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Son N, Kim H, Kim J, Park J, Byun D, Park SJ, Kim H, Park YM, Bourguet P, Berger F, Choi K. The histone variant H2A.W restricts heterochromatic crossovers in Arabidopsis. Proc Natl Acad Sci U S A 2025; 122:e2413698122. [PMID: 40184177 PMCID: PMC12002335 DOI: 10.1073/pnas.2413698122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 03/05/2025] [Indexed: 04/05/2025] Open
Abstract
Meiotic crossovers rearrange allele combinations and create offspring diversity. Crossovers occur nonrandomly along chromosomes, predominantly in distal euchromatin and less in pericentromeric heterochromatin marked with histone H3 lysine 9 dimethylation (H3K9me2) and the H2A variant H2A.W in Arabidopsis thaliana. Loss of H3K9me2 increases heterochromatic crossovers, but how H2A.W affects crossover formation in pericentromeric regions is unknown. Here, we report that H2A.W is required to restrict heterochromatic crossovers in Arabidopsis. Using meiosis-specific microRNA-induced gene silencing (meiMIGS) and fluorescence-tagged recombination reporters, we show that meiotic knockdown of H2A.W.6, H2A.W.7, and H2A.W.12 (meiMIGS-H2A.W.6/7/12) increases pericentromeric crossovers. High-resolution genomic maps of crossovers show that meiMIGS-H2A.W.6/7/12 enhances heterochromatic crossovers, similar to meiMIGS plants silencing the H3K9me2 pathway. Consistently, genome-wide crossover maps show that the mutants h2a.w.6, h2a.w.7, h2a.w.6 h2a.w.7, and h2a.w.6 h2a.w.7 h2a.w.12, but not h2a.w.12, exhibit a similar increase in heterochromatic crossovers to meiMIGS-H2A.W.6/7/12, demonstrating that H2A.W.6 and H2A.W.7 limit heterochromatic crossovers. Profiling of genome-wide nucleosome density using micrococcal nuclease sequencing reveals that h2a.w mutants with increased heterochromatic crossovers have increased heterochromatin accessibility, with lower H3K9me2 levels during meiosis. Our findings shed light on the role of H2A.W variants as heterochromatin compaction factors that suppress meiotic crossovers within the pericentromeric regions.
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Affiliation(s)
- Namil Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Jihye Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Dohwan Byun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Sang-jun Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Hyein Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Yeong Mi Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Pierre Bourguet
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna1030, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna1030, Austria
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
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2
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Parker MT, Amar S, Campoy JA, Krause K, Tusso S, Marek M, Huettel B, Schneeberger K. Scalable eQTL mapping using single-nucleus RNA-sequencing of recombined gametes from a small number of individuals. PLoS Biol 2025; 23:e3003085. [PMID: 40279341 PMCID: PMC12119024 DOI: 10.1371/journal.pbio.3003085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 05/28/2025] [Accepted: 02/25/2025] [Indexed: 04/27/2025] Open
Abstract
Phenotypic differences between individuals of a species are often caused by differences in gene expression, which are in turn caused by genetic variation. Expression quantitative trait locus (eQTL) analysis is a methodology by which we can identify such causal variants. Scaling eQTL analysis is costly due to the expense of generating mapping populations, and the collection of matched transcriptomic and genomic information. We developed a rapid eQTL analysis approach using single-cell/nucleus RNA sequencing of gametes from a small number of heterozygous individuals. Patterns of inherited polymorphisms are used to infer the recombinant genomes of thousands of individual gametes and identify how different haplotypes correlate with variation in gene expression. Applied to Arabidopsis pollen nuclei, our approach uncovers both cis- and trans-eQTLs, ultimately mapping variation in a master regulator of sperm cell development that affects the expression of hundreds of genes. This establishes snRNA-sequencing as a powerful, cost-effective method for the mapping of meiotic recombination, addressing the scalability challenges of eQTL analysis and enabling eQTL mapping in specific cell-types.
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Affiliation(s)
- Matthew T. Parker
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Samija Amar
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - José A. Campoy
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kristin Krause
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sergio Tusso
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | | | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
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3
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Pelé A, Falque M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Martin OC, Chèvre AM, Rousseau-Gueutin M. Genomic Divergence Shaped the Genetic Regulation of Meiotic Homologous Recombination in Brassica Allopolyploids. Mol Biol Evol 2025; 42:msaf073. [PMID: 40173423 PMCID: PMC11982612 DOI: 10.1093/molbev/msaf073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Revised: 03/05/2025] [Accepted: 03/06/2025] [Indexed: 04/04/2025] Open
Abstract
The tight regulation of meiotic recombination between homologs is disrupted in Brassica AAC allotriploids, a genomic configuration that may have facilitated the formation of rapeseed (Brassica napus L.) ∼7,500 years ago. Indeed, the presence of the haploid C genome induces supernumerary crossovers between homologous A chromosomes with dramatically reshaped distribution. However, the genetic mechanisms driving this phenomenon and their divergence between nascent and established lineages remain unclear. To address these concerns, we generated hybrids carrying additional C chromosomes derived either from an established lineage of the allotetraploid B. napus or from its diploid progenitor B. oleracea. We then assessed recombination variation across twelve populations by mapping male meiotic crossovers using single nucleotide polymorphism markers evenly distributed across the sequenced A genome. Our findings reveal that the C09 chromosome of B. oleracea is responsible for the formation of additional crossovers near pericentromeric regions. Interestingly, its counterpart from an established lineage of B. napus shows no significant effect on its own, despite having a similar content of meiotic genes. However, we showed that the B. napus C09 chromosome influences crossover formation through inter-chromosomal epistatic interactions with other specific C chromosomes. These results provide new insights into the genetic regulation of homologous recombination in Brassica and emphasize the role of genomic divergence since the formation of the allopolyploid B. napus.
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Affiliation(s)
- Alexandre Pelé
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Poznan 61-614, Poland
| | - Matthieu Falque
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | | | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu 35653, France
| | - Olivier C Martin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette 91190, France
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4
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Zhao Q, Xiong Z, Cheng C, Wang Y, Feng X, Yu X, Lou Q, Chen J. Meiotic crossovers revealed by differential visualization of homologous chromosomes using enhanced haplotype oligo-painting in cucumber. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:887-899. [PMID: 39661709 PMCID: PMC11869176 DOI: 10.1111/pbi.14546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 11/22/2024] [Accepted: 11/23/2024] [Indexed: 12/13/2024]
Abstract
The interaction dynamics of homologous chromosomes during meiosis, such as recognition, pairing, synapsis, recombination, and segregation are vital for species fertility and genetic diversity within populations. Meiotic crossover (CO), a prominent feature of meiosis, ensures the faithful segregation of homologous chromosomes and enriches genetic diversity within a population. Nevertheless, visually distinguishing homologous chromosomes and COs remains an intractable challenge in cytological studies, particularly in non-model or plants with small genomes, limiting insights into meiotic dynamics. In the present study, we developed a robust and reliable enhanced haplotype oligo-painting (EHOP) technique to image small amounts of oligos, enabling visual discrimination of homologous chromosomes. Using EHOP developed based on sequence polymorphisms and reconstructed oligonucleotides, we visually distinguished parental and most recombinant chromosomes in cucumber F1 hybrids and F2 populations. Results from EHOP revealed that meiotic CO events preferentially occur in the 30-60% intervals of chromosome arms with lower sequence polymorphisms and significant recombination bias exists between cultivated and ancestral chromosomes. Due to the occupation of extensive heterochromatin occupancy, it is not yet possible to precisely identify the meiotic COs present in the central portion of chr2 and chr4. Notably, CO accessibility was universally detected in the cytological centromere region in F2 populations, a feature rarely observed in crops with large genomes. EHOP demonstrated exceptional performance in distinguishing homologous chromosomes and holds significant potential for broad application in studying homologous chromosome interactions.
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Affiliation(s)
- Qinzheng Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
| | - Zhenhui Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
| | - Yuhui Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
| | - Xianbo Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of HorticultureNanjing Agricultural UniversityNanjing210095China
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5
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Gordon SG, Rodriguez AA, Gu Y, Corbett KD, Lee CF, Rog O. The synaptonemal complex aligns meiotic chromosomes by wetting. SCIENCE ADVANCES 2025; 11:eadt5675. [PMID: 40009663 PMCID: PMC11864179 DOI: 10.1126/sciadv.adt5675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 01/23/2025] [Indexed: 02/28/2025]
Abstract
During meiosis, the parental chromosomes are drawn together to enable exchange of genetic information. Chromosomes are aligned through the assembly of a conserved interface, the synaptonemal complex, composed of a central region that forms between two parallel chromosomal backbones called axes. Here, we identify the axis-central region interface in C. elegans, containing a conserved positive patch on the axis component HIM-3 and the negative C terminus of the central region protein SYP-5. Crucially, the canonical ultrastructure of the synaptonemal complex is altered upon weakening this interface using charge-reversal mutations. We developed a thermodynamic model that recapitulates our experimental observations, indicating that the liquid-like central region can assemble by wetting the axes without active energy consumption. More broadly, our data show that condensation drives tightly regulated nuclear reorganization during sexual reproduction.
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Affiliation(s)
- Spencer G. Gordon
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Alyssa A. Rodriguez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Chiu Fan Lee
- Department of Bioengineering, Imperial College London, London, UK
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA
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6
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Durand S, Lian Q, Solier V, Fernandes J, Mercier R. MutLγ enforces meiotic crossovers in Arabidopsis thaliana. Nucleic Acids Res 2025; 53:gkaf157. [PMID: 40105241 PMCID: PMC11920796 DOI: 10.1093/nar/gkaf157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 02/07/2025] [Accepted: 03/11/2025] [Indexed: 03/20/2025] Open
Abstract
During meiosis, each chromosome pair experiences at least one crossover (CO), which directs their balanced segregation in addition to shuffling genetic information. COs tend to be away from each other, a phenomenon known as CO interference. The main biochemical pathway for CO formation, which is conserved in distant eukaryotes, involves the ZMM proteins together with the MLH1-MLH3 complex (MutLγ). Here, we aim to clarify the role of MutLγ in CO formation in Arabidopsis thaliana. We show that AtMutLγ is partially dispensable for ZMM-dependent CO formation. HEI10 large foci-that mark CO sites in wild-type-form at a normal level in mlh1 and mlh3 mutants, but are inefficiently maturated into COs. Mutating the MUS81 nuclease in either mlh1 or mlh3 leads to chromosome fragmentation, which is suppressed by further mutating the zmm msh5. This suggests that in the absence of MutLγ, recombination intermediates produced by ZMMs are resolved by MUS81, which does not ensure CO formation. Finally, CO interference is marginally affected in mlh1, which is compatible with a random sub-sampling of normally patterned CO sites. We conclude that AtMutLγ imposes designated recombination intermediates to be resolved exclusively as COs, supporting the view that MutLγ asymmetrically resolves double-Holliday junctions, yielding COs.
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Affiliation(s)
- Stéphanie Durand
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Victor Solier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Joiselle Blanche Fernandes
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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7
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Kbiri N, Fernández-Jiménez N, Dziegielewski W, Sáez-Zárate E, Pelé A, Mata-Villanueva A, Dluzewska J, Santos J, Pradillo M, Ziolkowski P. Genetic dissection of MutL complexes in Arabidopsis meiosis. Nucleic Acids Res 2025; 53:gkaf187. [PMID: 40105242 PMCID: PMC11920794 DOI: 10.1093/nar/gkaf187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 02/16/2025] [Accepted: 02/25/2025] [Indexed: 03/20/2025] Open
Abstract
During meiosis, homologous chromosomes exchange genetic material through crossing over. The main crossover pathway relies on ZMM proteins, including ZIP4 and HEI10, and is typically resolved by the MLH1/MLH3 heterodimer, MutLγ. Our analysis shows that while MUS81 may partially compensate for MutLγ loss, its role remains uncertain. However, our multiple mutant analysis shows that MUS81 is unlikely to be the sole resolvase of ZMM-protected recombination intermediates when MutLγ is absent. Comparing genome-wide crossover maps of mlh1 mutants with ZMM-deficient mutants and lines with varying HEI10 levels reveals that crossover interference persists in mlh1 but is weakened. The significant crossover reduction in mlh1 also increases aneuploidy in offspring. The loss of MutLγ can be suppressed by eliminating the FANCM helicase. Combined with the lower-than-expected chiasma frequency, this suggests that in MutLγ absence, some ZMM-protected intermediates are ultimately resolved by DNA helicases and/or their complexes with Top3α. Elevated MLH1 or MLH3 expression moderately increases crossover frequency, while their misregulation drastically reduces crossover numbers and plant fertility, highlighting the importance for tight control of MLH1/MLH3 levels. By contrast, PMS1, a component of the MutLα endonuclease, appears uninvolved in crossing over. Together, these findings demonstrate the unique role of MutLγ in ZMM-dependent crossover regulation.
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Affiliation(s)
- Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Nadia Fernández-Jiménez
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Esperanza Sáez-Zárate
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Alexandre Pelé
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Ana Mata-Villanueva
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Juan L Santos
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
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Patel B, Grobler M, Herrera A, Logari E, Ortiz V, Bhalla N. The conserved ATPase PCH-2 controls the number and distribution of crossovers by antagonizing their formation in Caenorhabditis elegans. eLife 2025; 13:RP102409. [PMID: 39964851 PMCID: PMC11835387 DOI: 10.7554/elife.102409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2025] Open
Abstract
Meiotic crossover recombination is essential for both accurate chromosome segregation and the generation of new haplotypes for natural selection to act upon. This requirement is known as crossover assurance and is one example of crossover control. While the conserved role of the ATPase, PCH-2, during meiotic prophase has been enigmatic, a universal phenotype when pch-2 or its orthologs are mutated is a change in the number and distribution of meiotic crossovers. Here, we show that PCH-2 controls the number and distribution of crossovers by antagonizing their formation. This antagonism produces different effects at different stages of meiotic prophase: early in meiotic prophase, PCH-2 prevents double-strand breaks from becoming crossover-eligible intermediates, limiting crossover formation at sites of initial double-strand break formation and homolog interactions. Later in meiotic prophase, PCH-2 winnows the number of crossover-eligible intermediates, contributing to the designation of crossovers and ultimately, crossover assurance. We also demonstrate that PCH-2 accomplishes this regulation through the meiotic HORMAD, HIM-3. Our data strongly support a model in which PCH-2's conserved role is to remodel meiotic HORMADs throughout meiotic prophase to destabilize crossover-eligible precursors and coordinate meiotic recombination with synapsis, ensuring the progressive implementation of meiotic recombination and explaining its function in the pachytene checkpoint and crossover control.
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Affiliation(s)
- Bhumil Patel
- Department of Molecular, Cell and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Maryke Grobler
- Department of Molecular, Cell and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Alberto Herrera
- Department of Molecular, Cell and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Elias Logari
- Department of Molecular, Cell and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Valery Ortiz
- Department of Molecular, Cell and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Needhi Bhalla
- Department of Molecular, Cell and Developmental Biology, University of California, Santa CruzSanta CruzUnited States
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9
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Neves AR, Čavka I, Rausch T, Köhler S. Crossovers are regulated by a conserved and disordered synaptonemal complex domain. Nucleic Acids Res 2025; 53:gkaf095. [PMID: 39964475 PMCID: PMC11833701 DOI: 10.1093/nar/gkaf095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 01/30/2025] [Accepted: 02/04/2025] [Indexed: 02/21/2025] Open
Abstract
During meiosis, the number and distribution of crossovers (COs) must be precisely regulated through CO assurance and interference to prevent chromosome missegregation and genomic instability in the progeny. Here we show that this regulation of COs depends on a disordered and conserved domain within the synaptonemal complex (SC). This domain is located at the C-terminus of the central element protein SYP-4 in Caenorhabditis elegans. While not necessary for synapsis, the C-terminus of SYP-4 is crucial for both CO assurance and interference. Although the SYP-4 C-terminus contains many potential phosphorylation sites, we found that phosphorylation is not the primary regulator of CO events. Instead, we discovered that nine conserved phenylalanines are required to recruit a pro-CO factor predicted to be an E3 ligase and regulate the physical properties of the SC. We propose that this conserved and disordered domain plays a crucial role in maintaining the SC in a state that allows transmitting signals to regulate CO formation. While the underlying mechanisms remain to be fully understood, our findings align with existing models suggesting that the SC plays a critical role in determining the number and distribution of COs along chromosomes, thereby safeguarding the genome for future generations.
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Affiliation(s)
- Ana Rita Rodrigues Neves
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg University, Heidelberg, Germany
| | - Ivana Čavka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg University, Heidelberg, Germany
| | - Tobias Rausch
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- GeneCore, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Simone Köhler
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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10
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Köhler S, Wojcik M, Xu K, Dernburg AF. Dynamic molecular architecture of the synaptonemal complex. SCIENCE ADVANCES 2025; 11:eadq9374. [PMID: 39841849 PMCID: PMC11753403 DOI: 10.1126/sciadv.adq9374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 12/20/2024] [Indexed: 01/24/2025]
Abstract
During meiosis, pairing between homologous chromosomes is stabilized by the assembly of the synaptonemal complex (SC). The SC ensures the formation of crossovers between homologous chromosomes and regulates their distribution. However, how the SC regulates crossover formation remains elusive. We isolated an unusual mutation in Caenorhabditis elegans that disrupts crossover interference but not SC assembly. This mutation alters the unique C terminal domain of an essential SC protein, SYP-4, a likely ortholog of the vertebrate SC protein SIX6OS1. We use three-dimensional stochastic optical reconstruction microscopy (3D-STORM) to interrogate the molecular architecture of the SC from wild-type and mutant C. elegans animals. Using a probabilistic mapping approach to analyze super-resolution image data, we detect changes in the organization of the synaptonemal complex in wild-type animals that coincide with crossover designation. We also found that our syp-4 mutant perturbs SC architecture. Our findings add to growing evidence that the SC is an active material whose molecular organization contributes to chromosome-wide crossover regulation.
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Affiliation(s)
- Simone Köhler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Michal Wojcik
- Department of Chemistry, University of California, Berkeley, Berkeley CA 94720-3220, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley CA 94720-3220, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- California Institute for Quantitative Biosciences, Berkeley CA 94720, USA
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Abby F. Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
- California Institute for Quantitative Biosciences, Berkeley CA 94720, USA
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11
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Patel B, Grobler M, Herrera A, Logari E, Ortiz V, Bhalla N. The conserved ATPase PCH-2 controls the number and distribution of crossovers by antagonizing their formation in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607819. [PMID: 39185160 PMCID: PMC11343117 DOI: 10.1101/2024.08.13.607819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Meiotic crossover recombination is essential for both accurate chromosome segregation and the generation of new haplotypes for natural selection to act upon. This requirement is known as crossover assurance and is one example of crossover control. While the conserved role of the ATPase, PCH-2, during meiotic prophase has been enigmatic, a universal phenotype when pch-2 or its orthologs are mutated is a change in the number and distribution of meiotic crossovers. Here, we show that PCH-2 controls the number and distribution of crossovers by antagonizing their formation. This antagonism produces different effects at different stages of meiotic prophase: early in meiotic prophase, PCH-2 prevents double strand breaks from becoming crossover-eligible intermediates, limiting crossover formation at sites of initial double strand break formation and homolog interactions. Later in meiotic prophase, PCH-2 winnows the number of crossover-eligible intermediates, contributing to the designation of crossovers and ultimately, crossover assurance. We also demonstrate that PCH-2 accomplishes this regulation through the meiotic HORMAD, HIM-3. Our data strongly support a model in which PCH-2's conserved role is to remodel meiotic HORMADs throughout meiotic prophase to destabilize crossover-eligible precursors, coordinate meiotic recombination with synapsis, and contribute to the progressive implementation of meiotic recombination, guaranteeing crossover control.
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Affiliation(s)
- Bhumil Patel
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Maryke Grobler
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Alberto Herrera
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Elias Logari
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Valery Ortiz
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Needhi Bhalla
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
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12
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Rafiei N, Ronceret A. The plant early recombinosome: a high security complex to break DNA during meiosis. PLANT REPRODUCTION 2024; 37:421-440. [PMID: 39331138 PMCID: PMC11511760 DOI: 10.1007/s00497-024-00509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024]
Abstract
KEY MESSAGE The formacion of numerous unpredictable DNA Double Strand Breaks (DSBs) on chromosomes iniciates meiotic recombination. In this perspective, we propose a 'multi-key lock' model to secure the risky but necesary breaks as well as a 'one per pair of cromatids' model for the topoisomerase-like early recombinosome. During meiosis, homologous chromosomes recombine at few sites of crossing-overs (COs) to ensure correct segregation. The initiation of meiotic recombination involves the formation of DNA double strand breaks (DSBs) during prophase I. Too many DSBs are dangerous for genome integrity: if these DSBs are not properly repaired, it could potentially lead to chromosomal fragmentation. Too few DSBs are also problematic: if the obligate CO cannot form between bivalents, catastrophic unequal segregation of univalents lead to the formation of sterile aneuploid spores. Research on the regulation of the formation of these necessary but risky DSBs has recently advanced in yeast, mammals and plants. DNA DSBs are created by the enzymatic activity of the early recombinosome, a topoisomerase-like complex containing SPO11. This opinion paper reviews recent insights on the regulation of the SPO11 cofactors necessary for the introduction of temporally and spatially controlled DSBs. We propose that a 'multi-key-lock' model for each subunit of the early recombinosome complex is required to secure the formation of DSBs. We also discuss the hypothetical implications that the established topoisomerase-like nature of the SPO11 core-complex can have in creating DSB in only one of the two replicated chromatids of early prophase I meiotic chromosomes. This hypothetical 'one per pair of chromatids' DSB formation model could optimize the faithful repair of the self-inflicted DSBs. Each DSB could use three potential intact homologous DNA sequences as repair template: one from the sister chromatid and the two others from the homologous chromosomes.
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Affiliation(s)
- Nahid Rafiei
- Department of Plant Molecular Biology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Arnaud Ronceret
- Department of Plant Molecular Biology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México.
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13
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von Diezmann L, Bristow C, Rog O. Diffusion within the synaptonemal complex can account for signal transduction along meiotic chromosomes. Mol Biol Cell 2024; 35:ar148. [PMID: 39475711 PMCID: PMC11656479 DOI: 10.1091/mbc.e24-05-0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 10/15/2024] [Accepted: 10/21/2024] [Indexed: 11/09/2024] Open
Abstract
Meiotic chromosomes efficiently transduce information along their length to regulate the distribution of genetic exchanges (crossovers). However, the mode of signal transduction remains unknown. A conserved protein interface called the synaptonemal complex forms between the parental chromosomes. The synaptonemal complex exhibits liquid-like behaviors, suggesting that the diffusion of signaling molecules along its length could coordinate crossover formation. Here, we directly test the feasibility of such a mechanism by tracking a component of the synaptonemal complex (SYP-3) and a conserved regulator of exchanges (ZHP-3) in live Caenorhabditis elegans gonads. While we find that both proteins diffuse within the synaptonemal complex, ZHP-3 diffuses 4- and 9-fold faster than SYP-3 before and after crossover designation, respectively. We use these measurements to parameterize a physical model for signal transduction. We find that ZHP-3, but not SYP-3, can explore the lengths of chromosomes on the time scale of crossover designation, consistent with a role in the spatial regulation of exchanges. Given the conservation of ZHP-3 paralogues across eukaryotes, we propose that diffusion along the synaptonemal complex may be a conserved mechanism of meiotic regulation. More broadly, our work explores how diffusion compartmentalized by condensates could regulate crucial chromosomal functions.
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Affiliation(s)
- Lexy von Diezmann
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84114
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84114
| | - Chloe Bristow
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84114
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84114
| | - Ofer Rog
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84114
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84114
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14
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Morgan AP, Payseur BA. Genetic background affects the strength of crossover interference in house mice. Genetics 2024; 228:iyae146. [PMID: 39241112 PMCID: PMC11538424 DOI: 10.1093/genetics/iyae146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 08/22/2024] [Indexed: 09/08/2024] Open
Abstract
Meiotic recombination is required for faithful chromosome segregation in most sexually reproducing organisms and shapes the distribution of genetic variation in populations. Both the overall rate and the spatial distribution of crossovers vary within and between species. Adjacent crossovers on the same chromosome tend to be spaced more evenly than expected at random, a phenomenon known as crossover interference. Although interference has been observed in many taxa, the factors that influence the strength of interference are not well understood. We used house mice (Mus musculus), a well-established model system for understanding recombination, to study the effects of genetics and age on recombination rate and interference in the male germline. We analyzed crossover positions in 503 progeny from reciprocal F1 hybrids between inbred strains representing the three major subspecies of house mice. Consistent with previous studies, autosomal alleles from M. m. musculus tend to increase recombination rate, while inheriting a M. m. musculus X chromosome decreases recombination rate. Old males transmit an average of 0.6 more crossovers per meiosis (5.0%) than young males, though the effect varies across genetic backgrounds. We show that the strength of crossover interference depends on genotype, providing a rare demonstration that interference evolves over short timescales. Differences between reciprocal F1s suggest that X-linked factors modulate the strength of interference. Our findings motivate additional comparisons of interference among recently diverged species and further examination of the role of paternal age in determining the number and positioning of crossovers.
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Affiliation(s)
- Andrew P Morgan
- Department of Medicine, University of North Carolina, Campus Box #7085, Chapel Hill, NC 27599-7085, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
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15
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Zhou Y, Li Y, You H, Chen J, Wang B, Wen M, Zhang Y, Tang D, Shen Y, Yu H, Cheng Z. Kinesin-1-like protein PSS1 is essential for full-length homologous pairing and synapsis in rice meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:928-940. [PMID: 39283979 DOI: 10.1111/tpj.17025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/23/2024] [Accepted: 08/28/2024] [Indexed: 11/01/2024]
Abstract
The pairing and synapsis of homologous chromosomes are crucial for their correct segregation during meiosis. The LINC (Linker of Nucleoskeleton and Cytoskeleton) complex can recruit kinesin protein at the nuclear envelope, affecting telomere bouquet formation and homologous pairing. Kinesin-1-like protein Pollen Semi-Sterility1 (PSS1) plays a pivotal role in male meiotic chromosomal behavior and is essential for fertility in rice. However, its exact role in meiosis, especially as kinesin involved in homologous pairing and synapsis, has not been fully elucidated. Here, we generated three pss1 mutants by genome editing technology to dissect PSS1 biological functions in meiosis. The pss1 mutants exhibit alterations in the radial microtubule organization at pachytene and manifest a deficiency in telomere clustering, which is critical for full-length homologous pairing. We reveal that PSS1 serves as a key mediator between chromosomes and cytoskeleton, thereby regulating microtubule organization and transmitting the force to nuclei to facilitate homologous chromosome pairing and synapsis in meiosis.
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Affiliation(s)
- Yue Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yafei Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hanli You
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Jiawei Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingxin Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minsi Wen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yansong Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ding Tang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Shen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hengxiu Yu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhukuan Cheng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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16
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Ernst M, Mercier R, Zwicker D. Interference length reveals regularity of crossover placement across species. Nat Commun 2024; 15:8973. [PMID: 39419967 PMCID: PMC11487058 DOI: 10.1038/s41467-024-53054-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/27/2024] [Indexed: 10/19/2024] Open
Abstract
Crossover interference is a phenomenon that affects the number and positioning of crossovers in meiosis and thus affects genetic diversity and chromosome segregation. Yet, the underlying mechanism is not fully understood, partly because quantification is difficult. To overcome this challenge, we introduce the interference length Lint that quantifies changes in crossover patterning due to interference. We show that it faithfully captures known aspects of crossover interference and provides superior statistical power over previous measures such as the interference distance and the gamma shape parameter. We apply our analysis to empirical data and unveil a similar behavior of Lint across species, which hints at a common mechanism. A recently proposed coarsening model generally captures these aspects, providing a unified view of crossover interference. Consequently, Lint facilitates model refinements and general comparisons between alternative models of crossover interference.
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Affiliation(s)
- Marcel Ernst
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany.
- University of Göttingen, Institute for the Dynamics of Complex Systems, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany.
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany.
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17
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Boideau F, Huteau V, Maillet L, Brunet A, Coriton O, Deniot G, Trotoux G, Taburel-Lodé M, Eber F, Gilet M, Baron C, Boutte J, Richard G, Aury JM, Belser C, Labadie K, Morice J, Falentin C, Martin O, Falque M, Chèvre AM, Rousseau-Gueutin M. Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres. THE PLANT CELL 2024; 36:4472-4490. [PMID: 39121028 PMCID: PMC11449113 DOI: 10.1093/plcell/koae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/12/2024] [Indexed: 08/11/2024]
Abstract
Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA). Using the recently updated B. napus genome now including pericentromeres, we demonstrated that COs occur in these cold regions in allotriploids, as close as 375 kb from the centromere. Reverse transcription quantitative PCR (RT-qPCR) of various meiotic genes indicated that Class I COs are likely involved in the increased recombination frequency observed in allotriploids. We also demonstrated that this modified recombination landscape can be maintained via successive generations of allotriploidy (odd ploidy level). This deregulated meiotic behavior reverts to strict regulation in allotetraploid (even ploidy level) progeny in the second generation. Overall, we provide an easy way to manipulate tight recombination control in a polyploid crop.
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Affiliation(s)
- Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Virginie Huteau
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Anael Brunet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Olivier Coriton
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | | | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Marie Gilet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Cécile Baron
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Julien Boutte
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, 91057 Evry, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
| | - Olivier Martin
- Institute of Plant Sciences Paris-Saclay, Université de Paris-Saclay, Paris-Cité and Evry, CNRS, INRAE, 91192 Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, 91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, 91190 Gif-sur-Yvette, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35650 Le Rheu, France
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18
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Osman K, Desjardins SD, Simmonds J, Burridge AJ, Kanyuka K, Henderson IR, Edwards KJ, Uauy C, Franklin FCH, Higgins JD, Sanchez-Moran E. FIGL1 prevents aberrant chromosome associations and fragmentation and limits crossovers in polyploid wheat meiosis. THE NEW PHYTOLOGIST 2024; 244:528-541. [PMID: 38584326 DOI: 10.1111/nph.19716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Meiotic crossovers (COs) generate genetic diversity and are crucial for viable gamete production. Plant COs are typically limited to 1-3 per chromosome pair, constraining the development of improved varieties, which in wheat is exacerbated by an extreme distal localisation bias. Advances in wheat genomics and related technologies provide new opportunities to investigate, and possibly modify, recombination in this important crop species. Here, we investigate the disruption of FIGL1 in tetraploid and hexaploid wheat as a potential strategy for modifying CO frequency/position. We analysed figl1 mutants and virus-induced gene silencing lines cytogenetically. Genetic mapping was performed in the hexaploid. FIGL1 prevents abnormal meiotic chromosome associations/fragmentation in both ploidies. It suppresses class II COs in the tetraploid such that CO/chiasma frequency increased 2.1-fold in a figl1 msh5 quadruple mutant compared with a msh5 double mutant. It does not appear to affect class I COs based on HEI10 foci counts in a hexaploid figl1 triple mutant. Genetic mapping in the triple mutant suggested no significant overall increase in total recombination across examined intervals but revealed large increases in specific individual intervals. Notably, the tetraploid figl1 double mutant was sterile but the hexaploid triple mutant was moderately fertile, indicating potential utility for wheat breeding.
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Affiliation(s)
- Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stuart D Desjardins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amanda J Burridge
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Keith J Edwards
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
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19
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Morgan C, Howard M, Henderson IR. HEI10 coarsening, chromatin and sequence polymorphism shape the plant meiotic recombination landscape. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102570. [PMID: 38838583 DOI: 10.1016/j.pbi.2024.102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Meiosis is a conserved eukaryotic cell division that produces spores required for sexual reproduction. During meiosis, chromosomes pair and undergo programmed DNA double-strand breaks, followed by homologous repair that can result in reciprocal crossovers. Crossover formation is highly regulated with typically few events per homolog pair. Crossovers additionally show wider spacing than expected from uniformly random placement - defining the phenomenon of interference. In plants, the conserved HEI10 E3 ligase is initially loaded along meiotic chromosomes, before maturing into a small number of foci, corresponding to crossover locations. We review the coarsening model that explains these dynamics as a diffusion and aggregation process, resulting in approximately evenly spaced HEI10 foci. We review how underlying chromatin states, and the presence of interhomolog polymorphisms, shape the meiotic recombination landscape, in light of the coarsening model. Finally, we consider future directions to understand the control of meiotic recombination in plant genomes.
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Affiliation(s)
- Chris Morgan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.
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20
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Gordon SG, Rodriguez AA, Gu Y, Corbett KD, Lee CF, Rog O. The synaptonemal complex aligns meiotic chromosomes by wetting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607092. [PMID: 39149313 PMCID: PMC11326210 DOI: 10.1101/2024.08.07.607092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
During meiosis, the parental chromosomes are drawn together to enable exchange of genetic information. Chromosomes are aligned through the assembly of a conserved interface, the synaptonemal complex, composed of a central region that forms between two parallel chromosomal backbones called axes. Here we identify the axis-central region interface in C. elegans, containing a conserved positive patch on the axis component HIM-3 and the C-terminus of the central region protein SYP-5. Crucially, the canonical ultrastructure of the synaptonemal complex is altered upon weakening this interface. We developed a thermodynamic model that recapitulates our experimental observations, indicating that the liquid-like central region can assemble by wetting the axes without active energy consumption. More broadly, our data show that condensation drives tightly regulated nuclear reorganization during sexual reproduction.
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Affiliation(s)
- Spencer G. Gordon
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, United States
| | - Alyssa A. Rodriguez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA 92093
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA 92093
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA 92093
- Department of Molecular Biology, University of California San Diego, La Jolla CA 92093
| | - Chiu Fan Lee
- Department of Bioengineering, Imperial College London, United Kingdom
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, United States
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21
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Chu L, Zhuang J, Geng M, Zhang Y, Zhu J, Zhang C, Schnittger A, Yi B, Yang C. ASYNAPSIS3 has diverse dosage-dependent effects on meiotic crossover formation in Brassica napus. THE PLANT CELL 2024; 36:3838-3856. [PMID: 39047149 PMCID: PMC11371185 DOI: 10.1093/plcell/koae207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Crossovers create genetic diversity and are required for equal chromosome segregation during meiosis. Crossover number and distribution are highly regulated by different mechanisms that are not yet fully understood, including crossover interference. The chromosome axis is crucial for crossover formation. Here, we explore the function of the axis protein ASYNAPSIS3. To this end, we use the allotetraploid species Brassica napus; due to its polyploid nature, this system allows a fine-grained dissection of the dosage of meiotic regulators. The simultaneous mutation of all 4 ASY3 alleles results in defective synapsis and drastic reduction of crossovers, which is largely rescued by the presence of only one functional ASY3 allele. Crucially, while the number of class I crossovers in mutants with 2 functional ASY3 alleles is comparable to that in wild type, this number is significantly increased in mutants with only one functional ASY3 allele, indicating that reducing ASY3 dosage increases crossover formation. Moreover, the class I crossovers on each bivalent in mutants with 1 functional ASY3 allele follow a random distribution, indicating compromised crossover interference. These results reveal the distinct dosage-dependent effects of ASY3 on crossover formation and provide insights into the role of the chromosome axis in patterning recombination.
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Affiliation(s)
- Lei Chu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jixin Zhuang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Miaowei Geng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yashi Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Arp Schnittger
- Department of Developmental Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg 22609, Germany
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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22
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Morgan AP, Payseur BA. Genetic background affects the strength of crossover interference in house mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596233. [PMID: 38854148 PMCID: PMC11160618 DOI: 10.1101/2024.05.28.596233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Meiotic recombination is required for faithful chromosome segregation in most sexually reproducing organisms and shapes the distribution of genetic variation in populations. Both the overall rate and the spatial distribution of crossovers vary within and between species. Adjacent crossovers on the same chromosome tend to be spaced more evenly than expected at random, a phenomenon known as crossover interference. Although interference has been observed in many taxa, the factors that influence the strength of interference are not well understood. We used house mice (Mus musculus), a well-established model system for understanding recombination, to study the effects of genetics and age on recombination rate and interference in the male germline. We analyzed crossover positions in 503 progeny from reciprocal F1 hybrids between inbred strains representing the three major subspecies of house mice. Consistent with previous studies, autosomal alleles from M. m. musculus tend to increase recombination rate, while inheriting a M. m. musculus X chromosome decreases recombination rate. Old males transmit an average of 0.6 more crossovers per meiosis (5.0%) than young males, though the effect varies across genetic backgrounds. We show that the strength of crossover interference depends on genotype, providing a rare demonstration that interference evolves over short timescales. Differences between reciprocal F1s suggest that X-linked factors modulate the strength of interference. Our findings motivate additional comparisons of interference among recently diverged species and further examination of the role of paternal age in determining the number and positioning of crossovers.
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Affiliation(s)
- Andrew P Morgan
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI
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23
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Capilla-Pérez L, Solier V, Gilbault E, Lian Q, Goel M, Huettel B, Keurentjes JJB, Loudet O, Mercier R. Enhanced recombination empowers the detection and mapping of Quantitative Trait Loci. Commun Biol 2024; 7:829. [PMID: 38977904 PMCID: PMC11231358 DOI: 10.1038/s42003-024-06530-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
Modern plant breeding, such as genomic selection and gene editing, is based on the knowledge of the genetic architecture of desired traits. Quantitative trait loci (QTL) analysis, which combines high throughput phenotyping and genotyping of segregating populations, is a powerful tool to identify these genetic determinants and to decipher the underlying mechanisms. However, meiotic recombination, which shuffles genetic information between generations, is limited: Typically only one to two exchange points, called crossovers, occur between a pair of homologous chromosomes. Here we test the effect on QTL analysis of boosting recombination, by mutating the anti-crossover factors RECQ4 and FIGL1 in Arabidopsis thaliana full hybrids and lines in which a single chromosome is hybrid. We show that increasing recombination ~6-fold empowers the detection and resolution of QTLs, reaching the gene scale with only a few hundred plants. Further, enhanced recombination unmasks some secondary QTLs undetected under normal recombination. These results show the benefits of enhanced recombination to decipher the genetic bases of traits.
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Affiliation(s)
- Laia Capilla-Pérez
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Victor Solier
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Elodie Gilbault
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Qichao Lian
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Manish Goel
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Ludwig-Maximilians-Universität München, Fakultät für Biologie, Biozentrum Martinsried, 82152, Planegg-Martinsried, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, MPIPZ, Genome Center, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
| | - Raphael Mercier
- Max Planck Institute for Plant Breeding Research, MPIPZ, Department of Chromosome Biology, Carl-von-Linné Weg 10, 50829, Cologne, Germany.
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24
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Lian Q, Huettel B, Walkemeier B, Mayjonade B, Lopez-Roques C, Gil L, Roux F, Schneeberger K, Mercier R. A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat Genet 2024; 56:982-991. [PMID: 38605175 PMCID: PMC11096106 DOI: 10.1038/s41588-024-01715-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | | | - Lisa Gil
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
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25
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Kim H, Kim J, Son N, Kuo P, Morgan C, Chambon A, Byun D, Park J, Lee Y, Park YM, Fozard JA, Guérin J, Hurel A, Lambing C, Howard M, Hwang I, Mercier R, Grelon M, Henderson IR, Choi K. Control of meiotic crossover interference by a proteolytic chaperone network. NATURE PLANTS 2024; 10:453-468. [PMID: 38379086 DOI: 10.1038/s41477-024-01633-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Meiosis is a specialized eukaryotic division that produces genetically diverse gametes for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal exchanges, called crossovers, which recombine genetic variation. Meiotic crossovers are stringently controlled with at least one obligate exchange forming per chromosome pair, while closely spaced crossovers are inhibited by interference. In Arabidopsis, crossover positions can be explained by a diffusion-mediated coarsening model, in which large, approximately evenly spaced foci of the pro-crossover E3 ligase HEI10 grow at the expense of smaller, closely spaced clusters. However, the mechanisms that control HEI10 dynamics during meiosis remain unclear. Here, through a forward genetic screen in Arabidopsis, we identified high crossover rate3 (hcr3), a dominant-negative mutant that reduces crossover interference and increases crossovers genome-wide. HCR3 encodes J3, a co-chaperone related to HSP40, which acts to target protein aggregates and biomolecular condensates to the disassembly chaperone HSP70, thereby promoting proteasomal degradation. Consistently, we show that a network of HCR3 and HSP70 chaperones facilitates proteolysis of HEI10, thereby regulating interference and the recombination landscape. These results reveal a new role for the HSP40/J3-HSP70 chaperones in regulating chromosome-wide dynamics of recombination via control of HEI10 proteolysis.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Namil Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Chris Morgan
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Aurélie Chambon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Dohwan Byun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jihye Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngkyung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yeong Mi Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - John A Fozard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Julie Guérin
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Aurélie Hurel
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
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26
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Chen L, Weir JR. The molecular machinery of meiotic recombination. Biochem Soc Trans 2024; 52:379-393. [PMID: 38348856 PMCID: PMC10903461 DOI: 10.1042/bst20230712] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Meiotic recombination, a cornerstone of eukaryotic diversity and individual genetic identity, is essential for the creation of physical linkages between homologous chromosomes, facilitating their faithful segregation during meiosis I. This process requires that germ cells generate controlled DNA lesions within their own genome that are subsequently repaired in a specialised manner. Repair of these DNA breaks involves the modulation of existing homologous recombination repair pathways to generate crossovers between homologous chromosomes. Decades of genetic and cytological studies have identified a multitude of factors that are involved in meiotic recombination. Recent work has started to provide additional mechanistic insights into how these factors interact with one another, with DNA, and provide the molecular outcomes required for a successful meiosis. Here, we provide a review of the recent developments with a focus on protein structures and protein-protein interactions.
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Affiliation(s)
- Linda Chen
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - John R. Weir
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
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27
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Fernandes JB, Naish M, Lian Q, Burns R, Tock AJ, Rabanal FA, Wlodzimierz P, Habring A, Nicholas RE, Weigel D, Mercier R, Henderson IR. Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis. Genome Biol 2024; 25:30. [PMID: 38254210 PMCID: PMC10804481 DOI: 10.1186/s13059-024-03163-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within and between species. Despite variability in DNA sequence, centromeres are also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic and epigenetic factors responsible for suppression of centromeric crossovers remain to be completely defined. RESULTS To explore the centromere-proximal meiotic recombination landscape, we map 14,397 crossovers against fully assembled Arabidopsis thaliana (A. thaliana) genomes. A. thaliana centromeres comprise megabase satellite repeat arrays that load nucleosomes containing the CENH3 histone variant. Each chromosome contains a structurally polymorphic region of ~3-4 megabases, which lack crossovers and include the satellite arrays. This polymorphic region is flanked by ~1-2 megabase low-recombination zones. These recombination-suppressed regions are enriched for Gypsy/Ty3 retrotransposons, and additionally contain expressed genes with high genetic diversity that initiate meiotic recombination, yet do not crossover. We map crossovers at high-resolution in proximity to CEN3, which resolves punctate centromere-proximal hotspots that overlap gene islands embedded in heterochromatin. Centromeres are densely DNA methylated and the recombination landscape is remodelled in DNA methylation mutants. We observe that the centromeric low-recombining zones decrease and increase crossovers in CG (met1) and non-CG (cmt3) mutants, respectively, whereas the core non-recombining zones remain suppressed. CONCLUSION Our work relates the genetic and epigenetic organization of A. thaliana centromeres and flanking pericentromeric heterochromatin to the zones of crossover suppression that surround the CENH3-occupied satellite repeat arrays.
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Affiliation(s)
- Joiselle B Fernandes
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
| | - Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
| | - Robin Burns
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Biology, Tübingen, D-72076, Tübingen, Germany
| | - Piotr Wlodzimierz
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Anette Habring
- Department of Molecular Biology, Max Planck Institute for Biology, Tübingen, D-72076, Tübingen, Germany
| | - Robert E Nicholas
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, Tübingen, D-72076, Tübingen, Germany
- University of Tübingen, Institute for Bioinformatics and Medical Informatics, D-72076, Tübingen, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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28
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Tan Q, Zhang X, Luo Q, Xu YC, Zhang J, Liang WQ. The RING Domain of Rice HEI10 is Essential for Male, But Not Female Fertility. RICE (NEW YORK, N.Y.) 2024; 17:3. [PMID: 38180592 PMCID: PMC10769960 DOI: 10.1186/s12284-023-00681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
HEI10 is a conserved E3 ubiquitin ligase involved in crossover formation during meiosis, and is thus essential for both male and female gamete development. Here, we have discovered a novel allele of HEI10 in rice that produces a truncated HEI10 protein missing its N-terminal RING domain, namely sh1 (shorter hei10 1). Unlike previously reported hei10 null alleles that are completely sterile, sh1 exhibits complete male sterility but retains partial female fertility. The causative sh1 mutation is a 76 kb inversion between OsFYVE4 and HEI10, which breaks the integrity of both genes. Allelic tests and complementation assays revealed that the gamete developmental defects of sh1 were caused by disruption of HEI10. Further studies demonstrated that short HEI10 can correctly localise to the nucleus, where it could interact with other proteins that direct meiosis; expressing short HEI10 in hei10 null lines partially restores female fertility. Our data reveal an intriguing mutant allele of HEI10 with differential effects on male and female fertility, providing a new tool to explore similarities and differences between male and female meiosis.
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Affiliation(s)
- Qian Tan
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Luo
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Chun Xu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wan-Qi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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29
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Cseh A, Lenykó-Thegze A, Makai D, Szabados F, Hamow KÁ, Gulyás Z, Kiss T, Karsai I, Moncsek B, Mihók E, Sepsi A. Meiotic instability and irregular chromosome pairing underpin heat-induced infertility in bread wheat carrying the Rht-B1b or Rht-D1b Green Revolution genes. THE NEW PHYTOLOGIST 2024; 241:180-196. [PMID: 37691304 DOI: 10.1111/nph.19256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/12/2023] [Indexed: 09/12/2023]
Abstract
Mutations in the Rht-B1a and Rht-D1a genes of wheat (Triticum aestivum; resulting in Rht-B1b and Rht-D1b alleles) cause gibberellin-insensitive dwarfism and are one of the most important elements of increased yield introduced during the 'Green Revolution'. We measured the effects of a short period of heat imposed during the early reproductive stage on near-isogenic lines carrying Rht-B1b or Rht-D1b alleles, with respect to the wild-type (WT). The temperature shift caused a significant fertility loss within the ears of Rht-B1b and Rht-D1b wheats, greater than that observed for the WT. Defects in chromosome synapsis, reduced homologous recombination and a high frequency of chromosome mis-segregation were associated with reduced fertility. The transcription of TaGA3ox gene involved in the final stage of gibberellic acid (GA) biosynthesis was activated and ultra-performance liquid chromatography-tandem mass spectrometry identified GA1 as the dominant bioactive GA in developing ears, but levels were unaffected by the elevated temperature. Rht-B1b and Rht-D1b mutants were inclined to meiotic errors under optimal temperatures and showed a higher susceptibility to heat than their tall counterparts. Identification and introduction of new dwarfing alleles into modern breeding programmes is invaluable in the development of climate-resilient wheat varieties.
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Affiliation(s)
- András Cseh
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Andrea Lenykó-Thegze
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Egyetem tér 1-3, Budapest, 1053, Hungary
| | - Diána Makai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Fanni Szabados
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Kamirán Áron Hamow
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Zsolt Gulyás
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Tibor Kiss
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eszterházy tér 1, Eger, 3300, Hungary
| | - Ildikó Karsai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Blanka Moncsek
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Edit Mihók
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Adél Sepsi
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
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30
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Parra-Nunez P, Fernández-Jiménez N, Pachon-Penalba M, Sanchez-Moran E, Pradillo M, Santos JL. Synthetically induced Arabidopsis thaliana autotetraploids provide insights into the analysis of meiotic mutants with altered crossover frequency. THE NEW PHYTOLOGIST 2024; 241:197-208. [PMID: 37921581 DOI: 10.1111/nph.19366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/29/2023] [Indexed: 11/04/2023]
Abstract
Mutations affecting crossover (CO) frequency and distribution lead to the presence of univalents during meiosis, giving rise to aneuploid gametes and sterility. These mutations may have a different effect after chromosome doubling. The combination of altered ploidy and mutations could be potentially useful to gain new insights into the mechanisms and regulation of meiotic recombination; however, studies using autopolyploid meiotic mutants are scarce. Here, we have analyzed the cytogenetic consequences in colchicine-induced autotetraploids (colchiploids) from different Arabidopsis mutants with an altered CO frequency. We have found that there are three types of mutants: mutants in which chiasma frequency is doubled after chromosome duplication (zip4, mus81), as in the control; mutants in which polyploidy leads to a higher-than-expected increase in chiasma frequency (asy1, mer3, hei10, and mlh3); and mutants in which the rise in chiasma frequency produced by the presence of two extrachromosomal sets is less than doubled (msh5, fancm). In addition, the proportion of class I/class II COs varies after chromosome duplication in the control. The results obtained reveal the potential of colchiploid meiotic mutants for better understanding of the function of key proteins during plant meiosis. This is especially relevant considering that most crops are polyploids.
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Affiliation(s)
- Pablo Parra-Nunez
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nadia Fernández-Jiménez
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Madrid, 28040, Spain
| | - Miguel Pachon-Penalba
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | | | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Madrid, 28040, Spain
| | - Juan Luis Santos
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Madrid, 28040, Spain
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31
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Fozard J, Morgan C. Automated Quantification of Meiotic Recombination Foci Position and Intensity. Methods Mol Biol 2024; 2818:239-248. [PMID: 39126479 DOI: 10.1007/978-1-0716-3906-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
During meiosis, homologous chromosomes reciprocally exchange segments of DNA via the formation of crossovers. However, the frequency and position of crossover events along chromosomes are not random. Each chromosome must receive at least one crossover, and the formation of a crossover at one location inhibits the formation of additional crossovers nearby. These crossover patterning phenomena are referred to as "crossover assurance" and "crossover interference," respectively. One key method for quantifying meiotic crossover patterning is to immunocytologically measure the position and intensity of crossover-associated protein foci along the length of meiotic prophase I chromosomes. This approach was recently used to map the position of a conserved E3 ligase, HEI10, along Arabidopsis pachytene chromosomes, providing experimental support for a novel mechanistic "coarsening model" for crossover patterning. Here we describe a user-friendly method for automatically measuring the position and intensity of recombination-associated foci along meiotic prophase I chromosomes that is broadly applicable to studies in different eukaryotic species.
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Affiliation(s)
- John Fozard
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Chris Morgan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.
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32
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Wang T, Wang H, Lian Q, Jia Q, You C, Copenhaver GP, Wang C, Wang Y. HEI10 is subject to phase separation and mediates RPA1a degradation during meiotic interference-sensitive crossover formation. Proc Natl Acad Sci U S A 2023; 120:e2310542120. [PMID: 38134200 PMCID: PMC10756261 DOI: 10.1073/pnas.2310542120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/27/2023] [Indexed: 12/24/2023] Open
Abstract
Reciprocal exchanges of DNA between homologous chromosomes during meiosis, or crossovers (COs), shuffle genetic information in gametes and progeny. In many eukaryotes, the majority of COs (class I COs) are sensitive to a phenomenon called interference, which influences the occurrence of closely spaced double COs. Class I COs depend on a group of factors called ZMM (Zip, Msh, Mer) proteins including HEI10 (Human Enhancer of Invasion-10). However, how these proteins are recruited to class I CO sites is unclear. Here, we show that HEI10 forms foci on chromatin via a liquid-liquid phase separation (LLPS) mechanism that relies on residue Ser70. A HEI10S70F allele results in LLPS failure and a defect in class I CO formation. We further used immunoprecipitation-mass spectrometry to identify RPA1a (Replication Protein A 1) as a HEI10 interacting protein. Surprisingly, we find that RPA1a also undergoes phase separation and its ubiquitination and degradation are directly regulated by HEI10. We also show that HEI10 is required for the condensation of other class I CO factors. Thus, our results provide mechanistic insight into how meiotic class I CO formation is controlled by HEI10 coupling LLPS and ubiquitination.
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Affiliation(s)
- Tianyi Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
| | - Hongkuan Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI49503
| | - Qichao Lian
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Qian Jia
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
| | - Chenjiang You
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC27599-3280
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC27599-3280
| | - Cong Wang
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
- College of Life Sciences, South China Agricultural University, Guangzhou510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou510642, China
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Kursel LE, Martinez JEA, Rog O. A suppressor screen in C. elegans identifies a multiprotein interaction that stabilizes the synaptonemal complex. Proc Natl Acad Sci U S A 2023; 120:e2314335120. [PMID: 38055743 PMCID: PMC10723054 DOI: 10.1073/pnas.2314335120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/23/2023] [Indexed: 12/08/2023] Open
Abstract
Successful chromosome segregation into gametes depends on tightly regulated interactions between the parental chromosomes. During meiosis, chromosomes are aligned end-to-end by an interface called the synaptonemal complex, which also regulates exchanges between them. However, despite the functional and ultrastructural conservation of this essential interface, how protein-protein interactions within the synaptonemal complex regulate chromosomal interactions remains poorly understood. Here, we describe a genetic interaction in the C. elegans synaptonemal complex, comprised of short segments of three proteins, SYP-1, SYP-3, and SYP-4. We identified the interaction through a saturated suppressor screen of a mutant that destabilizes the synaptonemal complex. The specificity and tight distribution of suppressors suggest a charge-based interface that promotes interactions between synaptonemal complex subunits and, in turn, allows intimate interactions between chromosomes. Our work highlights the power of genetic studies to illuminate the mechanisms that underlie meiotic chromosome interactions.
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Affiliation(s)
- Lisa E. Kursel
- School of Biological Sciences and Center for Cell and Genome Sciences, The University of Utah, Salt Lake City, UT84112
| | - Jesus E. Aguayo Martinez
- School of Biological Sciences and Center for Cell and Genome Sciences, The University of Utah, Salt Lake City, UT84112
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, The University of Utah, Salt Lake City, UT84112
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Vrielynck N, Peuch M, Durand S, Lian Q, Chambon A, Hurel A, Guérin J, Guérois R, Mercier R, Grelon M, Mézard C. SCEP1 and SCEP2 are two new components of the synaptonemal complex central element. NATURE PLANTS 2023; 9:2016-2030. [PMID: 37973938 DOI: 10.1038/s41477-023-01558-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
The synaptonemal complex (SC) is a proteinaceous structure that forms between homologous chromosomes during meiosis prophase. The SC is widely conserved across species, but its structure and roles during meiotic recombination are still debated. While the SC central region is made up of transverse filaments and central element proteins in mammals and fungi, few central element proteins have been identified in other species. Here we report the identification of two coiled-coil proteins, SCEP1 and SCEP2, that form a complex and localize at the centre of the Arabidopsis thaliana SC. In scep1 and scep2 mutants, chromosomes are aligned but not synapsed (the ZYP1 transverse filament protein is not loaded), crossovers are increased compared with the wild type, interference is lost and heterochiasmy is strongly reduced. We thus report the identification of two plant SC central elements, and homologues of these are found in all major angiosperm clades.
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Affiliation(s)
- Nathalie Vrielynck
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Marion Peuch
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Stéphanie Durand
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Aurélie Chambon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Aurélie Hurel
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Julie Guérin
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Raphaël Guérois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Raphaël Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathilde Grelon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France.
| | - Christine Mézard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France.
- Université Paris-Saclay, INRAE, AgroParisTech, CNRS, Institut Jean-Pierre Bourgin, Versailles, France.
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35
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Chowdary KVSKA, Saini R, Singh AK. Epigenetic regulation during meiosis and crossover. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1945-1958. [PMID: 38222277 PMCID: PMC10784443 DOI: 10.1007/s12298-023-01390-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 01/16/2024]
Abstract
Meiosis is a distinctive type of cell division that reorganizes genetic material between generations. The initial stages of meiosis consist of several crucial steps which include double strand break, homologous chromosome pairing, break repair and crossover. Crossover frequency varies depending on the position on the chromosome, higher at euchromatin region and rare at heterochromatin, centromeres, telomeres and ribosomal DNA. Crossover positioning is dependent on various factors, especially epigenetic modifications. DNA methylation, histone post-translational modifications, histone variants and non-coding RNAs are most probably playing an important role in positioning of crossovers on a chromosomal level as well as hotspot level. DNA methylation negatively regulates crossover frequency and its effect is visible in centromeres, pericentromeres and heterochromatin regions. Pericentromeric chromatin and heterochromatin mark studies have been a centre of attraction in meiosis. Crossover hotspots are associated with euchromatin regions having specific chromatin modifications such as H3K4me3, H2A.Z. and H3 acetylation. This review will provide the current understanding of the epigenetic role in plants during meiotic recombination, chromosome synapsis, double strand break and hotspots with special attention to euchromatin and heterochromatin marks. Further, the role of epigenetic modifications in regulating meiosis and crossover in other organisms is also discussed.
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Affiliation(s)
- K. V. S. K. Arjun Chowdary
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Ramswaroop Saini
- Department of Biotechnology, Joy University, Vadakangulam, Tirunelveli, Tamil Nadu 627116 India
| | - Amit Kumar Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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36
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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37
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Dluzewska J, Dziegielewski W, Szymanska-Lejman M, Gazecka M, Henderson IR, Higgins JD, Ziolkowski PA. MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism. Nat Commun 2023; 14:6716. [PMID: 37872134 PMCID: PMC10593791 DOI: 10.1038/s41467-023-42511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism.
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Affiliation(s)
- Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Monika Gazecka
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
- Department of Molecular Virology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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38
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Cahoon CK, Richter CM, Dayton AE, Libuda DE. Sexual dimorphic regulation of recombination by the synaptonemal complex in C. elegans. eLife 2023; 12:e84538. [PMID: 37796106 PMCID: PMC10611432 DOI: 10.7554/elife.84538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/02/2023] [Indexed: 10/06/2023] Open
Abstract
In sexually reproducing organisms, germ cells faithfully transmit the genome to the next generation by forming haploid gametes, such as eggs and sperm. Although most meiotic proteins are conserved between eggs and sperm, many aspects of meiosis are sexually dimorphic, including the regulation of recombination. The synaptonemal complex (SC), a large ladder-like structure that forms between homologous chromosomes, is essential for regulating meiotic chromosome organization and promoting recombination. To assess whether sex-specific differences in the SC underpin sexually dimorphic aspects of meiosis, we examined Caenorhabditis elegans SC central region proteins (known as SYP proteins) in oogenesis and spermatogenesis and uncovered sex-specific roles for the SYPs in regulating meiotic recombination. We find that SC composition, specifically SYP-2, SYP-3, SYP-5, and SYP-6, is regulated by sex-specific mechanisms throughout meiotic prophase I. During pachytene, both oocytes and spermatocytes differentially regulate the stability of SYP-2 and SYP-3 within an assembled SC. Further, we uncover that the relative amount of SYP-2 and SYP-3 within the SC is independently regulated in both a sex-specific and a recombination-dependent manner. Specifically, we find that SYP-2 regulates the early steps of recombination in both sexes, while SYP-3 controls the timing and positioning of crossover recombination events across the genomic landscape in only oocytes. Finally, we find that SYP-2 and SYP-3 dosage can influence the composition of the other SYPs in the SC via sex-specific mechanisms during pachytene. Taken together, we demonstrate dosage-dependent regulation of individual SC components with sex-specific functions in recombination. These sexual dimorphic features of the SC provide insights into how spermatogenesis and oogenesis adapted similar chromosome structures to differentially regulate and execute recombination.
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Affiliation(s)
- Cori K Cahoon
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | - Colette M Richter
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | - Amelia E Dayton
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | - Diana E Libuda
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
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39
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Lian Q, Maestroni L, Gaudin M, Llorente B, Mercier R. Meiotic recombination is confirmed to be unusually high in the fission yeast Schizosaccharomyces pombe. iScience 2023; 26:107614. [PMID: 37664590 PMCID: PMC10474467 DOI: 10.1016/j.isci.2023.107614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/20/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
In most eukaryotes, meiotic crossovers (COs) are limited to 1-3 per chromosome, and are prevented from occurring close to one another by CO interference. The fission yeast Schizosaccharomyces pombe, an exception to these general rules, was reported to have the highest CO number per chromosome and no or weak interference. However, global CO frequency was indirectly estimated, calling for confirmation. Here, we used an innovative strategy to determine COs genome-wide in S. pombe. We confirmed weak CO interference, acting at physical distances compatible with the patterning of recombination precursors. We revealed a slight co-variation in CO number between chromosomes, suggesting that a limiting pro-CO factor varies between meiocytes. CO number per chromosome varies proportionally with chromosome size, with the three chromosomes having, on average, 15.9, 12.5, and 7.0 COs, respectively. This reinforces S. pombe's status as the eukaryote with the highest CO number per chromosome described to date.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Maxime Gaudin
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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40
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Kursel LE, Martinez JEA, Rog O. A suppressor screen in C. elegans identifies a multi-protein interaction interface that stabilizes the synaptonemal complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554166. [PMID: 37662357 PMCID: PMC10473659 DOI: 10.1101/2023.08.21.554166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Successful chromosome segregation into gametes depends on tightly-regulated interactions between the parental chromosomes. During meiosis, chromosomes are aligned end-to-end by an interface called the synaptonemal complex, which also regulates exchanges between them. However, despite the functional and ultrastructural conservation of this essential interface, how protein-protein interactions within the synaptonemal complex regulate chromosomal interactions remains poorly understood. Here we describe a novel interaction interface in the C. elegans synaptonemal complex, comprised of short segments of three proteins, SYP-1, SYP-3 and SYP-4. We identified the interface through a saturated suppressor screen of a mutant that destabilizes the synaptonemal complex. The specificity and tight distribution of suppressors point to a charge-based interface that promotes interactions between synaptonemal complex subunits and, in turn, allows intimate interactions between chromosomes. Our work highlights the power of genetic studies to illuminate the mechanisms that underly meiotic chromosome interactions.
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Affiliation(s)
- Lisa E. Kursel
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, United States
| | - Jesus E. Aguayo Martinez
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, United States
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, United States
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41
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Gonzalo A, Parra-Nunez P, Bachmann AL, Sanchez-Moran E, Bomblies K. Partial cytological diploidization of neoautotetraploid meiosis by induced cross-over rate reduction. Proc Natl Acad Sci U S A 2023; 120:e2305002120. [PMID: 37549263 PMCID: PMC10434300 DOI: 10.1073/pnas.2305002120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023] Open
Abstract
Polyploids, which arise from whole-genome duplication events, have contributed to genome evolution throughout eukaryotes. Among plants, novel features of neopolyploids include traits that can be evolutionarily or agriculturally beneficial, such as increased abiotic stress tolerance. Thus, in addition to being interesting from an evolutionary perspective, genome duplication is also increasingly recognized as a promising crop improvement tool. However, newly formed (neo)polyploids commonly suffer from fertility problems, which have been attributed to abnormal associations among the multiple homologous chromosome copies during meiosis (multivalents). Here, we test the long-standing hypothesis that reducing meiotic cross-over number may be sufficient to limit multivalent formation, favoring diploid-like bivalent associations (cytological diploidization). To do so, we developed Arabidopsis thaliana lines with low cross-over rates by combining mutations for HEI10 and TAF4b. Double mutants showed a reduction of ~33% in cross-over numbers in diploids without compromising meiotic stability. Neopolyploids derived from the double mutant show a cross-over rate reduction of about 40% relative to wild-type neotetraploids, and groups of four homologs indeed formed fewer multivalents and more bivalents. However, we also show that the reduction in multivalents comes with the cost of a slightly increased frequency of univalents and that it does not rescue neopolyploid fertility. Thus, while our results do show that reducing cross-over rates can reduce multivalent frequency in neopolyploids, they also emphasize that there are additional factors affecting both meiotic stability and neopolyploid fertility that will need to be considered in solving the neopolyploid fertility challenge.
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Affiliation(s)
- Adrián Gonzalo
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8092Zürich, Switzerland
| | - Pablo Parra-Nunez
- School of Biosciences, University of Birmingham, BirminghamB15 2TT, United Kingdom
| | - Andreas L. Bachmann
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8092Zürich, Switzerland
| | | | - Kirsten Bomblies
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8092Zürich, Switzerland
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42
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Rafiei N, Ronceret A. Crossover interference mechanism: New lessons from plants. Front Cell Dev Biol 2023; 11:1156766. [PMID: 37274744 PMCID: PMC10236007 DOI: 10.3389/fcell.2023.1156766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Plants are the source of our understanding of several fundamental biological principles. It is well known that Gregor Mendel discovered the laws of Genetics in peas and that maize was used for the discovery of transposons by Barbara McClintock. Plant models are still useful for the understanding of general key biological concepts. In this article, we will focus on discussing the recent plant studies that have shed new light on the mysterious mechanisms of meiotic crossover (CO) interference, heterochiasmy, obligatory CO, and CO homeostasis. Obligatory CO is necessary for the equilibrated segregation of homologous chromosomes during meiosis. The tight control of the different male and female CO rates (heterochiasmy) enables both the maximization and minimization of genome shuffling. An integrative model can now predict these observed aspects of CO patterning in plants. The mechanism proposed considers the Synaptonemal Complex as a canalizing structure that allows the diffusion of a class I CO limiting factor linearly on synapsed bivalents. The coarsening of this limiting factor along the SC explains the interfering spacing between COs. The model explains the observed coordinated processes between synapsis, CO interference, CO insurance, and CO homeostasis. It also easily explains heterochiasmy just considering the different male and female SC lengths. This mechanism is expected to be conserved in other species.
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43
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Mehdi SMM, Szczesniak MW, Ludwików A. The Bro1-like domain-containing protein, AtBro1, modulates growth and abiotic stress responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1157435. [PMID: 37251780 PMCID: PMC10213323 DOI: 10.3389/fpls.2023.1157435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023]
Abstract
Abscisic acid (ABA) affects plant physiology by altering gene expression, enabling plants to adapt to a wide range of environments. Plants have evolved protective mechanisms to allow seed germination in harsh conditions. Here, we explore a subset of these mechanisms involving the AtBro1 gene, which encodes one of a small family of poorly characterised Bro1-like domain-containing proteins, in Arabidopsis thaliana plants subjected to multiple abiotic stresses. AtBro1 transcripts were upregulated by salt, ABA and mannitol stress, while AtBro1-overexpression lines demonstrated robust tolerance to drought and salt stress. Furthermore, we found that ABA elicits stress-resistance responses in loss-of-function bro1-1 mutant plants and AtBro1 regulates drought resistance in Arabidopsis. When the AtBro1 promoter was fused to the β-glucuronidase (GUS) gene and introduced into plants, GUS was expressed mainly in rosette leaves and floral clusters, especially in anthers. Using a construct expressing an AtBro1-GFP fusion protein, AtBro1 was found to be localized in the plasma membrane in Arabidopsis protoplasts. A broad RNA-sequencing analysis revealed specific quantitative differences in the early transcriptional responses to ABA treatment between wild-type and loss-of-function bro1-1 mutant plants, suggesting that ABA stimulates stress-resistance responses via AtBro1. Additionally, transcripts levels of MOP9.5, MRD1, HEI10, and MIOX4 were altered in bro1-1 plants exposed to different stress conditions. Collectively, our results show that AtBro1 plays a significant role in the regulation of the plant transcriptional response to ABA and the induction of resistance responses to abiotic stress.
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Affiliation(s)
- Syed Muhammad Muntazir Mehdi
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Michal Wojciech Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Agnieszka Ludwików
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
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Girard C, Zwicker D, Mercier R. The regulation of meiotic crossover distribution: a coarse solution to a century-old mystery? Biochem Soc Trans 2023:233030. [PMID: 37145037 DOI: 10.1042/bst20221329] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Meiotic crossovers, which are exchanges of genetic material between homologous chromosomes, are more evenly and distantly spaced along chromosomes than expected by chance. This is because the occurrence of one crossover reduces the likelihood of nearby crossover events - a conserved and intriguing phenomenon called crossover interference. Although crossover interference was first described over a century ago, the mechanism allowing coordination of the fate of potential crossover sites half a chromosome away remains elusive. In this review, we discuss the recently published evidence supporting a new model for crossover patterning, coined the coarsening model, and point out the missing pieces that are still needed to complete this fascinating puzzle.
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Affiliation(s)
- Chloe Girard
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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Almanzar DE, Gordon SG, Bristow C, Hamrick A, von Diezmann L, Liu H, Rog O. Meiotic DNA exchanges in C. elegans are promoted by proximity to the synaptonemal complex. Life Sci Alliance 2023; 6:e202301906. [PMID: 36697255 PMCID: PMC9877436 DOI: 10.26508/lsa.202301906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
During meiosis, programmed double-strand DNA breaks are repaired to form exchanges between the parental chromosomes called crossovers. Chromosomes lacking a crossover fail to segregate accurately into the gametes, leading to aneuploidy. In addition to engaging the homolog, crossover formation requires the promotion of exchanges, rather than non-exchanges, as repair products. However, the mechanism underlying this meiosis-specific preference is not fully understood. Here, we study the regulation of meiotic sister chromatid exchanges in Caenorhabditis elegans by direct visualization. We find that a conserved chromosomal interface that promotes exchanges between the parental chromosomes, the synaptonemal complex, can also promote exchanges between the sister chromatids. In both cases, exchanges depend on the recruitment of the same set of pro-exchange factors to repair sites. Surprisingly, although the synaptonemal complex usually assembles between the two DNA molecules undergoing an exchange, its activity does not rely on a specific chromosome conformation. This suggests that the synaptonemal complex regulates exchanges-both crossovers and sister exchanges-by establishing a nuclear domain conducive to nearby recruitment of exchange-promoting factors.
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Affiliation(s)
- David E Almanzar
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Spencer G Gordon
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Chloe Bristow
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Antonia Hamrick
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Lexy von Diezmann
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Hanwenheng Liu
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
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Koury SA. Predicting recombination suppression outside chromosomal inversions in Drosophila melanogaster using crossover interference theory. Heredity (Edinb) 2023; 130:196-208. [PMID: 36721031 PMCID: PMC10076299 DOI: 10.1038/s41437-023-00593-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 02/02/2023] Open
Abstract
Recombination suppression in chromosomal inversion heterozygotes is a well-known but poorly understood phenomenon. Surprisingly, recombination suppression extends far outside of inverted regions where there are no intrinsic barriers to normal chromosome pairing, synapsis, double-strand break formation, or recovery of crossover products. The interference hypothesis of recombination suppression proposes heterozygous inversion breakpoints possess chiasma-like properties such that recombination suppression extends from these breakpoints in a process analogous to crossover interference. This hypothesis is qualitatively consistent with chromosome-wide patterns of recombination suppression extending to both inverted and uninverted regions of the chromosome. The present study generated quantitative predictions for this hypothesis using a probabilistic model of crossover interference with gamma-distributed inter-event distances. These predictions were then tested with experimental genetic data (>40,000 meioses) on crossing-over in intervals that are external and adjacent to four common inversions of Drosophila melanogaster. The crossover interference model accurately predicted the partially suppressed recombination rates in euchromatic intervals outside inverted regions. Furthermore, assuming interference does not extend across centromeres dramatically improved model fit and partially accounted for excess recombination observed in pericentromeric intervals. Finally, inversions with breakpoints closest to the centromere had the greatest excess of recombination in pericentromeric intervals, an observation that is consistent with negative crossover interference previously documented near Drosophila melanogaster centromeres. In conclusion, the experimental data support the interference hypothesis of recombination suppression, validate a mathematical framework for integrating distance-dependent effects of structural heterozygosity on crossover distribution, and highlight the need for improved modeling of crossover interference in pericentromeric regions.
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Affiliation(s)
- Spencer A Koury
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY, 11794, USA.
- 2613 Ashwood Ave, Nashville, TN, 37212, USA.
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Abstract
KEY MESSAGE Chromatin state, and dynamic loading of pro-crossover protein HEI10 at recombination intermediates shape meiotic chromosome patterning in plants. Meiosis is the basis of sexual reproduction, and its basic progression is conserved across eukaryote kingdoms. A key feature of meiosis is the formation of crossovers which result in the reciprocal exchange of segments of maternal and paternal chromosomes. This exchange generates chromosomes with new combinations of alleles, increasing the efficiency of both natural and artificial selection. Crossovers also form a physical link between homologous chromosomes at metaphase I which is critical for accurate chromosome segregation and fertility. The patterning of crossovers along the length of chromosomes is a highly regulated process, and our current understanding of its regulation forms the focus of this review. At the global scale, crossover patterning in plants is largely governed by the classically observed phenomena of crossover interference, crossover homeostasis and the obligatory crossover which regulate the total number of crossovers and their relative spacing. The molecular actors behind these phenomena have long remained obscure, but recent studies in plants implicate HEI10 and ZYP1 as key players in their coordination. In addition to these broad forces, a wealth of recent studies has highlighted how genomic and epigenomic features shape crossover formation at both chromosomal and local scales, revealing that crossovers are primarily located in open chromatin associated with gene promoters and terminators with low nucleosome occupancy.
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Affiliation(s)
- Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK.
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48
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Fozard JA, Morgan C, Howard M. Coarsening dynamics can explain meiotic crossover patterning in both the presence and absence of the synaptonemal complex. eLife 2023; 12:e79408. [PMID: 36847348 PMCID: PMC10036115 DOI: 10.7554/elife.79408] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 02/24/2023] [Indexed: 03/01/2023] Open
Abstract
The shuffling of genetic material facilitated by meiotic crossovers is a critical driver of genetic variation. Therefore, the number and positions of crossover events must be carefully controlled. In Arabidopsis, an obligate crossover and repression of nearby crossovers on each chromosome pair are abolished in mutants that lack the synaptonemal complex (SC), a conserved protein scaffold. We use mathematical modelling and quantitative super-resolution microscopy to explore and mechanistically explain meiotic crossover pattering in Arabidopsis lines with full, incomplete, or abolished synapsis. For zyp1 mutants, which lack an SC, we develop a coarsening model in which crossover precursors globally compete for a limited pool of the pro-crossover factor HEI10, with dynamic HEI10 exchange mediated through the nucleoplasm. We demonstrate that this model is capable of quantitatively reproducing and predicting zyp1 experimental crossover patterning and HEI10 foci intensity data. Additionally, we find that a model combining both SC- and nucleoplasm-mediated coarsening can explain crossover patterning in wild-type Arabidopsis and in pch2 mutants, which display partial synapsis. Together, our results reveal that regulation of crossover patterning in wild-type Arabidopsis and SC-defective mutants likely acts through the same underlying coarsening mechanism, differing only in the spatial compartments through which the pro-crossover factor diffuses.
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Affiliation(s)
- John A Fozard
- Computational and Systems Biology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Chris Morgan
- Cell and Developmental Biology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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Szymanska-Lejman M, Dziegielewski W, Dluzewska J, Kbiri N, Bieluszewska A, Poethig RS, Ziolkowski PA. The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids. Nat Commun 2023; 14:33. [PMID: 36596804 PMCID: PMC9810609 DOI: 10.1038/s41467-022-35722-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
In hybrid organisms, genetically divergent homologous chromosomes pair and recombine during meiosis; however, the effect of specific types of polymorphisms on crossover is poorly understood. Here, to analyze this in Arabidopsis, we develop the seed-typing method that enables the massively parallel fine-mapping of crossovers by sequencing. We show that structural variants, observed in one of the generated intervals, do not change crossover frequency unless they are located directly within crossover hotspots. Both natural and Cas9-induced deletions result in lower hotspot activity but are not compensated by increases in immediately adjacent hotspots. To examine the effect of single nucleotide polymorphisms on crossover formation, we analyze hotspot activity in mismatch detection-deficient msh2 mutants. Surprisingly, polymorphic hotspots show reduced activity in msh2. In lines where only the hotspot-containing interval is heterozygous, crossover numbers increase above those in the inbred (homozygous). We conclude that MSH2 shapes crossover distribution by stimulating hotspot activity at polymorphic regions.
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Affiliation(s)
- Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Nadia Kbiri
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Anna Bieluszewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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