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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. Nat 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chéron F, Petiot V, Lambing C, White C, Serra H. Incorrect recombination partner associations contribute to meiotic instability of neo-allopolyploid Arabidopsis suecica. New Phytol 2024; 241:2025-2038. [PMID: 38158491 DOI: 10.1111/nph.19487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
Combining two or more related homoeologous genomes in a single nucleus, newly formed allopolyploids must rapidly adapt meiosis to restore balanced chromosome segregation, production of euploid gametes and fertility. The poor fertility of such neo-allopolyploids thus strongly selects for the limitation or avoidance of genetic crossover formation between homoeologous chromosomes. In this study, we have reproduced the interspecific hybridization between Arabidopsis thaliana and Arabidopsis arenosa leading to the allotetraploid Arabidopsis suecica and have characterized the first allopolyploid meioses. First-generation neo-allopolyploid siblings vary considerably in fertility, meiotic behavior and levels of homoeologous recombination. We show that centromere dynamics at early meiosis is altered in synthetic neo-allopolyploids compared with evolved A. suecica, with a significant increase in homoeologous centromere interactions at zygotene. At metaphase I, the presence of multivalents involving homoeologous chromosomes confirms that homoeologous recombination occurs in the first-generation synthetic allopolyploid plants and this is associated with a significant reduction in homologous recombination, compared to evolved A. suecica. Together, these data strongly suggest that the fidelity of recombination partner choice, likely during the DNA invasion step, is strongly impaired during the first meiosis of neo-allopolyploids and requires subsequent adaptation.
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Affiliation(s)
- Floriane Chéron
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Valentine Petiot
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | | | - Charles White
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Heïdi Serra
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
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3
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Morgan C, Nayak A, Hosoya N, Smith GR, Lambing C. Meiotic chromosome organization and its role in recombination and cancer. Curr Top Dev Biol 2022; 151:91-126. [PMID: 36681479 PMCID: PMC10022578 DOI: 10.1016/bs.ctdb.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromosomes adopt specific conformations to regulate various cellular processes. A well-documented chromosome configuration is the highly compacted chromosome structure during metaphase. More regional chromatin conformations have also been reported, including topologically associated domains encompassing mega-bases of DNA and local chromatin loops formed by kilo-bases of DNA. In this review, we discuss the changes in chromatin conformation taking place between somatic and meiotic cells, with a special focus on the establishment of a proteinaceous structure, called the chromosome axis, at the beginning of meiosis. The chromosome axis is essential to support key meiotic processes such as chromosome pairing, homologous recombination, and balanced chromosome segregation to transition from a diploid to a haploid stage. We review the role of the chromosome axis in meiotic chromatin organization and provide a detailed description of its protein composition. We also review the conserved and distinct roles between species of axis proteins in meiotic recombination, which is a major factor contributing to the creation of genetic diversity and genome evolution. Finally, we discuss situations where the chromosome axis is deregulated and evaluate the effects on genome integrity and the consequences from protein deregulation in meiocytes exposed to heat stress, and aberrant expression of genes encoding axis proteins in mammalian somatic cells associated with certain types of cancers.
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Affiliation(s)
| | - Aditya Nayak
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zürich, Switzerland
| | - Noriko Hosoya
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Christophe Lambing
- Plant Science Department, Rothamsted Research, Harpenden, United Kingdom.
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Da Ines O, Choi K, Pradillo M, Lambing C. Editorial: Meiotic Recombination and DNA Repair: New Approaches to Solve Old Questions in Model and Non-model Plant Species. Front Plant Sci 2022; 13:841402. [PMID: 35222496 PMCID: PMC8864129 DOI: 10.3389/fpls.2022.841402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, Centre National de la Recherche Scientifique (CNRS), Institut national de la santé et de la recherche médicale (INSERM), Clermont-Ferrand, France
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Mónica Pradillo
- Department of Genetics, Faculty of Biology, Physiology and Microbiology, Universidad Complutense de Madrid, Madrid, Spain
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Kuo P, Darbyshire A, Lambing C. Super-resolution Chromatin Visualization Using a Combined Method of Fluorescence In Situ Hybridization and Structured Illumination Microscopy in Solanum lycopersicum. Methods Mol Biol 2022; 2484:85-92. [PMID: 35461446 DOI: 10.1007/978-1-0716-2253-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chromatin organization influences gene and transposon expression, and regulates various cellular processes. Higher order chromatin structure has been widely studied using genomic approaches and microscopy image analyses. Chromosome conformation capture and sequencing the junction of DNA fragments enables the study of both chromatin interaction and chromosome folding. However, certain cell types are embedded in other cell types which complicate the process of studying them using high-throughput genomic approaches. To overcome this limitation, high-resolution microscopy techniques are now available to investigate chromatin organization in single cells. In this chapter, we provide a detailed protocol to prepare chromosome spreading from tomato nuclei, to label genomic loci by fluorescence in situ hybridization, and to visualize these locations at high resolution with Structured Illumination microscopy.
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Affiliation(s)
- Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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Abstract
Reciprocal DNA crossovers between chromosomes form new allelic combinations and contribute to the formation of novel genetic diversity. Crossovers are formed during meiosis of germ cells and these recombination events have influenced plant genome evolution and are used during breeding to create improved plant varieties. Meiotic crossovers are not uniformly formed across the genome but instead occur in regions with low nucleosome density. The recombination landscape differs between the model plant organism Arabidopsis thaliana and crops such as rice and maize. Genotyping-by-sequencing is a technique that can detect crossover location and provide information on the recombination landscape genome-wide. This technique can be used to compare crossover position between ecotypes, species, and mutant lines to gain information on factors controlling meiotic recombination. In this protocol, we describe the steps to purify DNA from plant tissue, prepare 96 DNA libraries in parallel and perform quality control before next-generation sequencing.
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Affiliation(s)
- Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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Naish M, Alonge M, Wlodzimierz P, Tock AJ, Abramson BW, Schmücker A, Mandáková T, Jamge B, Lambing C, Kuo P, Yelina N, Hartwick N, Colt K, Smith LM, Ton J, Kakutani T, Martienssen RA, Schneeberger K, Lysak MA, Berger F, Bousios A, Michael TP, Schatz MC, Henderson IR. The genetic and epigenetic landscape of the Arabidopsis centromeres. Science 2021; 374:eabi7489. [PMID: 34762468 PMCID: PMC10164409 DOI: 10.1126/science.abi7489] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support CENTROMERE SPECIFIC HISTONE H3 (CENH3) occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites that show the least amount of divergence and occur in higher-order repeats. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization. Centromeric crossover recombination is suppressed, yet low levels of meiotic DNA double-strand breaks occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving through cycles of satellite homogenization and retrotransposon-driven diversification.
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Affiliation(s)
- Matthew Naish
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Piotr Wlodzimierz
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Andrew J. Tock
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Bradley W. Abramson
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Schmücker
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Bhagyshree Jamge
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Christophe Lambing
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Pallas Kuo
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Natasha Yelina
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nolan Hartwick
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kelly Colt
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Lisa M. Smith
- School of Biosciences and Institute for Sustainable Food, University of Sheffield, Sheffield S10 2TN, UK
| | - Jurriaan Ton
- School of Biosciences and Institute for Sustainable Food, University of Sheffield, Sheffield S10 2TN, UK
| | - Tetsuji Kakutani
- Department of Biological Sciences, University of Tokyo, Tokyo, Japan
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Korbinian Schneeberger
- Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | | | - Todd P. Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Ian R. Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
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Ali S, Zhang T, Lambing C, Wang W, Zhang P, Xie L, Wang J, Khan N, Zhang Q. Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana. Planta 2021; 254:107. [PMID: 34694462 DOI: 10.1007/s00425-021-03763-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
In ddm1 mutants, the DNA methylation is primarily affected in the heterochromatic region of the chromosomes, which is associated with the segregation distortion of SNPs in the F2 progenies. Segregation distortion (SD) is common in most genetic mapping experiments and a valuable resource to determine how gene loci induce deviation. Meiotic DNA crossing over and SD are under the control of several types of epigenetic modifications. DNA methylation is an important regulatory epigenetic modification that is inherited across generations. In the present study, we investigated the relationship between SD and DNA methylation. The ecotypes Col-0/C24 and chromatin remodeler mutants ddm1-10/Col and ddm1-15/C24 were reciprocally crossed to obtain F2 generations. A total of 300 plants for each reciprocally crossed plant in the F2 generations were subjected to next-generation sequencing to detect the single-nucleotide polymorphisms (SNPs) as DNA markers. All SNPs were analyzed using the Chi-square test method to determine their segregation ratio in F2 generations. Through the segregation ratio, whole-genome SNPs were classified into 16 classes. In class 10, the SNPs in the reciprocal crosses of wild type showed the expected Mendelian ratio of 1:2:1, while those in the reciprocal crosses of ddm1 mutants showed distortion. In contrast, all SNPs in class 16 displayed a normal 1:2:1 ratio, and class 1 showed SD, regardless of wild type or mutants, as assessed using CAPS (cleaved amplified polymorphic sequences) marker analysis to confirm the next-generation sequencing. In ddm1 mutants, the DNA methylation is highly reduced throughout the whole genome and more significantly in the heterochromatic regions of chromosomes. Our results showed that the ddm1 mutants exhibit low levels of DNA methylation, which facilitates the SD of SNPs primarily located in the heterochromatic region of chromosomes by reducing the heterozygous ratio. The present study will provide a strong base for future research focusing on the impact of DNA methylation on trait segregation and plant evolution.
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Affiliation(s)
- Shahid Ali
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | | | - Wanpeng Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Peng Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Linan Xie
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jiang Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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Abstract
Meiosis is a specialized cell division that contributes to halve the genome content and reshuffle allelic combinations between generations in sexually reproducing eukaryotes. During meiosis, a large number of programmed DNA double-strand breaks (DSBs) are formed throughout the genome. Repair of meiotic DSBs facilitates the pairing of homologs and forms crossovers which are the reciprocal exchange of genetic information between chromosomes. Meiotic recombination also influences centromere organization and is essential for proper chromosome segregation. Accordingly, meiotic recombination drives genome evolution and is a powerful tool for breeders to create new varieties important to food security. Modifying meiotic recombination has the potential to accelerate plant breeding but it can also have detrimental effects on plant performance by breaking beneficial genetic linkages. Therefore, it is essential to gain a better understanding of these processes in order to develop novel strategies to facilitate plant breeding. Recent progress in targeted recombination technologies, chromosome engineering, and an increasing knowledge in the control of meiotic chromosome segregation has significantly increased our ability to manipulate meiosis. In this review, we summarize the latest findings and technologies on meiosis in plants. We also highlight recent attempts and future directions to manipulate crossover events and control the meiotic division process in a breeding perspective.
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Affiliation(s)
- Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293 CNRS, U1103 INSERM, Clermont-Ferrand, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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11
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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. J Exp Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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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. Nat Plants 2021; 7:452-467. [PMID: 33846593 PMCID: PMC7610654 DOI: 10.1038/s41477-021-00889-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Blackwell AR, Dluzewska J, Szymanska-Lejman M, Desjardins S, Tock AJ, Kbiri N, Lambing C, Lawrence EJ, Bieluszewski T, Rowan B, Higgins JD, Ziolkowski PA, Henderson IR. MSH2 shapes the meiotic crossover landscape in relation to interhomolog polymorphism in Arabidopsis. EMBO J 2020; 39:e104858. [PMID: 32935357 PMCID: PMC7604573 DOI: 10.15252/embj.2020104858] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 11/09/2022] Open
Abstract
During meiosis, DNA double-strand breaks undergo interhomolog repair to yield crossovers between homologous chromosomes. To investigate how interhomolog sequence polymorphism affects crossovers, we sequenced multiple recombinant populations of the model plant Arabidopsis thaliana. Crossovers were elevated in the diverse pericentromeric regions, showing a local preference for polymorphic regions. We provide evidence that crossover association with elevated diversity is mediated via the Class I crossover formation pathway, although very high levels of diversity suppress crossovers. Interhomolog polymorphism causes mismatches in recombining molecules, which can be detected by MutS homolog (MSH) mismatch repair protein heterodimers. Therefore, we mapped crossovers in a msh2 mutant, defective in mismatch recognition, using multiple hybrid backgrounds. Although total crossover numbers were unchanged in msh2 mutants, recombination was remodelled from the diverse pericentromeres towards the less-polymorphic sub-telomeric regions. Juxtaposition of megabase heterozygous and homozygous regions causes crossover remodelling towards the heterozygous regions in wild type Arabidopsis, but not in msh2 mutants. Immunostaining showed that MSH2 protein accumulates on meiotic chromosomes during prophase I, consistent with MSH2 regulating meiotic recombination. Our results reveal a pro-crossover role for MSH2 in regions of higher sequence diversity in A. thaliana.
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Affiliation(s)
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Stuart Desjardins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | | | - Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Tomasz Bieluszewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Beth Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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14
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Lambing C, Tock AJ, Topp SD, Choi K, Kuo PC, Zhao X, Osman K, Higgins JD, Franklin FCH, Henderson IR. Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis. Plant Cell 2020; 32:1218-1239. [PMID: 32024691 PMCID: PMC7145502 DOI: 10.1105/tpc.19.00866] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/03/2020] [Accepted: 02/03/2020] [Indexed: 05/20/2023]
Abstract
Meiosis recombines genetic variation and influences eukaryote genome evolution. During meiosis, DNA double-strand breaks (DSBs) enter interhomolog repair to yield crossovers and noncrossovers. DSB repair occurs as replicated sister chromatids are connected to a polymerized axis. Cohesin rings containing the REC8 kleisin subunit bind sister chromatids and anchor chromosomes to the axis. Here, we report the genomic landscape of REC8 using chromatin immunoprecipitation sequencing (ChIP-seq) in Arabidopsis (Arabidopsis thaliana). REC8 associates with regions of high nucleosome occupancy in multiple chromatin states, including histone methylation at H3K4 (expressed genes), H3K27 (silent genes), and H3K9 (silent transposons). REC8 enrichment is associated with suppression of meiotic DSBs and crossovers at the chromosome and fine scales. As REC8 enrichment is greatest in transposon-dense heterochromatin, we repeated ChIP-seq in kyp suvh5 suvh6 H3K9me2 mutants. Surprisingly, REC8 enrichment is maintained in kyp suvh5 suvh6 heterochromatin and no defects in centromeric cohesion were observed. REC8 occupancy within genes anti-correlates with transcription and is reduced in COPIA transposons that reactivate expression in kyp suvh5 suvh6 Abnormal axis structures form in rec8 that recruit DSB-associated protein foci and undergo synapsis, which is followed by chromosome fragmentation. Therefore, REC8 occupancy correlates with multiple chromatin states and is required to organize meiotic chromosome architecture and interhomolog recombination.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Stephanie D Topp
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Pallas C Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Kim Osman
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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15
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Lambing C, Choi K, Blackwell AR, Henderson IR. Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol 2020; 2061:219-236. [PMID: 31583663 DOI: 10.1007/978-1-4939-9818-0_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During meiosis recombination occurs between homologous chromosomes which can result in reciprocal exchanges of genetic information, called crossovers. Crossover rate is heterogeneous within the genome, with local regions having a significantly higher recombination rate relative to the genome average. These regions are termed hotspots and typically occur with widths of kilobases. Therefore, there is a need to profile recombination factors at a similar resolution during meiosis via techniques such as chromatin immunoprecipitation (ChIP). Here we describe a ChIP protocol, combined with high throughput sequencing (ChIP-seq) optimised for analysis of meiotically expressed proteins in Arabidopsis thaliana flowers. We provide methods to (1) isolate nuclei and prepare the chromatin for shearing, (2) immunoprecipitate DNA molecules cross-linked to a protein of interest, (3) to size-select and purify immunoprecipitated DNA molecules, and (4) to prepare DNA sequencing libraries suitable for high-throughput sequencing. Together, these methods allow the detection of binding sites for meiotic proteins in the Arabidopsis genome at high resolution, which will provide insights into relationships between meiotic chromosome organization, chromatin and recombination.
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Affiliation(s)
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.,Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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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: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Choi K, Zhao X, Tock AJ, Lambing C, Underwood CJ, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR. Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res 2018. [PMID: 29530928 DOI: 10.1101/gr.225599.117.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access. A positive relationship was observed between SPO11-1-oligos and crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream from DSB formation. Although H3K4me3 is enriched in proximity to SPO11-1-oligo hotspots at gene 5' ends, H3K4me3 levels do not correlate with DSBs. Repetitive transposons are thought to be recombination silenced during meiosis, to prevent nonallelic interactions and genome instability. Unexpectedly, we found high SPO11-1-oligo levels in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin in SPO11-1-oligo distributions. Epigenetic activation of meiotic DSBs in proximity to centromeres and transposons occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription, and H3K4me3. Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant genomes.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Charles J Underwood
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Juhyun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Piotr A Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Robert A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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20
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Osman K, Yang J, Roitinger E, Lambing C, Heckmann S, Howell E, Cuacos M, Imre R, Dürnberger G, Mechtler K, Armstrong S, Franklin FCH. Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis. Plant J 2018; 93:17-33. [PMID: 29078019 PMCID: PMC5767750 DOI: 10.1111/tpj.13752] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 05/18/2023]
Abstract
During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functionally characterized. Our understanding of the physical and functional interactions between meiotic proteins is also limited. Here we use affinity proteomics to analyse the proteins that are associated with the meiotic chromosome axis protein, ASY1, in Brassica oleracea anthers and meiocytes. We show that during prophase I ASY1 and its interacting partner, ASY3, are extensively phosphorylated, and we precisely assign phosphorylation sites. We identify 589 proteins that co-immunoprecipitate with ASY1. These correspond to 492 Arabidopsis orthologues, over 90% of which form a coherent protein-protein interaction (PPI) network containing known and candidate meiotic proteins, including proteins more usually associated with other cellular processes such as DNA replication and proteolysis. Mutant analysis confirms that affinity proteomics is a viable strategy for revealing previously unknown meiotic proteins, and we show how the PPI network can be used to prioritise candidates for analysis. Finally, we identify another axis-associated protein with a role in meiotic recombination. Data are available via ProteomeXchange with identifier PXD006042.
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Affiliation(s)
- Kim Osman
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jianhua Yang
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Faculty of Engineering and ComputingCoventry UniversityCoventryCV1 5FBUK
| | | | - Christophe Lambing
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Stefan Heckmann
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | - Elaine Howell
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Maria Cuacos
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | | | - Gerhard Dürnberger
- IMP‐IMBA1030ViennaAustria
- Gregor Mendel Institute of Molecular Plant BiologyDr. Bohr‐Gasse 31030ViennaAustria
| | | | - Susan Armstrong
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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21
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Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Lambing C, Franklin FCH, Wang CJR. Understanding and Manipulating Meiotic Recombination in Plants. Plant Physiol 2017; 173:1530-1542. [PMID: 28108697 PMCID: PMC5338670 DOI: 10.1104/pp.16.01530] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/18/2017] [Indexed: 05/18/2023]
Abstract
Meiosis is a specialized cell division, essential in most reproducing organisms to halve the number of chromosomes, thereby enabling the restoration of ploidy levels during fertilization. A key step of meiosis is homologous recombination, which promotes homologous pairing and generates crossovers (COs) to connect homologous chromosomes until their separation at anaphase I. These CO sites, seen cytologically as chiasmata, represent a reciprocal exchange of genetic information between two homologous nonsister chromatids. This gene reshuffling during meiosis has a significant influence on evolution and also plays an essential role in plant breeding, because a successful breeding program depends on the ability to bring the desired combinations of alleles on chromosomes. However, the number and distribution of COs during meiosis is highly constrained. There is at least one CO per chromosome pair to ensure accurate segregation of homologs, but in most organisms, the CO number rarely exceeds three regardless of chromosome size. Moreover, their positions are not random on chromosomes but exhibit regional preference. Thus, genes in recombination-poor regions tend to be inherited together, hindering the generation of novel allelic combinations that could be exploited by breeding programs. Recently, much progress has been made in understanding meiotic recombination. In particular, many genes involved in the process in Arabidopsis (Arabidopsis thaliana) have been identified and analyzed. With the coming challenges of food security and climate change, and our enhanced knowledge of how COs are formed, the interest and needs in manipulating CO formation are greater than ever before. In this review, we focus on advances in understanding meiotic recombination and then summarize the attempts to manipulate CO formation. Last, we pay special attention to the meiotic recombination in polyploidy, which is a common genomic feature for many crop plants.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
| | - F Chris H Franklin
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
| | - Chung-Ju Rachel Wang
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (C.L.);
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (F.C.H.F.); and
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan (C.-J.R.W.)
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23
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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: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Yelina NE, Lambing C, Hardcastle TJ, Zhao X, Santos B, Henderson IR. DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis. Genes Dev 2016; 29:2183-202. [PMID: 26494791 PMCID: PMC4617981 DOI: 10.1101/gad.270876.115] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Yelina et al. show that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. This work demonstrates that DNA methylation plays a key role in establishing domains of meiotic recombination along chromosomes. During meiosis, homologous chromosomes undergo crossover recombination, which is typically concentrated in narrow hot spots that are controlled by genetic and epigenetic information. Arabidopsis chromosomes are highly DNA methylated in the repetitive centromeres, which are also crossover-suppressed. Here we demonstrate that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. However, loss of CG DNA methylation maintenance in met1 triggers epigenetic crossover remodeling at the chromosome scale, with pericentromeric decreases and euchromatic increases in recombination. We used recombination mutants that alter interfering and noninterfering crossover repair pathways (fancm and zip4) to demonstrate that remodeling primarily involves redistribution of interfering crossovers. Using whole-genome bisulfite sequencing, we show that crossover remodeling is driven by loss of CG methylation within the centromeric regions. Using cytogenetics, we profiled meiotic DNA double-strand break (DSB) foci in met1 and found them unchanged relative to wild type. We propose that met1 chromosome structure is altered, causing centromere-proximal DSBs to be inhibited from maturation into interfering crossovers. These data demonstrate that DNA methylation is sufficient to silence crossover hot spots and plays a key role in establishing domains of meiotic recombination along chromosomes.
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Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Bruno Santos
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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25
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Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FCH. Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers. PLoS Genet 2015; 11:e1005372. [PMID: 26182244 PMCID: PMC4504720 DOI: 10.1371/journal.pgen.1005372] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 06/19/2015] [Indexed: 11/30/2022] Open
Abstract
Meiotic chromosomes are organized into linear looped chromatin arrays by a protein axis localized along the loop-bases. Programmed remodelling of the axis occurs during prophase I of meiosis. Structured illumination microscopy (SIM) has revealed dynamic changes in the chromosome axis in Arabidopsis thaliana and Brassica oleracea. We show that the axis associated protein ASY1 is depleted during zygotene concomitant with synaptonemal complex (SC) formation. Study of an Atpch2 mutant demonstrates this requires the conserved AAA+ ATPase, PCH2, which localizes to the sites of axis remodelling. Loss of PCH2 leads to a failure to deplete ASY1 from the axes and compromizes SC polymerisation. Immunolocalization of recombination proteins in Atpch2 indicates that recombination initiation and CO designation during early prophase I occur normally. Evidence suggests that CO interference is initially functional in the mutant but there is a defect in CO maturation following designation. This leads to a reduction in COs and a failure to form COs between some homologous chromosome pairs leading to univalent chromosomes at metaphase I. Genetic analysis reveals that CO distribution is also affected in some chromosome regions. Together these data indicate that the axis remodelling defect in Atpch2 disrupts normal patterned formation of COs. In the reproductive cells of many eukaryotes, a process called meiosis generates haploid gametes. During meiosis, homologous parental chromosomes (homologs) recombine forming crossovers (CO) that provide genetic variation. CO formation generates physical links called chiasmata, which are essential for accurate homolog segregation. CO control designates a sub-set of recombination precursors that will mature to form at least one chiasma between each homolog pair. Recombination is accompanied by extensive chromosome reorganization. Formation of a proteinaceous axis organizes the pairs of sister chromatids of each homolog into conjoined linear looped chromatin arrays. Pairs of homologs then align and synapse becoming closely associated along their length by a protein structure, the synaptonemal complex (SC). The SC is disassembled at the end of prophase I and recombination is completed. We have investigated the link between recombination and chromosome remodelling by analysing the role of a protein, PCH2, which we show is required for remodelling of the chromosome axis during SC formation. In wild type, immunolocalization reveals depletion of the axis-associated signal of the axis component, ASY1, along synapsed regions of the chromosomes. In the absence of PCH2, the ASY1 signal is not depleted from the chromosome axis and the SC does not form normally. Although this defect in chromosome remodelling has no obvious effect on CO designation, CO maturation is perturbed such that the formation of at least one CO per homolog pair no longer occurs.
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Affiliation(s)
- Christophe Lambing
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Komsun Nuntasoontorn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Allan West
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - James D. Higgins
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Gregory P. Copenhaver
- Department of Biology and Carolina Center for Genome Scientists, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jianhua Yang
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Susan J. Armstrong
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | | | - F. Chris H. Franklin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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26
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Ziolkowski PA, Berchowitz LE, Lambing C, Yelina NE, Zhao X, Kelly KA, Choi K, Ziolkowska L, June V, Sanchez-Moran E, Franklin C, Copenhaver GP, Henderson IR. Juxtaposition of heterozygous and homozygous regions causes reciprocal crossover remodelling via interference during Arabidopsis meiosis. eLife 2015; 4:e03708. [PMID: 25815584 PMCID: PMC4407271 DOI: 10.7554/elife.03708] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 03/26/2015] [Indexed: 12/13/2022] Open
Abstract
During meiosis homologous chromosomes undergo crossover recombination. Sequence differences between homologs can locally inhibit crossovers. Despite this, nucleotide diversity and population-scaled recombination are positively correlated in eukaryote genomes. To investigate interactions between heterozygosity and recombination we crossed Arabidopsis lines carrying fluorescent crossover reporters to 32 diverse accessions and observed hybrids with significantly higher and lower crossovers than homozygotes. Using recombinant populations derived from these crosses we observed that heterozygous regions increase crossovers when juxtaposed with homozygous regions, which reciprocally decrease. Total crossovers measured by chiasmata were unchanged when heterozygosity was varied, consistent with homeostatic control. We tested the effects of heterozygosity in mutants where the balance of interfering and non-interfering crossover repair is altered. Crossover remodeling at homozygosity-heterozygosity junctions requires interference, and non-interfering repair is inefficient in heterozygous regions. As a consequence, heterozygous regions show stronger crossover interference. Our findings reveal how varying homolog polymorphism patterns can shape meiotic recombination.
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Affiliation(s)
- Piotr A Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Luke E Berchowitz
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, United States
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Krystyna A Kelly
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Liliana Ziolkowska
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Viviana June
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Chris Franklin
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Gregory P Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, United States
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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27
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Ferdous M, Higgins JD, Osman K, Lambing C, Roitinger E, Mechtler K, Armstrong SJ, Perry R, Pradillo M, Cuñado N, Franklin FCH. Inter-homolog crossing-over and synapsis in Arabidopsis meiosis are dependent on the chromosome axis protein AtASY3. PLoS Genet 2012; 8:e1002507. [PMID: 22319460 PMCID: PMC3271061 DOI: 10.1371/journal.pgen.1002507] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 12/11/2011] [Indexed: 12/13/2022] Open
Abstract
In this study we have analysed AtASY3, a coiled-coil domain protein that is required for normal meiosis in Arabidopsis. Analysis of an Atasy3-1 mutant reveals that loss of the protein compromises chromosome axis formation and results in reduced numbers of meiotic crossovers (COs). Although the frequency of DNA double-strand breaks (DSBs) appears moderately reduced in Atasy3-1, the main recombination defect is a reduction in the formation of COs. Immunolocalization studies in wild-type meiocytes indicate that the HORMA protein AtASY1, which is related to Hop1 in budding yeast, forms hyper-abundant domains along the chromosomes that are spatially associated with DSBs and early recombination pathway proteins. Loss of AtASY3 disrupts the axial organization of AtASY1. Furthermore we show that the AtASY3 and AtASY1 homologs BoASY3 and BoASY1, from the closely related species Brassica oleracea, are co-immunoprecipitated from meiocyte extracts and that AtASY3 interacts with AtASY1 via residues in its predicted coiled-coil domain. Together our results suggest that AtASY3 is a functional homolog of Red1. Since studies in budding yeast indicate that Red1 and Hop1 play a key role in establishing a bias to favor inter-homolog recombination (IHR), we propose that AtASY3 and AtASY1 may have a similar role in Arabidopsis. Loss of AtASY3 also disrupts synaptonemal complex (SC) formation. In Atasy3-1 the transverse filament protein AtZYP1 forms small patches rather than a continuous SC. The few AtMLH1 foci that remain in Atasy3-1 are found in association with the AtZYP1 patches. This is sufficient to prevent the ectopic recombination observed in the absence of AtZYP1, thus emphasizing that in addition to its structural role the protein is important for CO formation. Homologous recombination (HR) during prophase I of meiosis leads to the formation of physical connections, known as chiasmata, between homologous chromosomes (homologs). Chiasmata are essential for accurate homolog segregation at the first meiotic division. HR is initiated by the formation of DNA double-strand breaks (DSBs). As DNA replication prior to meiosis results in the duplication of each homolog to form two identical sister chromatids, a DSB in one sister chromatid could potentially be repaired using the other as the repair template rather than one of the two non-sister chromatids of the homolog. If this route were predominant, the formation of chiasmata would be disfavored and chromosome segregation would be compromised. However, during meiosis there is a strong bias towards inter-homolog recombination (IHR). In this study we have identified AtASY3, a component of the proteinaceous axes that organize the chromosomes during meiosis in Arabidopsis. We find that AtASY3 interacts with AtASY1, a previously identified axis protein that is essential for crossover formation. We show that loss of AtASY3 disrupts the axis-organization of AtASY1. This results in a substantial reduction in chiasmata, and there is extensive chromosome mis-segregation. We propose that loss of AtASY3 affects the efficiency of the inter-homolog bias.
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Affiliation(s)
- Maheen Ferdous
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - James D. Higgins
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Kim Osman
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Christophe Lambing
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Susan J. Armstrong
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Ruth Perry
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Mónica Pradillo
- Departamento de Génetica, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Nieves Cuñado
- Departamento de Génetica, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - F. Chris H. Franklin
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
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