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Wang Y, Chen Y, Gao J, Xie H, Guo Y, Yang J, Liu J, Chen Z, Li Q, Li M, Ren J, Wen L, Tang F. Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq. Cell Discov 2024; 10:26. [PMID: 38443370 PMCID: PMC10915157 DOI: 10.1038/s41421-023-00638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/11/2023] [Indexed: 03/07/2024] Open
Abstract
Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means the inability to detect both alleles simultaneously in an individual diploid cell, largely restricts the application of these methods particularly for medical applications. Here, we develop a new single-cell whole-genome sequencing method based on third-generation sequencing (TGS) platform named Refresh-seq (restriction fragment ligation-based genome amplification and TGS). It is based on restriction endonuclease cutting and ligation strategy in which two alleles in an individual cell can be cut into equal fragments and tend to be amplified simultaneously. As a new single-cell long-read genome sequencing method, Refresh-seq features much lower allele dropout rate compared with SMOOTH-seq. Furthermore, we apply Refresh-seq to 688 sperm cells and 272 female haploid cells (secondary polar bodies and parthenogenetic oocytes) from F1 hybrid mice. We acquire high-resolution genetic map of mouse meiosis recombination at low sequencing depth and reveal the sexual dimorphism in meiotic crossovers. We also phase the structure variations (deletions and insertions) in sperm cells and female haploid cells with high precision. Refresh-seq shows great performance in screening aneuploid sperm cells and oocytes due to the low allele dropout rate and has great potential for medical applications such as preimplantation genetic diagnosis.
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Affiliation(s)
- Yan Wang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yijun Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Junpeng Gao
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoling Xie
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqing Guo
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jingwei Yang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jun'e Liu
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Zonggui Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Changping Laboratory, Beijing, China
| | - Qingqing Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Mengyao Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jie Ren
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
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2
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Valero-Regalón FJ, Solé M, López-Jiménez P, Valerio-de Arana M, Martín-Ruiz M, de la Fuente R, Marín-Gual L, Renfree MB, Shaw G, Berríos S, Fernández-Donoso R, Waters PD, Ruiz-Herrera A, Gómez R, Page J. Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials. Front Cell Dev Biol 2023; 11:1147610. [PMID: 37181752 PMCID: PMC10166821 DOI: 10.3389/fcell.2023.1147610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
In eutherian mammals, hundreds of programmed DNA double-strand breaks (DSBs) are generated at the onset of meiosis. The DNA damage response is then triggered. Although the dynamics of this response is well studied in eutherian mammals, recent findings have revealed different patterns of DNA damage signaling and repair in marsupial mammals. To better characterize these differences, here we analyzed synapsis and the chromosomal distribution of meiotic DSBs markers in three different marsupial species (Thylamys elegans, Dromiciops gliorides, and Macropus eugenii) that represent South American and Australian Orders. Our results revealed inter-specific differences in the chromosomal distribution of DNA damage and repair proteins, which were associated with differing synapsis patterns. In the American species T. elegans and D. gliroides, chromosomal ends were conspicuously polarized in a bouquet configuration and synapsis progressed exclusively from the telomeres towards interstitial regions. This was accompanied by sparse H2AX phosphorylation, mainly accumulating at chromosomal ends. Accordingly, RAD51 and RPA were mainly localized at chromosomal ends throughout prophase I in both American marsupials, likely resulting in reduced recombination rates at interstitial positions. In sharp contrast, synapsis initiated at both interstitial and distal chromosomal regions in the Australian representative M. eugenii, the bouquet polarization was incomplete and ephemeral, γH2AX had a broad nuclear distribution, and RAD51 and RPA foci displayed an even chromosomal distribution. Given the basal evolutionary position of T. elegans, it is likely that the meiotic features reported in this species represent an ancestral pattern in marsupials and that a shift in the meiotic program occurred after the split of D. gliroides and the Australian marsupial clade. Our results open intriguing questions about the regulation and homeostasis of meiotic DSBs in marsupials. The low recombination rates observed at the interstitial chromosomal regions in American marsupials can result in the formation of large linkage groups, thus having an impact in the evolution of their genomes.
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Affiliation(s)
| | - Mireia Solé
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular, Universitat Autònoma de Barcelona, Spain
| | - Pablo López-Jiménez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Valerio-de Arana
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Roberto de la Fuente
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of The Polish Academy of Sciences, Jastrzębiec, Poland
| | - Laia Marín-Gual
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Soledad Berríos
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Raúl Fernández-Donoso
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Rocío Gómez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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3
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Predicting recombination frequency from map distance. Heredity (Edinb) 2023; 130:114-121. [PMID: 36566319 PMCID: PMC9981558 DOI: 10.1038/s41437-022-00585-3] [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: 10/14/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Map distance is one of the key measures in genetics and indicates the expected number of crossovers between two loci. Map distance is estimated from the observed recombination frequency using mapping functions, the most widely used of those, Haldane and Kosambi, being developed at the time when the number of markers was low and unobserved crossovers had a substantial effect on the recombination fractions. In contemporary high-density marker data, the probability of multiple crossovers between adjacent loci is negligible and different mapping functions yield the same result, that is, the recombination frequency between adjacent loci is equal to the map distance in Morgans. However, high-density linkage maps contain an interpretation problem: the map distance over a long interval is additive and its association with recombination frequency is not defined. Here, we demonstrate with high-density linkage maps from humans and stickleback fishes that the inverses of Haldane's and Kosambi's mapping functions systematically underpredict recombination frequencies from map distance. To remedy this, we formulate a piecewise function that yields more accurate predictions of recombination frequency from map distance. Our results demonstrate that the association between map distance and recombination frequency is context-dependent and without a universal solution.
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4
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Dissecting the Meiotic Recombination Patterns in a Brassica napus Double Haploid Population Using 60K SNP Array. Int J Mol Sci 2023; 24:ijms24054469. [PMID: 36901901 PMCID: PMC10003086 DOI: 10.3390/ijms24054469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Meiotic recombination not only maintains the stability of the chromosome structure but also creates genetic variations for adapting to changeable environments. A better understanding of the mechanism of crossover (CO) patterns at the population level is useful for crop improvement. However, there are limited cost-effective and universal methods to detect the recombination frequency at the population level in Brassica napus. Here, the Brassica 60K Illumina Infinium SNP array (Brassica 60K array) was used to systematically study the recombination landscape in a double haploid (DH) population of B. napus. It was found that COs were unevenly distributed across the whole genome, and a higher frequency of COs existed at the distal ends of each chromosome. A considerable number of genes (more than 30%) in the CO hot regions were associated with plant defense and regulation. In most tissues, the average gene expression level in the hot regions (CO frequency of greater than 2 cM/Mb) was significantly higher than that in the regions with a CO frequency of less than 1 cM/Mb. In addition, a bin map was constructed with 1995 recombination bins. For seed oil content, Bin 1131 to 1134, Bin 1308 to 1311, Bin 1864 to 1869, and Bin 2184 to 2230 were identified on chromosomes A08, A09, C03, and C06, respectively, which could explain 8.5%, 17.3%, 8.6%, and 3.9% of the phenotypic variation. These results could not only deepen our understanding of meiotic recombination in B. napus at the population level, and provide useful information for rapeseed breeding in the future, but also provided a reference for studying CO frequency in other species.
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5
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Soriano J, Belmonte-Tebar A, de la Casa-Esperon E. Synaptonemal & CO analyzer: A tool for synaptonemal complex and crossover analysis in immunofluorescence images. Front Cell Dev Biol 2023; 11:1005145. [PMID: 36743415 PMCID: PMC9894712 DOI: 10.3389/fcell.2023.1005145] [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: 07/28/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
During the formation of ova and sperm, homologous chromosomes get physically attached through the synaptonemal complex and exchange DNA at crossover sites by a process known as meiotic recombination. Chromosomes that do not recombine or have anomalous crossover distributions often separate poorly during the subsequent cell division and end up in abnormal numbers in ova or sperm, which can lead to miscarriage or developmental defects. Crossover numbers and distribution along the synaptonemal complex can be visualized by immunofluorescent microscopy. However, manual analysis of large numbers of cells is very time-consuming and a major bottleneck for recombination studies. Some image analysis tools have been created to overcome this situation, but they are not readily available, do not provide synaptonemal complex data, or do not tackle common experimental difficulties, such as overlapping chromosomes. To overcome these limitations, we have created and validated an open-source ImageJ macro routine that facilitates and speeds up the crossover and synaptonemal complex analyses in mouse chromosome spreads, as well as in other vertebrate species. It is free, easy to use and fulfills the recommendations for enhancing rigor and reproducibility in biomedical studies.
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Affiliation(s)
- Joaquim Soriano
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Albacete, Spain
| | - Angela Belmonte-Tebar
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Albacete, Spain
| | - Elena de la Casa-Esperon
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Albacete, Spain,Biology of Cell Growth, Differentiation and Activation Group, Department of Inorganic and Organic Chemistry and Biochemistry, School of Pharmacy, Universidad de Castilla-La Mancha, Albacete, Spain,*Correspondence: Elena de la Casa-Esperon,
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6
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TCFL5 deficiency impairs the pachytene to diplotene transition during spermatogenesis in the mouse. Sci Rep 2022; 12:10956. [PMID: 35768632 PMCID: PMC9242989 DOI: 10.1038/s41598-022-15167-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022] Open
Abstract
Spermatogenesis is a complex, multistep process during which spermatogonia give rise to spermatozoa. Transcription Factor Like 5 (TCFL5) is a transcription factor that has been described expressed during spermatogenesis. In order to decipher the role of TCFL5 during in vivo spermatogenesis, we generated two mouse models. Ubiquitous removal of TCFL5 generated by breeding TCFL5fl/fl with SOX2-Cre mice resulted in sterile males being unable to produce spermatozoa due to a dramatic alteration of the testis architecture presenting meiosis arrest and lack of spermatids. SYCP3, SYCP1 and H1T expression analysis showed that TCFL5 deficiency causes alterations during pachytene/diplotene transition resulting in a meiotic arrest in a diplotene-like stage. Even more, TCFL5 deficient pachytene showed alterations in the number of MLH1 foci and the condensation of the sexual body. In addition, tamoxifen-inducible TCFL5 knockout mice showed, besides meiosis phenotype, alterations in the spermatids elongation process resulting in aberrant spermatids. Furthermore, TCFL5 deficiency increased spermatogonia maintenance genes (Dalz, Sox2, and Dmrt1) but also increased meiosis genes (Syce1, Stag3, and Morc2a) suggesting that the synaptonemal complex forms well, but cannot separate and meiosis does not proceed. TCFL5 is able to bind to the promoter of Syce1, Stag3, Dmrt1, and Syce1 suggesting a direct control of their expression. In conclusion, TCFL5 plays an essential role in spermatogenesis progression being indispensable for meiosis resolution and spermatids maturation.
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7
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Shang Y, Tan T, Fan C, Nie H, Wang Y, Yang X, Zhai B, Wang S, Zhang L. Meiotic chromosome organization and crossover patterns. Biol Reprod 2022; 107:275-288. [PMID: 35191959 DOI: 10.1093/biolre/ioac040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/06/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Meiosis is the foundation of sexual reproduction, and crossover recombination is one hallmark of meiosis. Crossovers establish the physical connections between homolog chromosomes (homologs) for their proper segregation and exchange DNA between homologs to promote genetic diversity in gametes and thus progenies. Aberrant crossover patterns, e.g. absence of the obligatory crossover, are the leading cause of infertility, miscarriage, and congenital disease. Therefore, crossover patterns have to be tightly controlled. During meiosis, loop/axis organized chromosomes provide the structural basis and regulatory machinery for crossover patterning. Accumulating evidence shows that chromosome axis length regulates not only the numbers but also the positions of crossovers. In addition, recent studies suggest that alterations in axis length and the resultant alterations in crossover frequency may contribute to evolutionary adaptation. Here, current advances regarding these issues are reviewed, the possible mechanisms for axis length regulating crossover frequency are discussed, and important issues that need further investigations are suggested.
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Affiliation(s)
- Yongliang Shang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Taicong Tan
- State Key Laboratory of Microbial Technology, Shandong University, China
| | - Cunxian Fan
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Hui Nie
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Ying Wang
- State Key Laboratory of Microbial Technology, Shandong University, China
| | - Xiao Yang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China.,Center for Reproductive Medicine, Shandong University
| | - Binyuan Zhai
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Shandong University.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, 250012, China
| | - Liangran Zhang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China.,Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, Shandong, 250014, China
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8
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Malinovskaya LP, Tishakova KV, Bikchurina TI, Slobodchikova AY, Torgunakov NY, Torgasheva AA, Tsepilov YA, Volkova NA, Borodin PM. Negative heterosis for meiotic recombination rate in spermatocytes of the domestic chicken Gallus gallus. Vavilovskii Zhurnal Genet Selektsii 2021; 25:661-668. [PMID: 34782886 PMCID: PMC8558918 DOI: 10.18699/vj21.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Benef its and costs of meiotic recombination are a matter of discussion. Because recombination breaks
allele combinations already tested by natural selection and generates new ones of unpredictable f itness, a high
recombination rate is generally benef icial for the populations living in a f luctuating or a rapidly changing environment
and costly in a stable environment. Besides genetic benef its and costs, there are cytological effects of recombination,
both positive and negative. Recombination is necessary for chromosome synapsis and segregation. However,
it involves a massive generation of double-strand DNA breaks, erroneous repair of which may lead to germ
cell death or various mutations and chromosome rearrangements. Thus, the benef its of recombination (generation
of new allele combinations) would prevail over its costs (occurrence of deleterious mutations) as long as the population
remains suff iciently heterogeneous. Using immunolocalization of MLH1, a mismatch repair protein, at the
synaptonemal complexes, we examined the number and distribution of recombination nodules in spermatocytes
of two chicken breeds with high (Pervomai) and low (Russian Crested) recombination rates and their F1 hybrids and
backcrosses. We detected negative heterosis for recombination rate in the F1 hybrids. Backcrosses to the Pervomai
breed were rather homogenous and showed an intermediate recombination rate. The differences in overall recombination
rate between the breeds, hybrids and backcrosses were mainly determined by the differences in the crossing
over number in the seven largest macrochromosomes. The decrease in recombination rate in F1 is probably
determined by diff iculties in homology matching between the DNA sequences of genetically divergent breeds. The
suppression of recombination in the hybrids may impede gene f low between parapatric populations and therefore
accelerate their genetic divergence.
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Affiliation(s)
- L P Malinovskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - T I Bikchurina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A Yu Slobodchikova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N Yu Torgunakov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Torgasheva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y A Tsepilov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Moscow region, Russia
| | - P M Borodin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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9
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Tebar AB, Perez ESM, Nam-Cha SH, Valls AJS, Singh ND, de la Casa-Esperon E. Diet effects on mouse meiotic recombination: a warning for recombination studies. Genetics 2021; 220:6428542. [PMID: 34791205 DOI: 10.1093/genetics/iyab190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Meiotic recombination is a critical process for sexually reproducing organisms. This exchange of genetic information between homologous chromosomes during meiosis is important not only because it generates genetic diversity, but also because it is often required for proper chromosome segregation. Consequently, the frequency and distribution of crossovers are tightly controlled to ensure fertility and offspring viability. However, in many systems it has been shown that environmental factors can alter the frequency of crossover events. Two studies in flies and yeast point to nutritional status affecting the frequency of crossing over. However, this question remains unexplored in mammals. Here we test how crossover frequency varies in response to diet in Mus musculus males. We use immunohistochemistry to estimate crossover frequency in multiple genotypes under two diet treatments. Our results indicate that while crossover frequency was unaffected by diet in some strains, other strains were sensitive even to small composition changes between two common laboratory chows. Therefore, recombination is both resistant and sensitive to certain dietary changes in a strain-dependent manner and, hence, this response is genetically determined. Our study is the first to report a nutrition effect on genome-wide levels of recombination. Moreover, our work highlights the importance of controlling diet in recombination studies and may point to diet as a potential source of variability among studies, which is relevant for reproducibility.
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Affiliation(s)
- Angela Belmonte Tebar
- Regional Center for Biomedical Research (C.R.I.B.). University of Castilla-La Mancha. Albacete, 02008, Spain
| | - Estefania San Martin Perez
- Regional Center for Biomedical Research (C.R.I.B.). University of Castilla-La Mancha. Albacete, 02008, Spain
| | - Syong Hyun Nam-Cha
- Pathology Department and Biobank of Albacete. University Hospital Complex of Albacete. Albacete, 02006, Spain
| | | | - Nadia D Singh
- Department of Biology, Institute of Ecology and Evolution, University of Oregon. Eugene, Oregon 97403, USA
| | - Elena de la Casa-Esperon
- Regional Center for Biomedical Research (C.R.I.B.). University of Castilla-La Mancha. Albacete, 02008, Spain.,School of Pharmacy. University of Castilla-La Mancha. Albacete, 02071, Spain
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10
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Pazhayam NM, Turcotte CA, Sekelsky J. Meiotic Crossover Patterning. Front Cell Dev Biol 2021; 9:681123. [PMID: 34368131 PMCID: PMC8344875 DOI: 10.3389/fcell.2021.681123] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/28/2021] [Indexed: 12/02/2022] Open
Abstract
Proper number and placement of meiotic crossovers is vital to chromosome segregation, with failures in normal crossover distribution often resulting in aneuploidy and infertility. Meiotic crossovers are formed via homologous repair of programmed double-strand breaks (DSBs). Although DSBs occur throughout the genome, crossover placement is intricately patterned, as observed first in early genetic studies by Muller and Sturtevant. Three types of patterning events have been identified. Interference, first described by Sturtevant in 1915, is a phenomenon in which crossovers on the same chromosome do not occur near one another. Assurance, initially identified by Owen in 1949, describes the phenomenon in which a minimum of one crossover is formed per chromosome pair. Suppression, first observed by Beadle in 1932, dictates that crossovers do not occur in regions surrounding the centromere and telomeres. The mechanisms behind crossover patterning remain largely unknown, and key players appear to act at all scales, from the DNA level to inter-chromosome interactions. There is also considerable overlap between the known players that drive each patterning phenomenon. In this review we discuss the history of studies of crossover patterning, developments in methods used in the field, and our current understanding of the interplay between patterning phenomena.
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Affiliation(s)
- Nila M. Pazhayam
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carolyn A. Turcotte
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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11
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Fan X, Zhu Y, Wang N, Zhang B, Zhang C, Wang Y. Therapeutic Dose of Hydroxyurea-Induced Synaptic Abnormalities on the Mouse Spermatocyte. Front Physiol 2021; 12:666339. [PMID: 34305635 PMCID: PMC8299468 DOI: 10.3389/fphys.2021.666339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
Hydroxyurea (HU) is a widely used pharmacological therapy for sickle cell disease (SCD). However, replication stress caused by HU has been shown to inhibit premeiotic S-phase DNA, leading to reproductive toxicity in germ cells. In this study, we administered the therapeutic doses of HU (i.e., 25 and 50 mg/kg) to male mice to explore whether replication stress by HU affects pachytene spermatocytes and causes the abnormalities of homologous chromosomes pairing and recombination during prophase I of meiosis. In comparison with the control group, the proportions of spermatocyte gaps were significantly different in the experimental groups injected with 25 mg/kg (p < 0.05) and 50 mg/kg of HU (p < 0.05). Moreover, the proportions of unrepaired double-stranded breaks (DSBs) observed by γH2AX staining also corresponded to a higher HU dose with a greater number of breaks. Additionally, a reduction in the counts of recombination foci on the autosomal SCs was observed in the pachytene spermatocytes. Our results reveal that HU has some effects on synaptonemal complex (SC) formation and DSB repair which suggest possible problems in fertility. Therefore, this study provides new evidence of the mechanisms underlying HU reproductive toxicity.
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Affiliation(s)
- Xiaobo Fan
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Yunxia Zhu
- The Center of Reproductive Medicine, Xuzhou Maternity and Child Health Care Hospital, Xuzhou, China
| | - Naixin Wang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Bing Zhang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Cui Zhang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
| | - Yanan Wang
- Laboratory of Molecular Cytogenetics, School of Bioengineering, Xuzhou University of Technology, Xuzhou, China
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12
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The impact of chromosomal fusions on 3D genome folding and recombination in the germ line. Nat Commun 2021; 12:2981. [PMID: 34016985 PMCID: PMC8137915 DOI: 10.1038/s41467-021-23270-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/16/2021] [Indexed: 02/08/2023] Open
Abstract
The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome conformation capture in combination with single-nucleotide polymorphism (SNP) genotyping and analysis of crossover events to study how the higher-order chromatin organization and recombination landscapes are affected by chromosomal fusions in the mammalian germ line. We demonstrate that chromosomal fusions alter the nuclear architecture during meiosis, including an increased rate of heterologous interactions in primary spermatocytes, and alterations in both chromosome synapsis and axis length. These disturbances in topology were associated with changes in genomic landscapes of recombination, resulting in detectable genomic footprints. Overall, we show that chromosomal fusions impact the dynamic genome topology of germ cells in two ways: (i) altering chromosomal nuclear occupancy and synapsis, and (ii) reshaping landscapes of recombination.
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13
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Gil-Fernández A, Matveevsky S, Martín-Ruiz M, Ribagorda M, Parra MT, Viera A, Rufas JS, Kolomiets O, Bakloushinskaya I, Page J. Sex differences in the meiotic behavior of an XX sex chromosome pair in males and females of the mole vole Ellobius tancrei: turning an X into a Y chromosome? Chromosoma 2021; 130:113-131. [PMID: 33825031 DOI: 10.1007/s00412-021-00755-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 01/01/2023]
Abstract
Sex determination in mammals is usually provided by a pair of chromosomes, XX in females and XY in males. Mole voles of the genus Ellobius are exceptions to this rule. In Ellobius tancrei, both males and females have a pair of XX chromosomes that are indistinguishable from each other in somatic cells. Nevertheless, several studies on Ellobius have reported that the two X chromosomes may have a differential organization and behavior during male meiosis. It has not yet been demonstrated if these differences also appear in female meiosis. To test this hypothesis, we have performed a comparative study of chromosome synapsis, recombination, and histone modifications during male and female meiosis in E. tancrei. We observed that synapsis between the two X chromosomes is limited to the short distal (telomeric) regions of the chromosomes in males, leaving the central region completely unsynapsed. This uneven behavior of sex chromosomes during male meiosis is accompanied by structural modifications of one of the X chromosomes, whose axial element tends to appear fragmented, accumulates the heterochromatin mark H3K9me3, and is associated with a specific nuclear body that accumulates epigenetic marks and proteins such as SUMO-1 and centromeric proteins but excludes others such as H3K4me, ubiH2A, and γH2AX. Unexpectedly, sex chromosome synapsis is delayed in female meiosis, leaving the central region unsynapsed during early pachytene. This region accumulates γH2AX up to the stage in which synapsis is completed. However, there are no structural or epigenetic differences similar to those found in males in either of the two X chromosomes. Finally, we observed that recombination in the sex chromosomes is restricted in both sexes. In males, crossover-associated MLH1 foci are located exclusively in the distal regions, indicating incipient differentiation of one of the sex chromosomes into a neo-Y. Notably, in female meiosis, the central region of the X chromosome is also devoid of MLH1 foci, revealing a lack of recombination, possibly due to insufficient homology. Overall, these results reveal new clues about the origin and evolution of sex chromosomes.
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Affiliation(s)
- Ana Gil-Fernández
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Ribagorda
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Teresa Parra
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Viera
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Julio S Rufas
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Oxana Kolomiets
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
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14
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Torgunakov NY, Kizilova EA, Karamysheva TV, Malinovskaya LP, Bikchurina TI, Borodin PM. Homogeneously Staining Regions (HSR) in Chromosome 1 of the House Mouse: Synapsis and Recombination at Meiosis. Cytogenet Genome Res 2021; 161:14-22. [PMID: 33725692 DOI: 10.1159/000513266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/16/2020] [Indexed: 11/19/2022] Open
Abstract
Amplified sequences constitute a large part of mammalian genomes. A chromosome 1 containing 2 large (up to 50 Mb) homogeneously staining regions (HSRs) separated by a small inverted euchromatic region is present in many natural populations of the house mouse (Mus musculus musculus). The HSRs are composed of a long-range repeat cluster, Sp100-rs, with a repeat length of 100 kb. In order to understand the organization and function of HSRs in meiotic chromosomes, we examined synapsis and recombination in male mice hetero- and homozygous for the HSR-carrying chromosome using FISH with an HSR-specific DNA probe and immunolocalization of the key meiotic proteins. In all homozygous and heterozygous pachytene nuclei, we observed fully synapsed linear homomorphic bivalents 1 marked by the HSR FISH probe. The synaptic adjustment in the heterozygotes was bilateral: the HSR-carrying homolog was shortened and the wild-type homolog was elongated. The adjustment was reversible: desynapsis at diplotene was accompanied by elongation of the HSRs. Immunolocalization of H3K9me2/3 indicated that the HSRs in the meiotic chromosome retained the epigenetic modification typical for C-heterochromatin in somatic cells. MLH1 foci, marking mature recombination nodules, were detected in the proximal HSR band in heterozygotes and in both HSR bands of homozygotes. Unequal crossing over within the long-range repeat cluster can cause variation in size of the HSRs, which has been detected in the natural populations of the house mouse.
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Affiliation(s)
- Nikita Y Torgunakov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Elena A Kizilova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Tatyana V Karamysheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Lyubov P Malinovskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Tatiana I Bikchurina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, .,Novosibirsk State University, Novosibirsk, Russian Federation,
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15
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del Priore L, Pigozzi MI. DNA Organization along Pachytene Chromosome Axes and Its Relationship with Crossover Frequencies. Int J Mol Sci 2021; 22:ijms22052414. [PMID: 33673731 PMCID: PMC7957551 DOI: 10.3390/ijms22052414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022] Open
Abstract
During meiosis, the number of crossovers vary in correlation to the length of prophase chromosome axes at the synaptonemal complex stage. It has been proposed that the regular spacing of the DNA loops, along with the close relationship of the recombination complexes and the meiotic axes are at the basis of this covariation. Here, we use a cytogenomic approach to investigate the relationship between the synaptonemal complex length and the DNA content in chicken oocytes during the pachytene stage of the first meiotic prophase. The synaptonemal complex to DNA ratios of specific chromosomes and chromosome segments were compared against the recombination rates obtained by MLH1 focus mapping. The present results show variations in the DNA packing ratios of macro- and microbivalents and also between regions within the same bivalent. Chromosome or chromosome regions with higher crossover rates form comparatively longer synaptonemal complexes than expected based on their DNA content. These observations are compatible with the formation of higher number of shorter DNA loops along meiotic axes in regions with higher recombination levels.
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16
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Gil-Fernández A, Saunders PA, Martín-Ruiz M, Ribagorda M, López-Jiménez P, Jeffries DL, Parra MT, Viera A, Rufas JS, Perrin N, Veyrunes F, Page J. Meiosis reveals the early steps in the evolution of a neo-XY sex chromosome pair in the African pygmy mouse Mus minutoides. PLoS Genet 2020; 16:e1008959. [PMID: 33180767 PMCID: PMC7685469 DOI: 10.1371/journal.pgen.1008959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/24/2020] [Accepted: 10/06/2020] [Indexed: 01/30/2023] Open
Abstract
Sex chromosomes of eutherian mammals are highly different in size and gene content, and share only a small region of homology (pseudoautosomal region, PAR). They are thought to have evolved through an addition-attrition cycle involving the addition of autosomal segments to sex chromosomes and their subsequent differentiation. The events that drive this process are difficult to investigate because sex chromosomes in almost all mammals are at a very advanced stage of differentiation. Here, we have taken advantage of a recent translocation of an autosome to both sex chromosomes in the African pygmy mouse Mus minutoides, which has restored a large segment of homology (neo-PAR). By studying meiotic sex chromosome behavior and identifying fully sex-linked genetic markers in the neo-PAR, we demonstrate that this region shows unequivocal signs of early sex-differentiation. First, synapsis and resolution of DNA damage intermediates are delayed in the neo-PAR during meiosis. Second, recombination is suppressed or largely reduced in a large portion of the neo-PAR. However, the inactivation process that characterizes sex chromosomes during meiosis does not extend to this region. Finally, the sex chromosomes show a dual mechanism of association at metaphase-I that involves the formation of a chiasma in the neo-PAR and the preservation of an ancestral achiasmate mode of association in the non-homologous segments. We show that the study of meiosis is crucial to apprehend the onset of sex chromosome differentiation, as it introduces structural and functional constrains to sex chromosome evolution. Synapsis and DNA repair dynamics are the first processes affected in the incipient differentiation of X and Y chromosomes, and they may be involved in accelerating their evolution. This provides one of the very first reports of early steps in neo-sex chromosome differentiation in mammals, and for the first time a cellular framework for the addition-attrition model of sex chromosome evolution. Sex chromosomes seem to evolve and differentiate at different rates in different taxa. The reasons for this variability are still debated. It is well established that recombination suppression around the sex-determining region triggers differentiation, and several studies have investigated this process from a genetic point of view. However, the cellular context in which recombination arrest occurs has received little attention so far. In this report, we show that meiosis, the cellular division in which pairing and recombination between chromosomes takes place, can affect the incipient differentiation of X and Y chromosomes. Combining cytogenetic and genomic approaches, we found that in the African pygmy mouse Mus minutoides, which has recently undergone sex chromosome-autosome fusions, synapsis and DNA repair dynamics are disturbed along the newly added region of the sex chromosomes. We argue that these alterations are a by-product of the fusion itself, and cause recombination suppression across a large region of the neo-sex chromosome pair. Therefore, we propose that the meiotic context in which sex or neo-sex chromosomes arise is crucial to understand the very early stages of their differentiation, as it could promote or hinder recombination suppression, and therefore impact the rate at which these chromosomes differentiate.
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Affiliation(s)
- Ana Gil-Fernández
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paul A. Saunders
- Institut des Sciences de l'Evolution, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), Montpellier, France
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Ribagorda
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo López-Jiménez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - María Teresa Parra
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Viera
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Julio S. Rufas
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frederic Veyrunes
- Institut des Sciences de l'Evolution, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), Montpellier, France
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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17
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Palmer N, Talib SZA, Singh P, Goh CMF, Liu K, Schimenti JC, Kaldis P. A novel function for CDK2 activity at meiotic crossover sites. PLoS Biol 2020; 18:e3000903. [PMID: 33075054 PMCID: PMC7595640 DOI: 10.1371/journal.pbio.3000903] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/29/2020] [Accepted: 09/14/2020] [Indexed: 12/23/2022] Open
Abstract
Genetic diversity in offspring is induced by meiotic recombination, which is initiated between homologs at >200 sites originating from meiotic double-strand breaks (DSBs). Of this initial pool, only 1-2 DSBs per homolog pair will be designated to form meiotic crossovers (COs), where reciprocal genetic exchange occurs between parental chromosomes. Cyclin-dependent kinase 2 (CDK2) is known to localize to so-called "late recombination nodules" (LRNs) marking incipient CO sites. However, the role of CDK2 kinase activity in the process of CO formation remains uncertain. Here, we describe the phenotype of 2 Cdk2 point mutants with elevated or decreased activity, respectively. Elevated CDK2 activity was associated with increased numbers of LRN-associated proteins, including CDK2 itself and the MutL homolog 1 (MLH1) component of the MutLγ complex, but did not lead to increased numbers of COs. In contrast, reduced CDK2 activity leads to the complete absence of CO formation during meiotic prophase I. Our data suggest an important role for CDK2 in regulating MLH1 focus numbers and that the activity of this kinase is a key regulatory factor in the formation of meiotic COs.
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Affiliation(s)
- Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore, Republic of Singapore
- Department of Biochemistry, National University of Singapore (NUS), Singapore, Republic of Singapore
| | - S. Zakiah A. Talib
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore, Republic of Singapore
| | - Priti Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Christine M. F. Goh
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore, Republic of Singapore
| | - Kui Liu
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong—Shenzhen Hospital, Shenzhen, China
| | - John C. Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore, Republic of Singapore
- Department of Biochemistry, National University of Singapore (NUS), Singapore, Republic of Singapore
- Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
- * E-mail:
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18
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del Priore L, Pigozzi MI. MLH1 focus mapping in the guinea fowl (Numida meleagris) give insights into the crossover landscapes in birds. PLoS One 2020; 15:e0240245. [PMID: 33017431 PMCID: PMC7535058 DOI: 10.1371/journal.pone.0240245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/22/2020] [Indexed: 11/21/2022] Open
Abstract
Crossover rates and localization are not homogeneous throughout the genomes. Along the chromosomes of almost all species, domains with high crossover rates alternate with domains where crossover rates are significantly lower than the genome-wide average. The distribution of crossovers along chromosomes constitutes the recombination landscape of a given species and can be analyzed at broadscale using immunostaining of the MLH1 protein, a component of mature recombination nodules found on synaptonemal complexes during pachytene. We scored the MLH1 foci in oocytes of the chicken and the guinea fowl and compared their frequencies in the largest bivalents. The average autosomal number of foci is 62 in the chicken and 44 in the guinea fowl. The lower number in the guinea fowl responds to the occurrence of fewer crossovers in the six largest bivalents, where most MLH1 foci occur within one-fifth of the chromosome length with high polarization towards opposite ends. The skewed distribution of foci in the guinea fowl contrast with the more uniform distribution of numerous foci in the chicken, especially in the four largest bivalents. The crossover distribution observed in the guinea fowl is unusual among Galloanserae and also differs from other, more distantly related birds. We discussed the current evidence showing that the shift towards crossover localization, as observed in the guinea fowl, was not a unique event but also occurred at different moments of bird evolution. A comparative analysis of genome-wide average recombination rates in birds shows variations within narrower limits compared to mammals and the absence of a phylogenetic trend.
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Affiliation(s)
- Lucía del Priore
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Inés Pigozzi
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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19
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Hinch AG, Becker PW, Li T, Moralli D, Zhang G, Bycroft C, Green C, Keeney S, Shi Q, Davies B, Donnelly P. The Configuration of RPA, RAD51, and DMC1 Binding in Meiosis Reveals the Nature of Critical Recombination Intermediates. Mol Cell 2020; 79:689-701.e10. [PMID: 32610038 PMCID: PMC7447979 DOI: 10.1016/j.molcel.2020.06.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/07/2020] [Accepted: 06/04/2020] [Indexed: 01/05/2023]
Abstract
Meiotic recombination proceeds via binding of RPA, RAD51, and DMC1 to single-stranded DNA (ssDNA) substrates created after formation of programmed DNA double-strand breaks. Here we report high-resolution in vivo maps of RPA and RAD51 in meiosis, mapping their binding locations and lifespans to individual homologous chromosomes using a genetically engineered hybrid mouse. Together with high-resolution microscopy and DMC1 binding maps, we show that DMC1 and RAD51 have distinct spatial localization on ssDNA: DMC1 binds near the break site, and RAD51 binds away from it. We characterize inter-homolog recombination intermediates bound by RPA in vivo, with properties expected for the critical displacement loop (D-loop) intermediates. These data support the hypothesis that DMC1, not RAD51, performs strand exchange in mammalian meiosis. RPA-bound D-loops can be resolved as crossovers or non-crossovers, but crossover-destined D-loops may have longer lifespans. D-loops resemble crossover gene conversions in size, but their extent is similar in both repair pathways.
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Affiliation(s)
| | - Philipp W Becker
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tao Li
- Howard Hughes Medical Institute, Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Hefei National Laboratory for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gang Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Clare Bycroft
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Catherine Green
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Scott Keeney
- Howard Hughes Medical Institute, Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qinghua Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK.
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20
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Malinovskaya LP, Tishakova KV, Volkova NA, Torgasheva AA, Tsepilov YA, Borodin PM. Interbreed variation in meiotic recombination rate and distribution in the domestic chicken Gallus gallus. Arch Anim Breed 2019; 62:403-411. [PMID: 31807651 PMCID: PMC6859913 DOI: 10.5194/aab-62-403-2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/21/2019] [Indexed: 11/11/2022] Open
Abstract
The efficiency of natural and artificial selection is critically dependent on the recombination rate. However, interbreed and individual variation in recombination rate in poultry remains unknown. Conventional methods of analysis of recombination such as genetic linkage analysis, sperm genotyping and chiasma count at lampbrush chromosomes are expensive and time-consuming. In this study, we analyzed the number and distribution of recombination nodules in spermatocytes of the roosters of six chicken breeds using immunolocalization of key proteins involved in chromosome pairing and recombination. We revealed significant effects of breed ( R 2 = 0.17 ; p < 0.001 ) and individual ( R 2 = 0.28 ; p < 0.001 ) on variation in the number of recombination nodules. Both interbreed and individual variations in recombination rate were almost entirely determined by variation in recombination density on macrochromosomes, because almost all microchromosomes in each breed had one recombination nodule. Despite interbreed differences in the density of recombination nodules, the patterns of their distribution along homologous chromosomes were similar. The breeds examined in this study showed a correspondence between the age of the breed and its recombination rate. Those with high recombination rates (Pervomai, Russian White and Brahma) are relatively young breeds created by crossing several local breeds. The breeds displaying low recombination rate are ancient local breeds: Cochin (Indo-China), Brown Leghorn (Tuscany, Italy) and Russian Crested (the European part of Russia).
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Affiliation(s)
- Lyubov P Malinovskaya
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Katerina V Tishakova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
| | - Anna A Torgasheva
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yakov A Tsepilov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Pavel M Borodin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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21
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. Genome Biol Evol 2019; 11:1552-1572. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2019] [Indexed: 12/13/2022] Open
Abstract
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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22
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High-Throughput Single-Cell Sequencing with Linear Amplification. Mol Cell 2019; 76:676-690.e10. [PMID: 31495564 DOI: 10.1016/j.molcel.2019.08.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 05/22/2019] [Accepted: 08/01/2019] [Indexed: 11/22/2022]
Abstract
Conventional methods for single-cell genome sequencing are limited with respect to uniformity and throughput. Here, we describe sci-L3, a single-cell sequencing method that combines combinatorial indexing (sci-) and linear (L) amplification. The sci-L3 method adopts a 3-level (3) indexing scheme that minimizes amplification biases while enabling exponential gains in throughput. We demonstrate the generalizability of sci-L3 with proof-of-concept demonstrations of single-cell whole-genome sequencing (sci-L3-WGS), targeted sequencing (sci-L3-target-seq), and a co-assay of the genome and transcriptome (sci-L3-RNA/DNA). We apply sci-L3-WGS to profile the genomes of >10,000 sperm and sperm precursors from F1 hybrid mice, mapping 86,786 crossovers and characterizing rare chromosome mis-segregation events in meiosis, including instances of whole-genome equational chromosome segregation. We anticipate that sci-L3 assays can be applied to fully characterize recombination landscapes, to couple CRISPR perturbations and measurements of genome stability, and to other goals requiring high-throughput, high-coverage single-cell sequencing.
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23
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Conservation of the genome-wide recombination rate in white-footed mice. Heredity (Edinb) 2019; 123:442-457. [PMID: 31366913 PMCID: PMC6781155 DOI: 10.1038/s41437-019-0252-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
Despite being linked to the fundamental processes of chromosome segregation and offspring diversification, meiotic recombination rates vary within and between species. Recent years have seen progress in quantifying recombination rate evolution across multiple temporal and genomic scales. Nevertheless, the level of variation in recombination rate within wild populations-a key determinant of evolution in this trait-remains poorly documented on the genomic scale. To address this notable gap, we used immunofluorescent cytology to quantify genome-wide recombination rates in males from a wild population of the white-footed mouse, Peromyscus leucopus. For comparison, we measured recombination rates in a second population of male P. leucopus raised in the laboratory and in male deer mice from the subspecies Peromyscus maniculatus bairdii. Although we found differences between individuals in the genome-wide recombination rate, levels of variation were low-within populations, between populations, and between species. Quantification of synaptonemal complex length and crossover positions along chromosome 1 using a novel automated approach also revealed conservation in broad-scale crossover patterning, including strong crossover interference. We propose stabilizing selection targeting recombination or correlated processes as the explanation for these patterns.
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24
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. Genome Biol Evol 2019; 11:1573-1585. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is a highly conserved process that has profound effects on genome evolution. At a fine-scale, recombination rates can vary drastically across genomes, often localized into small recombination "hotspots" with highly elevated rates, surrounded by regions with little recombination. In most species studied, the location of hotspots within genomes is highly conserved across broad evolutionary timescales. The main exception to this pattern is in mammals, where hotspot location can evolve rapidly among closely related species and even among populations within a species. Hotspot position in mammals is controlled by the gene, Prdm9, whereas in species with conserved hotspots, a functional Prdm9 is typically absent. Due to a limited number of species where recombination rates have been estimated at a fine-scale, it remains unclear whether hotspot conservation is always associated with the absence of a functional Prdm9. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using a linkage disequilibrium-based approach, we found recombination rates indeed varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had highly divergent landscapes between stickleback populations, where only ∼15% of these hotspots were shared. Our results indicate that fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish. Interestingly, we found only a weak association of a PRDM9 binding motif within hotspots, which suggests that threespine stickleback fish may possess a novel mechanism for targeting recombination hotspots at a fine-scale.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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25
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Wang P, Jiang L, Ye M, Zhu X, Wu R. The Genomic Landscape of Crossover Interference in the Desert Tree Populus euphratica. Front Genet 2019; 10:440. [PMID: 31156703 PMCID: PMC6530421 DOI: 10.3389/fgene.2019.00440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/29/2019] [Indexed: 11/13/2022] Open
Abstract
Crossover (CO) interference is a universal phenomenon by which the occurrence of one CO event inhibits the simultaneous occurrence of other COs along a chromosome. Because of its critical role in the evolution of genome structure and organization, the cytological and molecular mechanisms underlying CO interference have been extensively investigated. However, the genome-wide distribution of CO interference and its interplay with sex-, stress-, and age-induced differentiation remain poorly understood. Multi-point linkage analysis has proven to be a powerful tool for landscaping CO interference, especially within species for which CO mutants are rarely available. We implemented four-point linkage analysis to landscape a detailed picture of how CO interference is distributed through the entire genome of Populus euphratica, the only forest tree that can survive and grow in saline desert. We identified an extensive occurrence of CO interference, and found that its strength depends on the length of chromosomes and the genomic locations within the chromosome. We detected high-order CO interference, possibly suggesting a highly complex mechanism crucial for P. euphratica to grow, reproduce, and evolve in its harsh environment.
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Affiliation(s)
- Ping Wang
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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26
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Hinch AG, Zhang G, Becker PW, Moralli D, Hinch R, Davies B, Bowden R, Donnelly P. Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm. Science 2019; 363:eaau8861. [PMID: 30898902 PMCID: PMC6445350 DOI: 10.1126/science.aau8861] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023]
Abstract
Recombination is critical to meiosis and evolution, yet many aspects of the physical exchange of DNA via crossovers remain poorly understood. We report an approach for single-cell whole-genome DNA sequencing by which we sequenced 217 individual hybrid mouse sperm, providing a kilobase-resolution genome-wide map of crossovers. Combining this map with molecular assays measuring stages of recombination, we identified factors that affect crossover probability, including PRDM9 binding on the non-initiating template homolog and telomere proximity. These factors also influence the time for sites of recombination-initiating DNA double-strand breaks to find and engage their homologs, with rapidly engaging sites more likely to form crossovers. We show that chromatin environment on the template homolog affects positioning of crossover breakpoints. Our results also offer insights into recombination in the pseudoautosomal region.
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Affiliation(s)
| | - Gang Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Philipp W Becker
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Robert Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Department of Statistics, University of Oxford, Oxford, UK
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27
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Veller C, Kleckner N, Nowak MA. A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel's second law. Proc Natl Acad Sci U S A 2019; 116:1659-1668. [PMID: 30635424 PMCID: PMC6358705 DOI: 10.1073/pnas.1817482116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. Such studies have been hampered by the absence of a direct measure of this quantity. Existing measures consider crossing-over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate, because the positions of crossovers along a chromosome are also critical: a crossover toward the middle of a chromosome causes more shuffling than a crossover toward the tip. Moreover, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel's second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter [Formula: see text] as the probability that the alleles at two randomly chosen loci are shuffled during gamete production. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that [Formula: see text] is larger when crossovers are more evenly spaced, which suggests a selective advantage of crossover interference. Utilization of [Formula: see text] is enabled by powerful emergent methods for determining crossover positions either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that (i) [Formula: see text] in humans is close to its maximum possible value of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortment, the contribution of which is ∼30 times greater than that of crossovers.
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Affiliation(s)
- Carl Veller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
| | - Martin A Nowak
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
- Department of Mathematics, Harvard University, Cambridge, MA 02138
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28
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Lukaszewicz A, Lange J, Keeney S, Jasin M. Control of meiotic double-strand-break formation by ATM: local and global views. Cell Cycle 2018; 17:1155-1172. [PMID: 29963942 PMCID: PMC6110601 DOI: 10.1080/15384101.2018.1464847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/19/2018] [Accepted: 04/08/2018] [Indexed: 10/28/2022] Open
Abstract
DNA double-strand breaks (DSBs) generated by the SPO11 protein initiate meiotic recombination, an essential process for successful chromosome segregation during gametogenesis. The activity of SPO11 is controlled by multiple factors and regulatory mechanisms, such that the number of DSBs is limited and DSBs form at distinct positions in the genome and at the right time. Loss of this control can affect genome integrity or cause meiotic arrest by mechanisms that are not fully understood. Here we focus on the DSB-responsive kinase ATM and its functions in regulating meiotic DSB numbers and distribution. We review the recently discovered roles of ATM in this context, discuss their evolutionary conservation, and examine future research perspectives.
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Affiliation(s)
- Agnieszka Lukaszewicz
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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29
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Matveevsky S, Ivanitskaya E, Spangenberg V, Bakloushinskaya I, Kolomiets O. Reorganization of the Y Chromosomes Enhances Divergence in Israeli Mole Rats Nannospalax ehrenbergi (Spalacidae, Rodentia): Comparative Analysis of Meiotic and Mitotic Chromosomes. Genes (Basel) 2018; 9:genes9060272. [PMID: 29794981 PMCID: PMC6027163 DOI: 10.3390/genes9060272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/14/2022] Open
Abstract
The Y chromosome in mammals is variable, even in closely related species. Middle East blind mole rats Nannospalax ehrenbergi demonstrate autosomal variability, which probably leads to speciation. Here, we compare the mitotic and meiotic chromosomes of mole rats. For the first time, we studied the behavior of their sex chromosomes in the meiotic prophase I using electron microscopy and immunocytochemical analysis. Unexpectedly, the sex chromosomes of the 52- and 60-chromosome forms of mole rats showed different synaptic and recombination patterns due to distinct locations of the centromeres on the Y chromosomes. The absence of recombination in the 60-chromosome form, the asymmetric synapsis, and the short-term disturbance in the synaptic co-orientation of the telomeric regions of the X and Y chromosomes were revealed as specific features of mole rat sex bivalents. We suggest several scenarios of Y chromosome alteration in connection with species differentiation in mole rats.
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Affiliation(s)
- Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
| | | | - Victor Spangenberg
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia.
| | - Oxana Kolomiets
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
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30
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del Priore L, Pigozzi MI. Broad-scale recombination pattern in the primitive bird Rhea americana (Ratites, Palaeognathae). PLoS One 2017; 12:e0187549. [PMID: 29095930 PMCID: PMC5667853 DOI: 10.1371/journal.pone.0187549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/20/2017] [Indexed: 12/02/2022] Open
Abstract
Birds have genomic and chromosomal features that make them an attractive group to analyze the evolution of recombination rate and the distribution of crossing over. Yet, analyses are biased towards certain species, especially domestic poultry and passerines. Here we analyze for the first time the recombination rate and crossover distribution in the primitive ratite bird, Rhea americana (Rheiformes, Palaeognathae). Using a cytogenetic approach for in situ mapping of crossovers we found that the total genetic map is 3050 cM with a global recombination rate of 2.1 cM/Mb for female rheas. In the five largest macrobivalents there were 3 or more crossovers in most bivalents. Recombination rates for macrobivalents ranges between 1.8-2.1 cM/Mb and the physical length of their synaptonemal complexes is highly predictive of their genetic lengths. The crossover rate at the pseudoautosomal region is 2.1 cM/Mb, similar to those of autosomal pairs 5 and 6 and only slightly higher compared to other macroautosomes. It is suggested that the presence of multiple crossovers on the largest macrobivalents is a feature common to many avian groups, irrespective of their position throughout phylogeny. These data provide new insights to analyze the heterogeneous recombination landscape of birds.
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Affiliation(s)
- Lucía del Priore
- INBIOMED Instituto de Investigaciones Biomédicas UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Inés Pigozzi
- INBIOMED Instituto de Investigaciones Biomédicas UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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31
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Lisachov AP, Trifonov VA, Giovannotti M, Ferguson-Smith MA, Borodin PM. Immunocytological analysis of meiotic recombination in two anole lizards (Squamata, Dactyloidae). COMPARATIVE CYTOGENETICS 2017; 11:129-141. [PMID: 28919954 PMCID: PMC5599703 DOI: 10.3897/compcytogen.v11i1.10916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/16/2017] [Indexed: 05/13/2023]
Abstract
Although the evolutionary importance of meiotic recombination is not disputed, the significance of interspecies differences in the recombination rates and recombination landscapes remains under-appreciated. Recombination rates and distribution of chiasmata have been examined cytologically in many mammalian species, whereas data on other vertebrates are scarce. Immunolocalization of the protein of the synaptonemal complex (SYCP3), centromere proteins and the mismatch-repair protein MLH1 was used, which is associated with the most common type of recombination nodules, to analyze the pattern of meiotic recombination in the male of two species of iguanian lizards, Anolis carolinensis Voigt, 1832 and Deiroptyx coelestinus (Cope, 1862). These species are separated by a relatively long evolutionary history although they retain the ancestral iguanian karyotype. In both species similar and extremely uneven distributions of MLH1 foci along the macrochromosome bivalents were detected: approximately 90% of crossovers were located at the distal 20% of the chromosome arm length. Almost total suppression of recombination in the intermediate and proximal regions of the chromosome arms contradicts the hypothesis that "homogenous recombination" is responsible for the low variation in GC content across the anole genome. It also leads to strong linkage disequilibrium between the genes located in these regions, which may benefit conservation of co-adaptive gene arrays responsible for the ecological adaptations of the anoles.
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Affiliation(s)
- Artem P. Lisachov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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32
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Meiotic Crossing Over in Maize Knob Heterochromatin. Genetics 2017; 205:1101-1112. [PMID: 28108587 DOI: 10.1534/genetics.116.196089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/10/2017] [Indexed: 12/31/2022] Open
Abstract
There is ample evidence that crossing over is suppressed in heterochromatin associated with centromeres and nucleolus organizers (NORs). This characteristic has been attributed to all heterochromatin, but the generalization may not be justified. To investigate the relationship of crossing over to heterochromatin that is not associated with centromeres or NORs, we used a combination of fluorescence in situ hybridization of the maize 180-bp knob repeat to show the locations of knob heterochromatin and fluorescent immunolocalization of MLH1 protein and AFD1 protein to show the locations of MLH1 foci on maize synaptonemal complexes (SCs, pachytene chromosomes). MLH1 foci correspond to the location of recombination nodules (RNs) that mark sites of crossing over. We found that MLH1 foci occur at similar frequencies per unit length of SC in interstitial knobs and in the 1 µm segments of SC in euchromatin immediately to either side of interstitial knobs. These results indicate not only that crossing over occurs within knob heterochromatin, but also that crossing over is not suppressed in the context of SC length in maize knobs. However, because there is more DNA per unit length of SC in knobs compared to euchromatin, crossing over is suppressed (but not eliminated) in knobs in the context of DNA length compared to adjacent euchromatin.
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33
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Ruiz-Herrera A, Vozdova M, Fernández J, Sebestova H, Capilla L, Frohlich J, Vara C, Hernández-Marsal A, Sipek J, Robinson TJ, Rubes J. Recombination correlates with synaptonemal complex length and chromatin loop size in bovids-insights into mammalian meiotic chromosomal organization. Chromosoma 2017; 126:615-631. [PMID: 28101670 DOI: 10.1007/s00412-016-0624-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/14/2016] [Accepted: 12/12/2016] [Indexed: 11/25/2022]
Abstract
Homologous chromosomes exchange genetic information through recombination during meiosis, a process that increases genetic diversity, and is fundamental to sexual reproduction. In an attempt to shed light on the dynamics of mammalian recombination and its implications for genome organization, we have studied the recombination characteristics of 112 individuals belonging to 28 different species in the family Bovidae. In particular, we analyzed the distribution of RAD51 and MLH1 foci during the meiotic prophase I that serve, respectively, as proxies for double-strand breaks (DSBs) which form in early stages of meiosis and for crossovers. In addition, synaptonemal complex length and meiotic DNA loop size were estimated to explore how genome organization determines DSBs and crossover patterns. We show that although the number of meiotic DSBs per cell and recombination rates observed vary between individuals of the same species, these are correlated with diploid number as well as with synaptonemal complex and DNA loop sizes. Our results illustrate that genome packaging, DSB frequencies, and crossover rates tend to be correlated, while meiotic chromosomal axis length and DNA loop size are inversely correlated in mammals. Moreover, axis length, DSB frequency, and crossover frequencies all covary, suggesting that these correlations are established in the early stages of meiosis.
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Affiliation(s)
- Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain. .,Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Miluse Vozdova
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Jonathan Fernández
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Hana Sebestova
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jan Frohlich
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Covadonga Vara
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Adrià Hernández-Marsal
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaroslav Sipek
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Jiri Rubes
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
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34
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Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals. Genetics 2016; 205:155-168. [PMID: 27838628 PMCID: PMC5223500 DOI: 10.1534/genetics.116.192690] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/03/2016] [Indexed: 01/08/2023] Open
Abstract
The segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the parameters that shape patterns of recombination rate evolution across species. Here, I use cytogenetic methods for in situ imaging of crossovers in karyotypically diverse house mice (Mus musculus domesticus) and voles (genus Microtus) to test how chromosome number and configuration constrain the distribution of crossovers in a genome. I show that the global distribution of crossovers in house mice is thresholded by a minimum of one crossover per chromosome arm, whereas the crossover landscape in voles is defined by a more relaxed requirement of one crossover per chromosome. I extend these findings in an evolutionary metaanalysis of published recombination and karyotype data for 112 mammalian species and demonstrate that the physical scale of the genomic crossover distribution has undergone multiple independent shifts from one crossover per chromosome arm to one per chromosome during mammalian evolution. Together, these results indicate that the chromosomal scale constraint on crossover rates is itself a trait that evolves among species, a finding that casts light on an important source of crossover rate variation in mammals.
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Lange J, Yamada S, Tischfield SE, Pan J, Kim S, Zhu X, Socci ND, Jasin M, Keeney S. The Landscape of Mouse Meiotic Double-Strand Break Formation, Processing, and Repair. Cell 2016; 167:695-708.e16. [PMID: 27745971 DOI: 10.1016/j.cell.2016.09.035] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/13/2016] [Accepted: 09/21/2016] [Indexed: 01/09/2023]
Abstract
Heritability and genome stability are shaped by meiotic recombination, which is initiated via hundreds of DNA double-strand breaks (DSBs). The distribution of DSBs throughout the genome is not random, but mechanisms molding this landscape remain poorly understood. Here, we exploit genome-wide maps of mouse DSBs at unprecedented nucleotide resolution to uncover previously invisible spatial features of recombination. At fine scale, we reveal a stereotyped hotspot structure-DSBs occur within narrow zones between methylated nucleosomes-and identify relationships between SPO11, chromatin, and the histone methyltransferase PRDM9. At large scale, DSB formation is suppressed on non-homologous portions of the sex chromosomes via the DSB-responsive kinase ATM, which also shapes the autosomal DSB landscape at multiple size scales. We also provide a genome-wide analysis of exonucleolytic DSB resection lengths and elucidate spatial relationships between DSBs and recombination products. Our results paint a comprehensive picture of features governing successive steps in mammalian meiotic recombination.
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Affiliation(s)
- Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shintaro Yamada
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Memorial Sloan Kettering Cancer Center, Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Sam E Tischfield
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jing Pan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Seoyoung Kim
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xuan Zhu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maria Jasin
- Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Memorial Sloan Kettering Cancer Center, Howard Hughes Medical Institute, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
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36
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Matveevsky S, Bakloushinskaya I, Kolomiets O. Unique sex chromosome systems in Ellobius: How do male XX chromosomes recombine and undergo pachytene chromatin inactivation? Sci Rep 2016; 6:29949. [PMID: 27425629 PMCID: PMC4947958 DOI: 10.1038/srep29949] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/27/2016] [Indexed: 01/09/2023] Open
Abstract
Most mammalian species have heteromorphic sex chromosomes in males, except for a few enigmatic groups such as the mole voles Ellobius, which do not have the Y chromosome and Sry gene. The Ellobius (XX ♀♂) system of sex chromosomes has no analogues among other animals. The structure and meiotic behaviour of the two X chromosomes were investigated for males of the sibling species Ellobius talpinus and Ellobius tancrei. Their sex chromosomes, despite their identical G-structure, demonstrate short synaptic fragments and crossover-associated MLH1 foci in both telomeric regions only. The chromatin undergoes modifications in the meiotic sex chromosomes. SUMO-1 marks a small nucleolus-like body of the meiotic XX. ATR and ubiH2A are localized in the asynaptic area and the histone γH2AFX covers the entire XX bivalent. The distribution of some markers of chromatin inactivation differentiates sex chromosomes of mole voles from those of other mammals. Sex chromosomes of both studied species have identical recombination and meiotic inactivation patterns. In Ellobius, similar chromosome morphology masks the functional heteromorphism of the male sex chromosomes, which can be seen at meiosis.
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Affiliation(s)
- Sergey Matveevsky
- Cytogenetics Laboratory, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Irina Bakloushinskaya
- Evolutionary and Developmental Genetics Laboratory, N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Oxana Kolomiets
- Cytogenetics Laboratory, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
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37
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Pigozzi MI, Del Priore L. Meiotic recombination analysis in female ducks (Anas platyrhynchos). Genetica 2016; 144:307-12. [PMID: 27115519 DOI: 10.1007/s10709-016-9899-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/20/2016] [Indexed: 11/28/2022]
Abstract
Meiotic recombination in female ducks was directly studied by immunolocalization of MLH1 protein, a mismatch repair protein of mature recombination nodules. In total, 6820 crossovers were scored along the autosomal synaptonemal complexes in 122 meiotic nuclei. From this analysis we predict that the female map length of the duck is 2845 cM, with a genome wide recombination rate of 2 cM/Mb. MLH1-focus mapping along the six largest bivalents shows regional variations of recombination frequencies that can be linked to differences in chromosome morphology. From this MLH1 mapping it can be inferred that distally located markers will appear more separated in genetic maps than physically equidistant markers located near the centromeres on bivalents 1 and 2. Instead, markers at interstitial positions on the acrocentric bivalents 3-6 will appear more tightly linked than expected on the basis of their physical distance because recombination is comparatively lower at the mid region of these chromosomes. The present results provide useful information to complement linkage mapping in ducks and extend previous knowledge about the variation of recombination rates among domestic Galloanserae.
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Affiliation(s)
- M I Pigozzi
- INBIOMED-Instituto de Investigaciones Biomédicas, UBA, CONICET, Facultad de Medicina (UBA), Paraguay 2155, Piso 10, C1121ABG, Buenos Aires, Argentina.
| | - L Del Priore
- INBIOMED-Instituto de Investigaciones Biomédicas, UBA, CONICET, Facultad de Medicina (UBA), Paraguay 2155, Piso 10, C1121ABG, Buenos Aires, Argentina
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38
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Förster DW, Jones EP, Jóhannesdóttir F, Gabriel SI, Giménez MD, Panithanarak T, Hauffe HC, Searle JB. Genetic differentiation within and away from the chromosomal rearrangements characterising hybridising chromosomal races of the western house mouse (Mus musculus domesticus). Chromosome Res 2016; 24:271-80. [PMID: 27048372 DOI: 10.1007/s10577-016-9520-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/19/2016] [Accepted: 03/22/2016] [Indexed: 01/19/2023]
Abstract
The importance of chromosomal rearrangements for speciation can be inferred from studies of genetic exchange between hybridising chromosomal races within species. Reduced fertility or recombination suppression in karyotypic hybrids has the potential to maintain or promote genetic differentiation in genomic regions near rearrangement breakpoints. We studied genetic exchange between two hybridising groups of chromosomal races of house mouse in Upper Valtellina (Lombardy, Italy), using microsatellites. These groups differ by Robertsonian fusions and/or whole-arm reciprocal translocations such that F1 hybrids have a chain-of-five meiotic configuration. Previous studies showed genetic differentiation in two chromosomes in the chain-of-five (10 and 12) close to their centromeres (i.e. the rearrangement breakpoints); we have shown here that the centromeric regions of the other two chromosomes in the chain (2 and 8) are similarly differentiated. The internal chromosomes of the chain (8 and 12) show the greatest differentiation, which may reflect pairing and recombination properties of internal and external elements in a meiotic chain. Importantly, we found that centromeric regions of some non-rearranged chromosomes also showed genetic differentiation between the hybridising groups, indicating a complex interplay between chromosomal rearrangements and other parts of the genome in maintaining or promoting differentiation and potentially driving speciation between chromosomal races.
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Affiliation(s)
- Daniel W Förster
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str.17, 10315, Berlin, Germany
| | - Eleanor P Jones
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,Fera Science, Sand Hutton, York, YO41 1LZ, UK
| | - Fríða Jóhannesdóttir
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,Department of Ecology and Genetics, Uppsala University, Norbyv 18 D, 752 36, Uppsala, Sweden.,Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY, 14853-2701, USA
| | - Sofia I Gabriel
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Mabel D Giménez
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,Instituto de Biología Subtropical, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Félix de Azara 1552, N3300LQH, Posadas, Misiones, Argentina
| | | | - Heidi C Hauffe
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, TN, Italy
| | - Jeremy B Searle
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK. .,Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY, 14853-2701, USA.
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Abstract
During meiotic recombination, double-strand breaks (DSBs) are formed in chromosomal DNA and then repaired as either crossovers (COs) or non-crossovers (NCOs). In most taxa, the number of DSBs vastly exceeds the number of COs. COs are required for generating genetic diversity in the progeny, as well as proper chromosome segregation. Their formation is tightly controlled so that there is at least one CO per pair of homologous chromosomes whereas the maximum number of COs per chromosome pair is fairly limited. One of the main mechanisms controlling the number of recombination events per meiosis is CO homeostasis, which maintains a stable CO number even when the DSB number is dramatically altered. The existence of CO homeostasis has been reported in several species, including mouse, yeast, and Caenorhabditis elegans. However, it is not known whether homeostasis exists in the same form in all species. In addition, the studies of homeostasis have been conducted using mutants and/or transgenic lines exhibiting fairly severe meiotic phenotypes, and it is unclear how important homeostasis is under normal physiological conditions. We found that, in maize, CO control is robust only to ensure one CO per chromosome pair. However, once this limit is reached, the CO number is linearly related to the DSB number. We propose that CO control is a multifaceted process whose different aspects have a varying degree of importance in different species.
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40
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Fröhlich J, Vozdova M, Kubickova S, Cernohorska H, Sebestova H, Rubes J. Variation of Meiotic Recombination Rates and MLH1 Foci Distribution in Spermatocytes of Cattle, Sheep and Goats. Cytogenet Genome Res 2015; 146:211-21. [PMID: 26406935 DOI: 10.1159/000439452] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
Despite similar genome sizes, a great variability in recombination rates is observed in mammals. We used antibodies against SYCP3, MLH1 and centromeres to compare crossover frequency, position along chromosome arms and the effect of crossover interference in spermatocytes of 4 species from the family Bovidae (Bos taurus, 2n = 60, tribe Bovini; Ovis aries, 2n = 54, Capra hircus, 2n = 60 and Ammotragus lervia, 2n = 58, tribe Caprini). Despite significant individual variability, our results also show significant differences in both recombination rates and the total length of autosomal synaptonemal complexes (SC) between cattle (47.53 MLH1 foci/cell, 244.59 µm) and members of the tribe Caprini (61.83 MLH1 foci, 296.19 µm) which can be explained by the length of time that has passed since their evolutionary divergence. Sheep displayed the highest number of MLH1 foci per cell and recombination density, although they have a lower diploid chromosome number caused by centric fusions corresponding to cattle chromosomes 1;3, 2;8 and 5;11. However, the proportion of MLH1 foci observed on the fused chromosomes in sheep (26.14%) was significantly lower than on the orthologous acrocentrics in cattle (27.6%) and goats (28.2%), and their distribution along the SC arms differed significantly. The reduced recombination rate in metacentrics is probably caused by interference acting across the centromere.
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Affiliation(s)
- Jan Fröhlich
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
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41
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Sebestova H, Vozdova M, Kubickova S, Cernohorska H, Kotrba R, Rubes J. Effect of species-specific differences in chromosome morphology on chromatin compaction and the frequency and distribution of RAD51 and MLH1 foci in two bovid species: cattle (Bos taurus) and the common eland (Taurotragus oryx). Chromosoma 2015; 125:137-49. [PMID: 26194101 DOI: 10.1007/s00412-015-0533-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Abstract
Meiotic recombination between homologous chromosomes is crucial for their correct segregation into gametes and for generating diversity. We compared the frequency and distribution of MLH1 foci and RAD51 foci, synaptonemal complex (SC) length and DNA loop size in two related Bovidae species that share chromosome arm homology but show an extreme difference in their diploid chromosome number: cattle (Bos taurus, 2n = 60) and the common eland (Taurotragus oryx, 2nmale = 31). Compared to cattle, significantly fewer MLH1 foci per cell were observed in the common eland, which can be attributed to the lower number of initial double-strand breaks (DSBs) detected as RAD51 foci in leptonema. Despite the significantly shorter total autosomal SC length and longer DNA loop size of the common eland bi-armed chromosomes compared to those of bovine acrocentrics, the overall crossover density in the common eland was still lower than in cattle, probably due to the reduction in the number of MLH1 foci in the proximal regions of the bi-armed chromosomes. The formation of centric fusions during karyotype evolution of the common eland accompanied by meiotic chromatin compaction has greater implications in the reduction in the number of DSBs in leptonema than in the decrease of MLH1 foci number in pachynema.
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Affiliation(s)
- Hana Sebestova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Miluse Vozdova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic.
| | - Svatava Kubickova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Halina Cernohorska
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Radim Kotrba
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Prague, Czech Republic
| | - Jiri Rubes
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
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42
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Keeney S, Lange J, Mohibullah N. Self-organization of meiotic recombination initiation: general principles and molecular pathways. Annu Rev Genet 2015; 48:187-214. [PMID: 25421598 DOI: 10.1146/annurev-genet-120213-092304] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recombination in meiosis is a fascinating case study for the coordination of chromosomal duplication, repair, and segregation with each other and with progression through a cell-division cycle. Meiotic recombination initiates with formation of developmentally programmed DNA double-strand breaks (DSBs) at many places across the genome. DSBs are important for successful meiosis but are also dangerous lesions that can mutate or kill, so cells ensure that DSBs are made only at the right times, places, and amounts. This review examines the complex web of pathways that accomplish this control. We explore how chromosome breakage is integrated with meiotic progression and how feedback mechanisms spatially pattern DSB formation and make it homeostatic, robust, and error correcting. Common regulatory themes recur in different organisms or in different contexts in the same organism. We review this evolutionary and mechanistic conservation but also highlight where control modules have diverged. The framework that emerges helps explain how meiotic chromosomes behave as a self-organizing system.
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Affiliation(s)
- Scott Keeney
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
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43
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Del Priore L, Pigozzi MI. Sex-specific recombination maps for individual macrochromosomes in the Japanese quail (Coturnix japonica). Chromosome Res 2015; 23:199-210. [PMID: 25596820 DOI: 10.1007/s10577-014-9448-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Abstract
Meiotic recombination in the Japanese quail was directly studied by immunolocalization of mutL homolog 1 (MLH1), a mismatch repair protein of mature recombination nodules. In total, 15,862 crossovers were scored along the autosomal synaptonemal complexes in 308 meiotic nuclei from males and females. Crossover frequencies calculated from MLH1 foci show wide similitude between males and females with slightly higher number of foci in females. From this analysis, we predict that the sex-averaged map length of the Japanese quail is 2580 cM, with a genome-wide recombination rate of 1.9 cM/Mb. MLH1 focus mapping along the six largest bivalents showed few intersex differences in the distribution of crossovers along with variant patterns in metacentric and acrocentric macrobivalents. These results provide valuable information to complement linkage map analysis in the species while providing insight into our understanding of the mechanisms of crossover distribution along chromosome arms.
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Affiliation(s)
- Lucía Del Priore
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10, C1121ABG, Buenos Aires, Argentina
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44
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Capilla L, Medarde N, Alemany-Schmidt A, Oliver-Bonet M, Ventura J, Ruiz-Herrera A. Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background. Proc Biol Sci 2015; 281:rspb.2014.0297. [PMID: 24850922 DOI: 10.1098/rspb.2014.0297] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite the existence of formal models to explain how chromosomal rearrangements can be fixed in a population in the presence of gene flow, few empirical data are available regarding the mechanisms by which genome shuffling contributes to speciation, especially in mammals. In order to shed light on this intriguing evolutionary process, here we present a detailed empirical study that shows how Robertsonian (Rb) fusions alter the chromosomal distribution of recombination events during the formation of the germline in a Rb system of the western house mouse (Mus musculus domesticus). Our results indicate that both the total number of meiotic crossovers and the chromosomal distribution of recombination events are reduced in mice with Rb fusions and that this can be related to alterations in epigenetic signatures for heterochromatinization. Furthermore, we detected novel house mouse Prdm9 allelic variants in the Rb system. Remarkably, mean recombination rates were positively correlated with a decrease in the number of ZnF domains in the Prdm9 gene. The suggestion that recombination can be modulated by both chromosomal reorganizations and genetic determinants that control the formation of double-stranded breaks during meiosis opens new avenues for understanding the role of recombination in chromosomal speciation.
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Affiliation(s)
- Laia Capilla
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | - Nuria Medarde
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | | | - Maria Oliver-Bonet
- Unitat d'Investigació, Hospital Universitari Son Espases, Ctra Valldemossa 79, Palma 07010, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
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45
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Anderson LK, Lohmiller LD, Tang X, Hammond DB, Javernick L, Shearer L, Basu-Roy S, Martin OC, Falque M. Combined fluorescent and electron microscopic imaging unveils the specific properties of two classes of meiotic crossovers. Proc Natl Acad Sci U S A 2014; 111:13415-20. [PMID: 25197066 PMCID: PMC4169947 DOI: 10.1073/pnas.1406846111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Crossovers (COs) shuffle genetic information and allow balanced segregation of homologous chromosomes during the first division of meiosis. In several organisms, mutants demonstrate that two molecularly distinct pathways produce COs. One pathway produces class I COs that exhibit interference (lowered probability of nearby COs), and the other pathway produces class II COs with little or no interference. However, the relative contributions, genomic distributions, and interactions of these two pathways are essentially unknown in nonmutant organisms because marker segregation only indicates that a CO has occurred, not its class type. Here, we combine the efficiency of light microscopy for revealing cellular functions using fluorescent probes with the high resolution of electron microscopy to localize and characterize COs in the same sample of meiotic pachytene chromosomes from wild-type tomato. To our knowledge, for the first time, every CO along each chromosome can be identified by class to unveil specific characteristics of each pathway. We find that class I and II COs have different recombination profiles along chromosomes. In particular, class II COs, which represent about 18% of all COs, exhibit no interference and are disproportionately represented in pericentric heterochromatin, a feature potentially exploitable in plant breeding. Finally, our results demonstrate that the two pathways are not independent because there is interference between class I and II COs.
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Affiliation(s)
- Lorinda K Anderson
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878; and
| | - Leslie D Lohmiller
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878; and
| | - Xiaomin Tang
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878; and
| | - D Boyd Hammond
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878; and
| | - Lauren Javernick
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878; and
| | - Lindsay Shearer
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878; and
| | - Sayantani Basu-Roy
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Olivier C Martin
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
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46
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de la Fuente R, Manterola M, Viera A, Parra MT, Alsheimer M, Rufas JS, Page J. Chromatin organization and remodeling of interstitial telomeric sites during meiosis in the Mongolian gerbil (Meriones unguiculatus). Genetics 2014; 197:1137-51. [PMID: 24907260 PMCID: PMC4125389 DOI: 10.1534/genetics.114.166421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/01/2014] [Indexed: 12/16/2022] Open
Abstract
Telomeric DNA repeats are key features of chromosomes that allow the maintenance of integrity and stability in the telomeres. However, interstitial telomere sites (ITSs) can also be found along the chromosomes, especially near the centromere, where they may appear following chromosomal rearrangements like Robertsonian translocations. There is no defined role for ITSs, but they are linked to DNA damage-prone sites. We were interested in studying the structural organization of ITSs during meiosis, a kind of cell division in which programmed DNA damage events and noticeable chromatin reorganizations occur. Here we describe the presence of highly amplified ITSs in the pericentromeric region of Mongolian gerbil (Meriones unguiculatus) chromosomes. During meiosis, ITSs show a different chromatin conformation than DNA repeats at telomeres, appearing more extended and accumulating heterochromatin markers. Interestingly, ITSs also recruit the telomeric proteins RAP1 and TRF1, but in a stage-dependent manner, appearing mainly at late prophase I stages. We did not find a specific accumulation of DNA repair factors to the ITSs, such as γH2AX or RAD51 at these stages, but we could detect the presence of MLH1, a marker for reciprocal recombination. However, contrary to previous reports, we did not find a specific accumulation of crossovers at ITSs. Intriguingly, some centromeric regions of metacentric chromosomes may bind the nuclear envelope through the association to SUN1 protein, a feature usually performed by telomeres. Therefore, ITSs present a particular and dynamic chromatin configuration in meiosis, which could be involved in maintaining their genetic stability, but they additionally retain some features of distal telomeres, provided by their capability to associate to telomere-binding proteins.
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Affiliation(s)
| | - Marcia Manterola
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
| | - Alberto Viera
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - María Teresa Parra
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Manfred Alsheimer
- Department of Cell and Developmental Biology, University of Würzburg, Würzburg D-97074, Germany
| | - Julio S Rufas
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jesús Page
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid 28049, Spain
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Basheva EA, Torgasheva AA, Golenischev FN, Frisman LV, Borodin PM. Chromosome synapsis and recombination in the hybrids between chromosome races of the common vole Microtus aravalis: "arvalis" and "obscurus". DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2014; 456:206-8. [PMID: 24985517 DOI: 10.1134/s0012496614030144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Indexed: 11/23/2022]
Affiliation(s)
- E A Basheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
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Ullastres A, Farré M, Capilla L, Ruiz-Herrera A. Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions. BMC Genomics 2014; 15:530. [PMID: 24969235 PMCID: PMC4082625 DOI: 10.1186/1471-2164-15-530] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 06/19/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution. RESULTS We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages. CONCLUSIONS Our data suggest that adaptive alleles - in this case, genes involved in the immune response - might have been favored by genome rearrangements in the macaque lineage.
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Affiliation(s)
| | | | | | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain.
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Mary N, Barasc H, Ferchaud S, Billon Y, Meslier F, Robelin D, Calgaro A, Loustau-Dudez AM, Bonnet N, Yerle M, Acloque H, Ducos A, Pinton A. Meiotic recombination analyses of individual chromosomes in male domestic pigs (Sus scrofa domestica). PLoS One 2014; 9:e99123. [PMID: 24919066 PMCID: PMC4053413 DOI: 10.1371/journal.pone.0099123] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/09/2014] [Indexed: 01/05/2023] Open
Abstract
For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes.
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Affiliation(s)
- Nicolas Mary
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Harmonie Barasc
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Stéphane Ferchaud
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Yvon Billon
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Frédéric Meslier
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - David Robelin
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anne Calgaro
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anne-Marie Loustau-Dudez
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Nathalie Bonnet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Martine Yerle
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Hervé Acloque
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Ducos
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Pinton
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
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Hot regions of noninterfering crossovers coexist with a nonuniformly interfering pathway in Arabidopsis thaliana. Genetics 2013; 195:769-79. [PMID: 24026099 DOI: 10.1534/genetics.113.155549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In most organisms that have been studied, crossovers formed during meiosis exhibit interference: nearby crossovers are rare. Here we provide an in-depth study of crossover interference in Arabidopsis thaliana, examining crossovers genome-wide in >1500 backcrosses for both male and female meiosis. This unique data set allows us to take a two-pathway modeling approach based on superposing a fraction p of noninterfering crossovers and a fraction (1 - p) of interfering crossovers generated using the gamma model characterized by its interference strength nu. Within this framework, we fit the two-pathway model to the data and compare crossover interference strength between chromosomes and then along chromosomes. We find that the interfering pathway has markedly higher interference strength nu in female than in male meiosis and also that male meiosis has a higher proportion p of noninterfering crossovers. Furthermore, we test for possible intrachromosomal variations of nu and p. Our conclusion is that there are clear differences between left and right arms as well as between central and peripheral regions. Finally, statistical tests unveil a genome-wide picture of small-scale heterogeneities, pointing to the existence of hot regions in the genome where crossovers form preferentially without interference.
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