91405 Orsay, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
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25
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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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26
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De Storme N, Geelen D. High temperatures alter cross-over distribution and induce male meiotic restitution in Arabidopsis thaliana. Commun Biol 2020; 3:187. [PMID: 32327690 PMCID: PMC7181631 DOI: 10.1038/s42003-020-0897-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 03/16/2020] [Indexed: 12/03/2022] Open
Abstract
Plant fertility is highly sensitive to elevated temperature. Here, we report that hot spells induce the formation of dyads and triads by disrupting the biogenesis or stability of the radial microtubule arrays (RMAs) at telophase II. Heat-induced meiotic restitution in Arabidopsis is predominantly SDR-type (Second Division Restitution) indicating specific interference with RMAs formed between separated sister chromatids. In addition, elevated temperatures caused distinct deviations in cross-over formation in male meiosis. Synapsis at pachytene was impaired and the obligate cross-over per chromosome was discarded, resulting in partial univalency in meiosis I (MI). At diakinesis, interconnections between non-homologous chromosomes tied separate bivalents together, suggesting heat induces ectopic events of non-homologous recombination. Summarized, heat interferes with male meiotic cross-over designation and cell wall formation, providing a mechanistic basis for plant karyotype change and genome evolution under high temperature conditions. de Storme and Geelen show that heat stress has pleiotropic effects on male meiosis in Arabidopsis, causing deviations in cross-over formations, reproduction, and fertility. They show that heat also affects cell wall formation, providing mechanistic insights into karyotype change under high temperatures.
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Affiliation(s)
- Nico De Storme
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University (UGent), Coupure Links 653, 9000, Ghent, Belgium.,Laboratory for Plant Genetics and Crop Improvement (PGCI), Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001, Heverlee, Leuven, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University (UGent), Coupure Links 653, 9000, Ghent, Belgium.
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27
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Lim EC, Kim J, Park J, Kim EJ, Kim J, Park YM, Cho HS, Byun D, Henderson IR, Copenhaver GP, Hwang I, Choi K. DeepTetrad: high-throughput image analysis of meiotic tetrads by deep learning in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:473-483. [PMID: 31536659 DOI: 10.1111/tpj.14543] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/03/2019] [Accepted: 09/09/2019] [Indexed: 06/10/2023]
Abstract
Meiotic crossovers facilitate chromosome segregation and create new combinations of alleles in gametes. Crossover frequency varies along chromosomes and crossover interference limits the coincidence of closely spaced crossovers. Crossovers can be measured by observing the inheritance of linked transgenes expressing different colors of fluorescent protein in Arabidopsis pollen tetrads. Here we establish DeepTetrad, a deep learning-based image recognition package for pollen tetrad analysis that enables high-throughput measurements of crossover frequency and interference in individual plants. DeepTetrad will accelerate the genetic dissection of mechanisms that control meiotic recombination.
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Affiliation(s)
- Eun-Cheon Lim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Jihye Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Eun-Jung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Yeong Mi Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Dohwan Byun
- 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, CB2 3EA, UK
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ildoo Hwang
- 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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28
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Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Curr Biol 2019; 29:2676-2686.e3. [PMID: 31378616 DOI: 10.1016/j.cub.2019.06.084] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Abstract
Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.
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Affiliation(s)
- Emma J Lawrence
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Hongbo Gao
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Andrew J Tock
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Christophe Lambing
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Alexander R Blackwell
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
| | - Ian R Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK.
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29
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Bolaños-Villegas P, Xu W, Martínez-García M, Pradillo M, Wang Y. Insights Into the Role of Ubiquitination in Meiosis: Fertility, Adaptation and Plant Breeding. THE ARABIDOPSIS BOOK 2018; 16:e0187. [PMID: 31068764 PMCID: PMC6501859 DOI: 10.1199/tab.0187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Ubiquitination is a post-translational modification process that plays a central role in protein degradation in eukaryotic cell cell division, including meiosis. This modification affects different cellular processes on a global scale by its pleiotropic ability to modify numerous proteins. Meiosis is essential for sexual reproduction and involves two rounds of nuclear division following a single round of DNA replication to produce haploid gametes. Unlike mitosis, meiosis has a unique prophase I, which involves homologous chromosome interaction including pairing, synapsis, recombination and segregation. Over the last several decades, molecular genetic studies have identified many proteins that participate in meiotic progression. In this review, we focus on the recent advances regarding the role of ubiquitination during plant meiotic cell cycle progression and recombination, especially the role played by the Anaphase-Promoting Complex and E3 ligases in modulating crossover formation and its impact on evolution and plant breeding.
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Affiliation(s)
- Pablo Bolaños-Villegas
- Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela 20102, Costa Rica
| | - Wanyue Xu
- 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
| | - Marina Martínez-García
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States of America
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Universidad Complutense, C/José Antonio Novais, 12, Madrid 28040, Spain
| | - 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
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30
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Gohar M, Gäbelein R, Mason AS. A quartet pollen phenotype identified in a population of Brassica interspecific hybrids shows incomplete penetrance and variable response to temperature. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:894-901. [PMID: 29883021 DOI: 10.1111/plb.12854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/03/2018] [Indexed: 06/08/2023]
Abstract
Quartet pollen, where pollen grains remain attached to each other post-meiosis, is useful for tetrad analysis, crossover assessment and centromere mapping. We observed the quartet pollen phenotype for the first time in the agriculturally significant Brassica genus, in an experimental population of allohexaploid Brassica hybrids derived from the cross (Brassica napus × B. carinata) × B. juncea followed by two self-pollination generations. Quartet pollen production was assessed in 144 genotypes under glasshouse conditions, following which a set of 16 genotypes were selected to further investigate the effect of environment (warm: 25 °C and cold: 10 °C temperatures) on quartet pollen production in growth cabinets. Under glasshouse phenotyping conditions, only 92 out of 144 genotypes produced enough pollen to score: of these, 30 did not produce any observable quartet pollen, while 62 genotypes produced quartet pollen at varying frequencies. Quartet pollen production appeared quantitative and did not clearly fall into phenotypic or qualitative categories indicative of major gene expression. No consistent effect of temperature on quartet pollen production was identified, with some genotypes producing more and some producing less quartet pollen under different temperature treatments. The genetic heterogeneity and frequent pollen infertility of this population prevents strong conclusions being made. However, it is clear that the quartet phenotype in this Brassica population does not show complete penetrance and shows variable (likely genotype-specific) response to temperature stress. In future, identification of quartet phenotypes in Brassica would perhaps best be carried out via screening of diploid (e.g. B. rapa) TILLING populations.
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Affiliation(s)
- M Gohar
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - R Gäbelein
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - A S Mason
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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31
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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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32
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Fernandes JB, Duhamel M, Seguéla-Arnaud M, Froger N, Girard C, Choinard S, Solier V, De Winne N, De Jaeger G, Gevaert K, Andrey P, Grelon M, Guerois R, Kumar R, Mercier R. FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination. PLoS Genet 2018; 14:e1007317. [PMID: 29608566 PMCID: PMC5897033 DOI: 10.1371/journal.pgen.1007317] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 04/12/2018] [Accepted: 03/19/2018] [Indexed: 02/07/2023] Open
Abstract
Homologous recombination is central to repair DNA double-strand breaks, either accidently arising in mitotic cells or in a programed manner at meiosis. Crossovers resulting from the repair of meiotic breaks are essential for proper chromosome segregation and increase genetic diversity of the progeny. However, mechanisms regulating crossover formation remain elusive. Here, we identified through genetic and protein-protein interaction screens FIDGETIN-LIKE-1 INTERACTING PROTEIN (FLIP) as a new partner of the previously characterized anti-crossover factor FIDGETIN-LIKE-1 (FIGL1) in Arabidopsis thaliana. We showed that FLIP limits meiotic crossover together with FIGL1. Further, FLIP and FIGL1 form a protein complex conserved from Arabidopsis to human. FIGL1 interacts with the recombinases RAD51 and DMC1, the enzymes that catalyze the DNA strand exchange step of homologous recombination. Arabidopsis flip mutants recapitulate the figl1 phenotype, with enhanced meiotic recombination associated with change in counts of DMC1 and RAD51 foci. Our data thus suggests that FLIP and FIGL1 form a conserved complex that regulates the crucial step of strand invasion in homologous recombination. Homologous recombination is a DNA repair mechanism that is essential to preserve the integrity of genetic information and thus to prevent cancer formation. Homologous recombination is also used during sexual reproduction to generate genetic diversity in the offspring by shuffling parental chromosomes. Here, we identified a novel protein complex (FLIP-FIGL1) that regulates homologous recombination and is conserved from plants to mammals. This suggests the existence of a novel mode of regulation at a central step of homologous recombination.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
- Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Marine Duhamel
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Mathilde Seguéla-Arnaud
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Nicole Froger
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Chloé Girard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Sandrine Choinard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Victor Solier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, CEA-Saclay, Gif-sur-Yvette, France
| | - Rajeev Kumar
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
- * E-mail: (RK); (RM)
| | - Raphaël Mercier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, RD10,Versailles, France
- * E-mail: (RK); (RM)
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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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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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35
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Raffoux X, Bourge M, Dumas F, Martin OC, Falque M. High-throughput measurement of recombination rates and genetic interference in Saccharomyces cerevisiae. Yeast 2018; 35:431-442. [PMID: 29577404 DOI: 10.1002/yea.3315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 01/23/2023] Open
Abstract
Allelic recombination owing to meiotic crossovers is a major driver of genome evolution, as well as a key player for the selection of high-performing genotypes in economically important species. Therefore, we developed a high-throughput and low-cost method to measure recombination rates and crossover patterning (including interference) in large populations of the budding yeast Saccharomyces cerevisiae. Recombination and interference were analysed by flow cytometry, which allows time-consuming steps such as tetrad microdissection or spore growth to be avoided. Moreover, our method can also be used to compare recombination in wild-type vs. mutant individuals or in different environmental conditions, even if the changes in recombination rates are small. Furthermore, meiotic mutants often present recombination and/or pairing defects affecting spore viability but our method does not involve growth steps and thus avoids filtering out non-viable spores.
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Affiliation(s)
- Xavier Raffoux
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mickael Bourge
- Cytometry/Electronic Microscopy/Light Microcopy Facility, Imagerie-Gif, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Fabrice Dumas
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier C Martin
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Matthieu Falque
- GQE- Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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36
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Fernandes JB, Séguéla-Arnaud M, Larchevêque C, Lloyd AH, Mercier R. Unleashing meiotic crossovers in hybrid plants. Proc Natl Acad Sci U S A 2018; 115:2431-2436. [PMID: 29183972 DOI: 10.1101/159640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in recq4 figl1 (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in recq4 figl1 hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Andrew H Lloyd
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France;
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37
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Fernandes JB, Séguéla-Arnaud M, Larchevêque C, Lloyd AH, Mercier R. Unleashing meiotic crossovers in hybrid plants. Proc Natl Acad Sci U S A 2018; 115:2431-2436. [PMID: 29183972 PMCID: PMC5877974 DOI: 10.1073/pnas.1713078114] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713-4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in recq4 figl1 (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in recq4 figl1 hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
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Affiliation(s)
- Joiselle Blanche Fernandes
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Andrew H Lloyd
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France;
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38
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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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39
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Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
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40
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Liu B, De Storme N, Geelen D. Cold-Induced Male Meiotic Restitution in Arabidopsis thaliana Is Not Mediated by GA-DELLA Signaling. FRONTIERS IN PLANT SCIENCE 2018; 9:91. [PMID: 29459879 PMCID: PMC5807348 DOI: 10.3389/fpls.2018.00091] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/17/2018] [Indexed: 05/20/2023]
Abstract
Short periods of cold stress induce male meiotic restitution and diploid pollen formation in Arabidopsis thaliana by specifically interfering with male meiotic cytokinesis. Similar alterations in male meiotic cell division and gametophytic ploidy stability occur when gibberellic acid (GA) signaling is perturbed in developing anthers. In this study, we found that exogenous application of GA primarily induces second division restitution (SDR)-type pollen in Arabidopsis, similar to what cold does. Driven by the close similarity in cellular defects, we tested the hypothesis that cold-induced meiotic restitution is mediated by GA-DELLA signaling. Using a combination of chemical, genetic and cytological approaches, however, we found that both exogenously and endogenously altered GA signaling do not affect the cold sensitivity of male meiotic cytokinesis. Moreover, in vivo localization study using a GFP-tagged version of RGA protein revealed that cold does not affect the expression pattern and abundance of DELLA in Arabidopsis anthers at tetrad stage. Expression study found that transcript of RGA appears enhanced in cold-stressed young flower buds. Since our previous work demonstrated that loss of function of DELLA causes irregular male meiotic cytokinesis, we here conclude that cold-induced meiotic restitution is not mediated by DELLA-dependent GA signaling.
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Affiliation(s)
- Bing Liu
- Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Nico De Storme
- Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium
| | - Danny Geelen
- Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium
- *Correspondence: Danny Geelen,
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41
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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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42
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Séguéla-Arnaud M, Choinard S, Larchevêque C, Girard C, Froger N, Crismani W, Mercier R. RMI1 and TOP3α limit meiotic CO formation through their C-terminal domains. Nucleic Acids Res 2017; 45:1860-1871. [PMID: 27965412 PMCID: PMC5389728 DOI: 10.1093/nar/gkw1210] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/23/2016] [Indexed: 01/04/2023] Open
Abstract
At meiosis, hundreds of programmed DNA double-strand breaks (DSBs) form and are repaired by homologous recombination. From this large number of DSBs, only a subset yields crossovers (COs), with a minimum of one CO per chromosome pair. All DSBs must be repaired and every recombination intermediate must be resolved to avoid subsequent entanglement and chromosome breakage. The conserved BLM-TOP3α-RMI1 (BTR) complex acts on early and late meiotic recombination intermediates to both limit CO outcome and promote chromosome integrity. In Arabidopsis, the BLM homologues RECQ4A and RECQ4B act redundantly to prevent meiotic extra COs, but recombination intermediates are fully resolved in their absence. In contrast, TOP3α is needed for both processes. Here we show through the characterization of specific mutants that RMI1 is a major anti-CO factor, in addition to being essential to prevent chromosome breakage and entanglement. Further, our findings suggest a specific role of the C-terminal domains of RMI1 and TOP3α, that respectively contain an Oligo Binding domain (OB2) and ZINC finger motifs, in preventing extra-CO. We propose that these domains of TOP3α and RMI1 define a sub-domain of the BTR complex which is dispensable for the resolution of recombination intermediates but crucial to limit extra-COs.
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Affiliation(s)
- Mathilde Séguéla-Arnaud
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Sandrine Choinard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Cécile Larchevêque
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Chloé Girard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Nicole Froger
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Wayne Crismani
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France
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Singh G, Da Ines O, Gallego ME, White CI. Analysis of the impact of the absence of RAD51 strand exchange activity in Arabidopsis meiosis. PLoS One 2017; 12:e0183006. [PMID: 28797117 PMCID: PMC5552350 DOI: 10.1371/journal.pone.0183006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/27/2017] [Indexed: 11/21/2022] Open
Abstract
The ploidy of eukaryote gametes must be halved to avoid doubling of numbers of chromosomes with each generation and this is carried out by meiosis, a specialized cell division in which a single chromosomal replication phase is followed by two successive nuclear divisions. With some exceptions, programmed recombination ensures the proper pairing and distribution of homologous pairs of chromosomes in meiosis and recombination defects thus lead to sterility. Two highly related recombinases are required to catalyse the key strand-invasion step of meiotic recombination and it is the meiosis-specific DMC1 which is generally believed to catalyse the essential non-sister chromatid crossing-over, with RAD51 catalysing sister-chromatid and non-cross-over events. Recent work in yeast and plants has however shown that in the absence of RAD51 strand-exchange activity, DMC1 is able to repair all meiotic DNA breaks and surprisingly, that this does not appear to affect numbers of meiotic cross-overs. In this work we confirm and extend this conclusion. Given that more than 95% of meiotic homologous recombination in Arabidopsis does not result in inter-homologue crossovers, Arabidopsis is a particularly sensitive model for testing the relative importance of the two proteins-even minor effects on the non-crossover event population should produce detectable effects on crossing-over. Although the presence of RAD51 protein provides essential support for the action of DMC1, our results show no significant effect of the absence of RAD51 strand-exchange activity on meiotic crossing-over rates or patterns in different chromosomal regions or across the whole genome of Arabidopsis, strongly supporting the argument that DMC1 catalyses repair of all meiotic DNA breaks, not only non-sister cross-overs.
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Affiliation(s)
- Gunjita Singh
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Olivier Da Ines
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Charles I. White
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
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Arabidopsis RAD51, RAD51C and XRCC3 proteins form a complex and facilitate RAD51 localization on chromosomes for meiotic recombination. PLoS Genet 2017; 13:e1006827. [PMID: 28562599 PMCID: PMC5470734 DOI: 10.1371/journal.pgen.1006827] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/14/2017] [Accepted: 05/17/2017] [Indexed: 11/22/2022] Open
Abstract
Meiotic recombination is required for proper homologous chromosome segregation in plants and other eukaryotes. The eukaryotic RAD51 gene family has seven ancient paralogs with important roles in mitotic and meiotic recombination. Mutations in mammalian RAD51 homologs RAD51C and XRCC3 lead to embryonic lethality. In the model plant Arabidopsis thaliana, RAD51C and XRCC3 homologs are not essential for vegetative development but are each required for somatic and meiotic recombination, but the mechanism of RAD51C and XRCC3 in meiotic recombination is unclear. The non-lethal Arabidopsis rad51c and xrcc3 null mutants provide an opportunity to study their meiotic functions. Here, we show that AtRAD51C and AtXRCC3 are components of the RAD51-dependent meiotic recombination pathway and required for normal AtRAD51 localization on meiotic chromosomes. In addition, AtRAD51C interacts with both AtRAD51 and AtXRCC3 in vitro and in vivo, suggesting that these proteins form a complex (es). Comparison of AtRAD51 foci in meiocytes from atrad51, atrad51c, and atxrcc3 single, double and triple heterozygous mutants further supports an interaction between AtRAD51C and AtXRCC3 that enhances AtRAD51 localization. Moreover, atrad51c-/+atxrcc3-/+ double and atrad51-/+atrad51c-/+atxrcc3-/+ triple heterozygous mutants have defects in meiotic recombination, suggesting the role of the AtRAD51C-AtXRCC3 complex in meiotic recombination is in part AtRAD51-dependent. Together, our results support a model in which direct interactions between the RAD51C-XRCC3 complex and RAD51 facilitate RAD51 localization on meiotic chromosomes and RAD51-dependent meiotic recombination. Finally, we hypothesize that maintenance of RAD51 function facilitated by the RAD51C-XRCC3 complex could be highly conserved in eukaryotes. Meiotic recombination and sister chromatid cohesion are important for maintaining the association between homologous chromosomes and ensuring their accurate segregation. Meiotic recombination starts with a set of programmed DNA double-strand breaks (DSBs), catalyzed by the SPO11 endonuclease. Processing of DSB ends produces 3′ single-stranded DNA tails, which form nucleoprotein filaments with RAD51 and DMC1, homologs of the prokaryotic RecA protein. The eukaryotic RAD51 gene family has seven ancient paralogs, in addition to RAD51 and DMC1, the other five members in mammals form two complexes: RAD51B-RAD51C-RAD51D- XRCC2 (BCDX2) and RAD51C-XRCC3 (CX3). To date, the molecular mechanism of CX3 in animal meiosis remains largely unknown due to the essential roles of these two proteins in embryo development. In Arabidopsis, RAD51C and XRCC3 are required for meiosis and fertility, but their specific mechanisms are unclear. Here we present strong evidence that Arabidopsis RAD51 forms a protein complex with AtRAD51C-AtXRCC3 in vivo. Our data also support the previous hypothesis that CX3 promotes RAD51-denpendet meiotic recombination by affecting its localization on chromosomes. Given that the RAD51, RAD51C and XRCC3 proteins are highly conserved in plants and vertebrates, the mechanism we present here could be important for the regulation of meiotic recombination in both plants and vertebrate animals.
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Variation in Recombination Rate: Adaptive or Not? Trends Genet 2017; 33:364-374. [DOI: 10.1016/j.tig.2017.03.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 01/30/2023]
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Li F, De Storme N, Geelen D. Dynamics of male meiotic recombination frequency during plant development using Fluorescent Tagged Lines in Arabidopsis thaliana. Sci Rep 2017; 7:42535. [PMID: 28211906 PMCID: PMC5304153 DOI: 10.1038/srep42535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/10/2017] [Indexed: 12/11/2022] Open
Abstract
Meiotic homologous recombination plays a central role in creating genetic variability, making it an essential biological process relevant to evolution and crop breeding. In this study, we used pollen-specific fluorescent tagged lines (FTLs) to measure male meiotic recombination frequency during the development of Arabidopsis thaliana. Interestingly, a subset of pollen grains consistently shows loss of fluorescence expression in tested lines. Using nine independent FTL intervals, the spatio-temporal dynamics of male recombination frequency was assessed during plant development, considering both shoot type and plant age as independent parameters. In most genomic intervals assayed, male meiotic recombination frequency is highly consistent during plant development, showing no significant change between different shoot types and during plant aging. However, in some genomic regions, such as I1a and I5a, a small but significant effect of either developmental position or plant age were observed, indicating that the meiotic CO frequency in those intervals varies during plant development. Furthermore, from an overall view of all nine genomic intervals assayed, both primary and tertiary shoots show a similar dynamics of increasing recombination frequency during development, while secondary and lateral shoots remain highly stable. Our results provide new insights in the dynamics of male meiotic recombination frequency during plant development.
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Affiliation(s)
- Fan Li
- In vitroBiology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Nico De Storme
- In vitroBiology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Danny Geelen
- In vitroBiology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
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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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Huang J, Copenhaver GP, Ma H, Wang Y. New insights into the role of DNA synthesis in meiotic recombination. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1126-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Choi K, Reinhard C, Serra H, Ziolkowski PA, Underwood CJ, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP, Henderson IR. Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet 2016; 12:e1006179. [PMID: 27415776 PMCID: PMC4945094 DOI: 10.1371/journal.pgen.1006179] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/15/2016] [Indexed: 12/31/2022] Open
Abstract
Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Carsten Reinhard
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Piotr A. Ziolkowski
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Charles J. Underwood
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Xiaohui Zhao
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Thomas J. Hardcastle
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Nataliya E. Yelina
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Griffin
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Jackson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles, France
| | - Gil McVean
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - 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
| | - Ian R. Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
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Vrielynck N, Chambon A, Vezon D, Pereira L, Chelysheva L, De Muyt A, Mezard C, Mayer C, Grelon M. A DNA topoisomerase VI-like complex initiates meiotic recombination. Science 2016; 351:939-43. [DOI: 10.1126/science.aad5196] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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