1
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Niu Y, Fan X, Yang Y, Li J, Lian J, Wang L, Zhang Y, Tang Y, Tang Z. Haplotype-resolved assembly of a pig genome using single-sperm sequencing. Commun Biol 2024; 7:738. [PMID: 38890535 PMCID: PMC11189477 DOI: 10.1038/s42003-024-06397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/29/2024] [Indexed: 06/20/2024] Open
Abstract
Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was developed based on long-read sequencing and sperm-phased markers. The chromosome-level phased assembly showed higher phasing accuracy than methods that rely only on HiFi reads. The use of single-sperm sequencing data enabled the construction of a genetic map, successfully mapping the sperm motility trait to a specific region on chromosome 1 (105.40-110.70 Mb). Furthermore, with the assistance of Y chromosome-bearing sperm data, 26.16 Mb Y chromosome sequences were assembled. We report a reliable approach for assembling chromosome-level phased genomes and reveal the potential of sperm population in basic biology research and sperm phenotype research.
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Affiliation(s)
- Yongchao Niu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiang Li
- Biozeron Shenzhen, Inc., Shenzhen, China
| | | | - Liu Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
| | - Yongjin Zhang
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China.
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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2
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Venu V, Harjunmaa E, Dreau A, Brady S, Absher D, Kingsley DM, Jones FC. Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish. Nat Ecol Evol 2024:10.1038/s41559-024-02434-4. [PMID: 38839849 DOI: 10.1038/s41559-024-02434-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 05/02/2024] [Indexed: 06/07/2024]
Abstract
Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine-freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene 'cassettes'. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.
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Affiliation(s)
- Vrinda Venu
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- Los Alamos National Laboratory, New Mexico, NM, USA.
| | - Enni Harjunmaa
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- CeGAT GmbH, Tübingen, Germany
| | - Andreea Dreau
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Evotec SE 'Campus Curie', Toulouse, France
| | - Shannon Brady
- Deptartment of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - David M Kingsley
- Deptartment of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, the Netherlands.
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3
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Joseph J, Prentout D, Laverré A, Tricou T, Duret L. High prevalence of PRDM9-independent recombination hotspots in placental mammals. Proc Natl Acad Sci U S A 2024; 121:e2401973121. [PMID: 38809707 PMCID: PMC11161765 DOI: 10.1073/pnas.2401973121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
In many mammals, recombination events are concentrated in hotspots directed by a sequence-specific DNA-binding protein named PRDM9. Intriguingly, PRDM9 has been lost several times in vertebrates, and notably among mammals, it has been pseudogenized in the ancestor of canids. In the absence of PRDM9, recombination hotspots tend to occur in promoter-like features such as CpG islands. It has thus been proposed that one role of PRDM9 could be to direct recombination away from PRDM9-independent hotspots. However, the ability of PRDM9 to direct recombination hotspots has been assessed in only a handful of species, and a clear picture of how much recombination occurs outside of PRDM9-directed hotspots in mammals is still lacking. In this study, we derived an estimator of past recombination activity based on signatures of GC-biased gene conversion in substitution patterns. We quantified recombination activity in PRDM9-independent hotspots in 52 species of boreoeutherian mammals. We observe a wide range of recombination rates at these loci: several species (such as mice, humans, some felids, or cetaceans) show a deficit of recombination, while a majority of mammals display a clear peak of recombination. Our results demonstrate that PRDM9-directed and PRDM9-independent hotspots can coexist in mammals and that their coexistence appears to be the rule rather than the exception. Additionally, we show that the location of PRDM9-independent hotspots is relatively more stable than that of PRDM9-directed hotspots, but that PRDM9-independent hotspots nevertheless evolve slowly in concert with DNA hypomethylation.
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Affiliation(s)
- Julien Joseph
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne69100, France
| | - Djivan Prentout
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Alexandre Laverré
- Department of Ecology and Evolution, University of Lausanne, LausanneCH-1015, Switzerland
- Swiss Institute of Bioinformatics, LausanneCH-1015, Switzerland
| | - Théo Tricou
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne69100, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne69100, France
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4
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Genestier A, Duret L, Lartillot N. Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis: A model based exploration of the PRDM9 intra-genomic Red Queen. PLoS Genet 2024; 20:e1011274. [PMID: 38768268 PMCID: PMC11142677 DOI: 10.1371/journal.pgen.1011274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/31/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Molecular dissection of meiotic recombination in mammals, combined with population-genetic and comparative studies, have revealed a complex evolutionary dynamic characterized by short-lived recombination hotspots. Hotspots are chromosome positions containing DNA sequences where the protein PRDM9 can bind and cause crossing-over. To explain these fast evolutionary dynamic, a so-called intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hotspot extinction (the hotspot conversion paradox), followed by positive selection favoring mutant PRDM9 alleles recognizing new sequence motifs. Although this model predicts many empirical observations, the exact causes of the positive selection acting on new PRDM9 alleles is still not well understood. In this direction, experiment on mouse hybrids have suggested that, in addition to targeting double strand breaks, PRDM9 has another role during meiosis. Specifically, PRDM9 symmetric binding (simultaneous binding at the same site on both homologues) would facilitate homology search and, as a result, the pairing of the homologues. Although discovered in hybrids, this second function of PRDM9 could also be involved in the evolutionary dynamic observed within populations. To address this point, here, we present a theoretical model of the evolutionary dynamic of meiotic recombination integrating current knowledge about the molecular function of PRDM9. Our modeling work gives important insights into the selective forces driving the turnover of recombination hotspots. Specifically, the reduced symmetrical binding of PRDM9 caused by the loss of high affinity binding sites induces a net positive selection eliciting new PRDM9 alleles recognizing new targets. The model also offers new insights about the influence of the gene dosage of PRDM9, which can paradoxically result in negative selection on new PRDM9 alleles entering the population, driving their eviction and thus reducing standing variation at this locus.
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Affiliation(s)
- Alice Genestier
- Universite Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, France
| | - Laurent Duret
- Universite Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, France
| | - Nicolas Lartillot
- Universite Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, France
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5
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Yin L, Jiang N, Li T, Zhang Y, Yuan S. Telomeric function and regulation during male meiosis in mice and humans. Andrology 2024. [PMID: 38511802 DOI: 10.1111/andr.13631] [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: 07/06/2023] [Revised: 02/26/2024] [Accepted: 03/03/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Telomeres are unique structures situated at the ends of chromosomes. Preserving the structure and function of telomeres is essential for maintaining genomic stability and promoting genetic diversity during male meiosis in mammals. MATERIAL-METHODS This review compiled recent literature on the function and regulation of telomeres during male meiosis in both mice and humans, and also highlighted the critical roles of telomeres in reproductive biology and medicine. RESULTS-DISCUSSION Various structures, consisting of the LINC complex (SUN-KASH), SPDYA-CDK2, TTM trimer (TERB1-TERB2-MAJIN), and shelterin, are critical in controlling telomeric activities, such as nuclear envelope attachment and bouquet formation. Other than telomere-related proteins, cohesins and genes responsible for regulating telomere function are also highlighted, though the exact mechanism remains unclear. The gene-mutant mouse models with meiotic defects directly reveal the essential roles of telomeres in male meiosis. Recently reported mutant genes associated with telomere activity in clinical practice have also been illustrated in detail. CONCLUSIONS Proper regulation of telomere activities is essential for male meiosis progression in mice and humans.
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Affiliation(s)
- Lisha Yin
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Jiang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Youzhi Zhang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology; Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, Xianning, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan, China
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6
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Przeworski M. 2023 ASHG Scientific Achievement Award. Am J Hum Genet 2024; 111:425-427. [PMID: 38458164 PMCID: PMC10995464 DOI: 10.1016/j.ajhg.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 03/10/2024] Open
Abstract
This article is based on the address given by the author at the 2023 meeting of The American Society of Human Genetics (ASHG) in Washington, D.C. A video of the original address can be found at the ASHG website.
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Affiliation(s)
- Molly Przeworski
- Departments of Biological Sciences and Systems Biology, Columbia University, New York, NY, USA.
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7
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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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8
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Huang X, Zhu TN, Liu YC, Qi GA, Zhang JN, Chen GB. Efficient estimation for large-scale linkage disequilibrium patterns of the human genome. eLife 2023; 12:RP90636. [PMID: 38149842 PMCID: PMC10752592 DOI: 10.7554/elife.90636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
In this study, we proposed an efficient algorithm (X-LD) for estimating linkage disequilibrium (LD) patterns for a genomic grid, which can be of inter-chromosomal scale or of small segments. Compared with conventional methods, the proposed method was significantly faster, dropped from O(nm2) to O(n2m)-n the sample size and m the number of SNPs, and consequently we were permitted to explore in depth unknown or reveal long-anticipated LD features of the human genome. Having applied the algorithm for 1000 Genome Project (1KG), we found (1) the extended LD, driven by population structure, universally existed, and the strength of inter-chromosomal LD was about 10% of their respective intra-chromosomal LD in relatively homogeneous cohorts, such as FIN, and to nearly 56% in admixed cohort, such as ASW. (2) After splitting each chromosome into upmost of more than a half million grids, we elucidated the LD of the HLA region was nearly 42 folders higher than chromosome 6 in CEU and 11.58 in ASW; on chromosome 11, we observed that the LD of its centromere was nearly 94.05 folders higher than chromosome 11 in YRI and 42.73 in ASW. (3) We uncovered the long-anticipated inversely proportional linear relationship between the length of a chromosome and the strength of chromosomal LD, and their Pearson's correlation was on average over 0.80 for 26 1KG cohorts. However, this linear norm was so far perturbed by chromosome 11 given its more completely sequenced centromere region. Uniquely chromosome 8 of ASW was found most deviated from the linear norm than any other autosomes. The proposed algorithm has been realized in C++ (called X-LD) and is available at https://github.com/gc5k/gear2, and can be applied to explore LD features in any sequenced populations.
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Affiliation(s)
- Xin Huang
- Institute of Bioinformatics, Zhejiang UniversityHangzhouChina
- Center for General Practice Medicine, Department of General Practice Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical CollegeHangzhouChina
- Center for Reproductive Medicine, Department of Genetic and Genomic Medicine, and Clinical Research Institute, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical CollegeZhejiangChina
| | - Tian-Neng Zhu
- Institute of Bioinformatics, Zhejiang UniversityHangzhouChina
| | - Ying-Chao Liu
- Institute of Bioinformatics, Zhejiang UniversityHangzhouChina
| | - Guo-An Qi
- Institute of Bioinformatics, Zhejiang UniversityHangzhouChina
- Hainan Institute of Zhejiang UniversityHainanChina
| | | | - Guo-Bo Chen
- Center for General Practice Medicine, Department of General Practice Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical CollegeHangzhouChina
- Center for Reproductive Medicine, Department of Genetic and Genomic Medicine, and Clinical Research Institute, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical CollegeZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouChina
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9
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Hinch R, Donnelly P, Hinch AG. Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line. Science 2023; 382:eadh2531. [PMID: 38033082 PMCID: PMC7615360 DOI: 10.1126/science.adh2531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/29/2023] [Indexed: 12/02/2023]
Abstract
Meiotic recombination commences with hundreds of programmed DNA breaks; however, the degree to which they are accurately repaired remains poorly understood. We report that meiotic break repair is eightfold more mutagenic for single-base substitutions than was previously understood, leading to de novo mutation in one in four sperm and one in 12 eggs. Its impact on indels and structural variants is even higher, with 100- to 1300-fold increases in rates per break. We uncovered new mutational signatures and footprints relative to break sites, which implicate unexpected biochemical processes and error-prone DNA repair mechanisms, including translesion synthesis and end joining in meiotic break repair. We provide evidence that these mechanisms drive mutagenesis in human germ lines and lead to disruption of hundreds of genes genome wide.
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Affiliation(s)
- Robert Hinch
- Big Data Institute, University of Oxford; Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford; Oxford, UK
- Genomics plc; Oxford, UK
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10
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Davies B, Zhang G, Moralli D, Alghadban S, Biggs D, Preece C, Donnelly P, Hinch AG. Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice. Genome Res 2023; 33:gr.278024.123. [PMID: 37977820 PMCID: PMC10760447 DOI: 10.1101/gr.278024.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Mammalian meiotic recombination proceeds via repair of hundreds of programmed DNA double-strand breaks, which requires choreographed binding of RPA, DMC1, and RAD51 to single-stranded DNA substrates. High-resolution in vivo binding maps of these proteins provide insights into the underlying molecular mechanisms. When assayed in F1-hybrid mice, these maps can distinguish the broken chromosome from the chromosome used as template for repair, revealing more mechanistic detail and enabling the structure of the recombination intermediates to be inferred. By applying CRISPR-Cas9 mutagenesis directly on F1-hybrid embryos, we have extended this approach to explore the molecular detail of recombination when a key component is knocked out. As a proof of concept, we have generated hybrid biallelic knockouts of Dmc1 and built maps of meiotic binding of RAD51 and RPA in them. DMC1 is essential for meiotic recombination, and comparison of these maps with those from wild-type mice is informative about the structure and timing of critical recombination intermediates. We observe redistribution of RAD51 binding and complete abrogation of D-loop recombination intermediates at a molecular level in Dmc1 mutants. These data provide insight on the configuration of RPA in D-loop intermediates and suggest that stable strand exchange proceeds via multiple rounds of strand invasion with template switching in mouse. Our methodology provides a high-throughput approach for characterization of gene function in meiotic recombination at low animal cost.
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Affiliation(s)
- Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Gang Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Samy Alghadban
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Chris Preece
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
- Genomics PLC, Oxford OX1 1JD, United Kingdom
| | - Anjali Gupta Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom;
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11
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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Brooks Crickard J, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566911. [PMID: 38014100 PMCID: PMC10680668 DOI: 10.1101/2023.11.13.566911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80 percent of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction (dHJ) intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates and whether it interacts with other meiotic factors prior to its role in crossover resolution. We performed a haploinsufficiency screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3 using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. We identified several genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and at times in meiotic prophase when Dmc1 acts as a recombinase. Interestingly, restricting MLH3 expression to roughly the time of crossover resolution resulted in a mlh3 null-like phenotype for crossing over. Our data are consistent with a model in which Dmc1 nucleates a polymer of Mlh1-Mlh3 to promote crossing over.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
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12
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Baker Z, Przeworski M, Sella G. Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence. eLife 2023; 12:e83769. [PMID: 37830496 DOI: 10.7554/elife.83769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/12/2023] [Indexed: 10/14/2023] Open
Abstract
In many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. This assumption, however, does not align with current evidence. Recent experimental work indicates that PRDM9 binding on both homologs facilitates DSB repair, and that the absence of sufficient symmetric binding disrupts meiosis. We therefore consider an alternative hypothesis: that rapid PRDM9 evolution is driven by the need to restore symmetric binding because of its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population genetic processes that govern the evolution of the zinc finger array and its binding sites. We show that the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease, in turn, drives rapid PRDM9 evolutionary turnover. Our results therefore suggest that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
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Affiliation(s)
- Zachary Baker
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
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13
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Xie H, Li W, Guo Y, Su X, Chen K, Wen L, Tang F. Long-read-based single sperm genome sequencing for chromosome-wide haplotype phasing of both SNPs and SVs. Nucleic Acids Res 2023; 51:8020-8034. [PMID: 37351613 PMCID: PMC10450174 DOI: 10.1093/nar/gkad532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Although localized haploid phasing can be achieved using long read genome sequencing without parental data, reliable chromosome-scale phasing remains a great challenge. Given that sperm is a natural haploid cell, single-sperm genome sequencing can provide a chromosome-wide phase signal. Due to the limitation of read length, current short-read-based single-sperm genome sequencing methods can only achieve SNP haplotyping and come with difficulties in detecting and haplotyping structural variations (SVs) in complex genomic regions. To overcome these limitations, we developed a long-read-based single-sperm genome sequencing method and a corresponding data analysis pipeline that can accurately identify crossover events and chromosomal level aneuploidies in single sperm and efficiently detect SVs within individual sperm cells. Importantly, without parental genome information, our method can accurately conduct de novo phasing of heterozygous SVs as well as SNPs from male individuals at the whole chromosome scale. The accuracy for phasing of SVs was as high as 98.59% using 100 single sperm cells, and the accuracy for phasing of SNPs was as high as 99.95%. Additionally, our method reliably enabled deduction of the repeat expansions of haplotype-resolved STRs/VNTRs in single sperm cells. Our method provides a new opportunity for studying haplotype-related genetics in mammals.
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Affiliation(s)
- Haoling Xie
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
- Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
| | - Wen Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Yuqing Guo
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Xinjie Su
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Kexuan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Lu Wen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
- Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
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14
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Tsui V, Lyu R, Novakovic S, Stringer JM, Dunleavy JE, Granger E, Semple T, Leichter A, Martelotto LG, Merriner DJ, Liu R, McNeill L, Zerafa N, Hoffmann ER, O’Bryan MK, Hutt K, Deans AJ, Heierhorst J, McCarthy DJ, Crismani W. Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals. CELL GENOMICS 2023; 3:100349. [PMID: 37601968 PMCID: PMC10435384 DOI: 10.1016/j.xgen.2023.100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/30/2023] [Accepted: 06/02/2023] [Indexed: 08/22/2023]
Abstract
Meiotic crossovers are required for accurate chromosome segregation and producing new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. Here, we reveal the tumor suppressor FANCM as a meiotic anti-crossover factor in mammals. We use unique large-scale crossover analyses with both single-gamete sequencing and pedigree-based bulk-sequencing datasets to identify a genome-wide increase in crossover frequencies in Fancm-deficient mice. Gametogenesis is heavily perturbed in Fancm loss-of-function mice, which is consistent with the reproductive defects reported in humans with biallelic FANCM mutations. A portion of the gametogenesis defects can be attributed to the cGAS-STING pathway after birth. Despite the gametogenesis phenotypes in Fancm mutants, both sexes are capable of producing offspring. We propose that the anti-crossover function and role in gametogenesis of Fancm are separable and will inform diagnostic pathways for human genomic instability disorders.
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Affiliation(s)
- Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Stevan Novakovic
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jessica M. Stringer
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Jessica E.M. Dunleavy
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Elissah Granger
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Tim Semple
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Anna Leichter
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Luciano G. Martelotto
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - D. Jo Merriner
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruijie Liu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Lucy McNeill
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Nadeen Zerafa
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Eva R. Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Moira K. O’Bryan
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Deans
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Genome Stability Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jörg Heierhorst
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Molecular Genetics Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
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15
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Teterina AA, Willis JH, Lukac M, Jovelin R, Cutter AD, Phillips PC. Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes. PLoS Genet 2023; 19:e1010879. [PMID: 37585484 PMCID: PMC10461856 DOI: 10.1371/journal.pgen.1010879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/28/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.
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Affiliation(s)
- Anastasia A. Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matt Lukac
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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16
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Kudryavtseva N, Ermolaev A, Pivovarov A, Simanovsky S, Odintsov S, Khrustaleva L. The Control of the Crossover Localization in Allium. Int J Mol Sci 2023; 24:ijms24087066. [PMID: 37108228 PMCID: PMC10138942 DOI: 10.3390/ijms24087066] [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: 12/14/2022] [Revised: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Meiotic crossovers/chiasmata are not randomly distributed and strictly controlled. The mechanisms behind crossover (CO) patterning remain largely unknown. In Allium cepa, as in the vast majority of plants and animals, COs predominantly occur in the distal 2/3 of the chromosome arm, while in Allium fistulosum they are strictly localized in the proximal region. We investigated the factors that may contribute to the pattern of COs in A. cepa, A. fistulosum and their F1 diploid (2n = 2x = 8C + 8F) and F1 triploid (2n = 3x = 16F + 8C) hybrids. The genome structure of F1 hybrids was confirmed using genomic in situ hybridization (GISH). The analysis of bivalents in the pollen mother cells (PMCs) of the F1 triploid hybrid showed a significant shift in the localization of COs to the distal and interstitial regions. In F1 diploid hybrid, the COs localization was predominantly the same as that of the A. cepa parent. We found no differences in the assembly and disassembly of ASY1 and ZYP1 in PMCs between A. cepa and A. fistulosum, while F1 diploid hybrid showed a delay in chromosome pairing and a partial absence of synapsis in paired chromosomes. Immunolabeling of MLH1 (class I COs) and MUS81 (class II COs) proteins showed a significant difference in the class I/II CO ratio between A. fistulosum (50%:50%) and A. cepa (73%:27%). The MLH1:MUS81 ratio at the homeologous synapsis of F1 diploid hybrid (70%:30%) was the most similar to that of the A. cepa parent. F1 triploid hybrid at the A. fistulosum homologous synapsis showed a significant increase in MLH1:MUS81 ratio (60%:40%) compared to the A. fistulosum parent. The results suggest possible genetic control of CO localization. Other factors affecting the distribution of COs are discussed.
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Affiliation(s)
- Natalia Kudryavtseva
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Aleksey Ermolaev
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Anton Pivovarov
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Sergey Simanovsky
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prosp., Moscow 119071, Russia
| | - Sergey Odintsov
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Ludmila Khrustaleva
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
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17
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Donnelly P. 2022 William Allan Award. Am J Hum Genet 2023; 110:404-408. [PMID: 36868201 PMCID: PMC10036731 DOI: 10.1016/j.ajhg.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
This article is based on the address given by the author at the 2022 meeting of The American Society of Human Genetics (ASHG) in Los Angeles, CA. The video of the original address can be found at the ASHG website.
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Affiliation(s)
- Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK; Genomics plc, Oxford, UK.
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18
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Wang X, Li Z, Feng T, Luo X, Xue L, Mao C, Cui K, Li H, Huang J, Huang K, Rehman SU, Shi D, Wu D, Ruan J, Liu Q. Chromosome-level genome and recombination map of the male buffalo. Gigascience 2022; 12:giad063. [PMID: 37589307 PMCID: PMC10433102 DOI: 10.1093/gigascience/giad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/20/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND The swamp buffalo (Bubalus bubalis carabanesis) is an economically important livestock supplying milk, meat, leather, and draft power. Several female buffalo genomes have been available, but the lack of high-quality male genomes hinders studies on chromosome evolution, especially Y, as well as meiotic recombination. RESULTS Here, a chromosome-level genome with a contig N50 of 72.2 Mb and a fine-scale recombination map of male buffalo were reported. We found that transposable elements (TEs) and structural variants (SVs) may contribute to buffalo evolution by influencing adjacent gene expression. We further found that the pseudoautosomal region (PAR) of the Y chromosome is subject to stronger purification selection. The meiotic recombination map showed that there were 2 obvious recombination hotspots on chromosome 8, and the genes around them were mainly related to tooth development, which may have helped to enhance the adaption of buffalo to inferior feed. Among several genomic features, TE density has the strongest correlation with recombination rates. Moreover, the TE subfamily, SINE/tRNA, is likely to play a role in driving recombination into SVs. CONCLUSIONS The male genome and sperm sequencing will facilitate the understanding of the buffalo genomic evolution and functional research.
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Affiliation(s)
- Xiaobo Wang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Lintao Xue
- Reproductive Medical and Genetic Center, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - Chonghui Mao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Saif-ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
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19
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Wooldridge LK, Dumont BL. Rapid Evolution of the Fine-scale Recombination Landscape in Wild House Mouse (Mus musculus) Populations. Mol Biol Evol 2022; 40:6889355. [PMID: 36508360 PMCID: PMC9825251 DOI: 10.1093/molbev/msac267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Meiotic recombination is an important evolutionary force and an essential meiotic process. In many species, recombination events concentrate into hotspots defined by the site-specific binding of PRMD9. Rapid evolution of Prdm9's zinc finger DNA-binding array leads to remarkably abrupt shifts in the genomic distribution of hotspots between species, but the question of how Prdm9 allelic variation shapes the landscape of recombination between populations remains less well understood. Wild house mice (Mus musculus) harbor exceptional Prdm9 diversity, with >150 alleles identified to date, and pose a particularly powerful system for addressing this open question. We employed a coalescent-based approach to construct broad- and fine-scale sex-averaged recombination maps from contemporary patterns of linkage disequilibrium in nine geographically isolated wild house mouse populations, including multiple populations from each of three subspecies. Comparing maps between wild mouse populations and subspecies reveals several themes. First, we report weak fine- and broad-scale recombination map conservation across subspecies and populations, with genetic divergence offering no clear prediction for recombination map divergence. Second, most hotspots are unique to one population, an outcome consistent with minimal sharing of Prdm9 alleles between surveyed populations. Finally, by contrasting aggregate hotspot activity on the X versus autosomes, we uncover evidence for population-specific differences in the degree and direction of sex dimorphism for recombination. Overall, our findings illuminate the variability of both the broad- and fine-scale recombination landscape in M. musculus and underscore the functional impact of Prdm9 allelic variation in wild mouse populations.
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20
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Novakovic S, Tsui V, Semple T, Martelotto L, McCarthy DJ, Crismani W. SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing. PLoS One 2022; 17:e0275168. [PMID: 36173986 PMCID: PMC9521801 DOI: 10.1371/journal.pone.0275168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
We developed a simple and reliable method for the isolation of haploid nuclei from fresh and frozen testes. The described protocol uses readily available reagents in combination with flow cytometry to separate haploid and diploid nuclei. The protocol can be completed within 1 hour and the resulting individual haploid nuclei have intact morphology. The isolated nuclei are suitable for library preparation for high-throughput DNA and RNA sequencing using bulk or single nuclei. The protocol was optimised with mouse testes and we anticipate that it can be applied for the isolation of mature sperm from other mammals including humans.
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Affiliation(s)
- Stevan Novakovic
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
| | - Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tim Semple
- Single Cell Innovation Laboratory, Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Luciano Martelotto
- Single Cell Innovation Laboratory, Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St. Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Melbourne, Victoria, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
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21
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Tan T, Tan Y, Wang Y, Yang X, Zhai B, Zhang S, Yang X, Nie H, Gao J, Zhou J, Zhang L, Wang S. Negative supercoils regulate meiotic crossover patterns in budding yeast. Nucleic Acids Res 2022; 50:10418-10435. [PMID: 36107772 PMCID: PMC9561271 DOI: 10.1093/nar/gkac786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/21/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
Interference exists ubiquitously in many biological processes. Crossover interference patterns meiotic crossovers, which are required for faithful chromosome segregation and evolutionary adaption. However, what the interference signal is and how it is generated and regulated is unknown. We show that yeast top2 alleles which cannot bind or cleave DNA accumulate a higher level of negative supercoils and show weaker interference. However, top2 alleles which cannot religate the cleaved DNA or release the religated DNA accumulate less negative supercoils and show stronger interference. Moreover, the level of negative supercoils is negatively correlated with crossover interference strength. Furthermore, negative supercoils preferentially enrich at crossover-associated Zip3 regions before the formation of meiotic DNA double-strand breaks, and regions with more negative supercoils tend to have more Zip3. Additionally, the strength of crossover interference and homeostasis change coordinately in mutants. These findings suggest that the accumulation and relief of negative supercoils pattern meiotic crossovers.
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Affiliation(s)
- Taicong Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Yingjin Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Ying Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Xiao Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- 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
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
| | - Binyuan Zhai
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- 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
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
| | - Shuxian Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- Advanced Medical Research Institute, Shandong University , Jinan, Shandong 250012, China
| | - Xuan Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Hui Nie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Jinmin Gao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Liangran Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- Advanced Medical Research Institute, Shandong University , Jinan, Shandong 250012, China
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- 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
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
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22
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Lyu R, Tsui V, Crismani W, Liu R, Shim H, McCarthy D. sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data. Nucleic Acids Res 2022; 50:e118. [PMID: 36107768 PMCID: PMC9723612 DOI: 10.1093/nar/gkac764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/17/2022] [Accepted: 09/06/2022] [Indexed: 12/24/2022] Open
Abstract
Profiling gametes of an individual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologies. However, high-throughput single-gamete data commonly have low depth of coverage per gamete, which challenges existing gamete-based haplotype phasing methods. In addition, haplotyping a large number of single gametes from high-throughput single-cell DNA sequencing data and constructing meiotic crossover profiles using existing methods requires intensive processing. Here, we introduce efficient software tools for the essential tasks of generating personalised haplotypes and calling crossovers in gametes from single-gamete DNA sequencing data (sgcocaller), and constructing, visualising, and comparing individualised crossover landscapes from single gametes (comapr). With additional data pre-possessing, the tools can also be applied to bulk-sequenced samples. We demonstrate that sgcocaller is able to generate impeccable phasing results for high-coverage datasets, on which it is more accurate and stable than existing methods, and also performs well on low-coverage single-gamete sequencing datasets for which current methods fail. Our tools achieve highly accurate results with user-friendly installation, comprehensive documentation, efficient computation times and minimal memory usage.
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Affiliation(s)
- Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia,Melbourne Integrative Genomics/School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Building 184, Royal Parade, Parkville, Victoria 3010, Australia
| | - Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia,The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia,The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Ruijie Liu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | | | - Davis J McCarthy
- To whom correspondence should be addressed. Tel: +61 3 9231 2480; Fax: +61 3 9416 2676;
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23
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Diversity and determinants of recombination landscapes in flowering plants. PLoS Genet 2022; 18:e1010141. [PMID: 36040927 PMCID: PMC9467342 DOI: 10.1371/journal.pgen.1010141] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 09/12/2022] [Accepted: 08/05/2022] [Indexed: 11/19/2022] Open
Abstract
During meiosis, crossover rates are not randomly distributed along the chromosome and their location may have a strong impact on the functioning and evolution of the genome. To date, the broad diversity of recombination landscapes among plants has rarely been investigated and a formal comparative genomic approach is still needed to characterize and assess the determinants of recombination landscapes among species and chromosomes. We gathered genetic maps and genomes for 57 flowering plant species, corresponding to 665 chromosomes, for which we estimated large-scale recombination landscapes. We found that the number of crossover per chromosome spans a limited range (between one to five/six) whatever the genome size, and that there is no single relationship across species between genetic map length and chromosome size. Instead, we found a general relationship between the relative size of chromosomes and recombination rate, while the absolute length constrains the basal recombination rate for each species. At the chromosome level, we identified two main patterns (with a few exceptions) and we proposed a conceptual model explaining the broad-scale distribution of crossovers where both telomeres and centromeres play a role. These patterns correspond globally to the underlying gene distribution, which affects how efficiently genes are shuffled at meiosis. These results raised new questions not only on the evolution of recombination rates but also on their distribution along chromosomes. Meiotic recombination is a universal feature of sexually reproducing species. During meiosis, crossovers play a fundamental role for the proper segregation of chromosomes during meiosis and reshuffles alleles among chromosomes. How much variation in recombination is expected within a genome and among different species remains a central question for understanding the evolution of recombination. We characterized and compared recombination landscapes in a large set of plant species with a wide range of genome size. We found that the number of crossovers varied little among species, from one mandatory to no more than five or six crossovers per chromosomes, whatever the genome size. However, we identified two main patterns of variation along chromosomes (with a few exceptions) that can be explained by a new conceptual model where chromosome length, chromosome structure and gene density play a role. The strong association between gene density and recombination was already known, but raised new questions not only about the evolution of recombination rates but also on their distribution along chromosomes.
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24
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Damm E, Odenthal-Hesse L. Orchestrating recombination initiation in mice and men. Curr Top Dev Biol 2022; 151:27-42. [PMID: 36681473 DOI: 10.1016/bs.ctdb.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recent discoveries have advanced our understanding of recombination initiation beyond the placement of double-stranded DNA breaks (DSBs) from germline replication timing to the dynamic reorganization of chromatin, and defined critical players of recombination initiation. This article focuses on recombination initiation in mammals utilizing the PRDM9 protein to orchestrate crucial stages of meiotic recombination initiation by interacting with the local DNA environment and several protein complexes. The Pioneer Complex with the SNF2-type chromatin remodeling enzyme HELLS, exposes PRDM9-bound DNA. At the same time, a Compass-Complex containing EWSR1, CXXC1, CDYL, EHMT2 and PRDM9 facilitates the association of putative hotspot sites in DNA loops with the chromosomal axis where DSB-promoting complexes are located, and DSBs are catalyzed by the SPO11/TOPOVIBL complex. Finally, homology search is facilitated at PRDM9-directed sites by ANKRD31. The Reader-Writer system consists of PRDM9 writing characteristic histone methylation signatures, which are read by ZCWPW1, promoting efficient homology engagement.
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Affiliation(s)
- Elena Damm
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön, Germany.
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25
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Valiskova B, Gregorova S, Lustyk D, Šimeček P, Jansa P, Forejt J. Genic and Chromosomal Components of Prdm9-Driven Hybrid Male Sterility in Mice (Mus musculus). Genetics 2022; 222:6655690. [PMID: 35924978 PMCID: PMC9434306 DOI: 10.1093/genetics/iyac116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/27/2022] [Indexed: 11/14/2022] Open
Abstract
Hybrid sterility contributes to speciation by preventing gene flow between related taxa. Prdm9, the first and only hybrid male sterility (HMS) gene known in vertebrates, predetermines the sites of recombination between homologous chromosomes and their synapsis in early meiotic prophase. The asymmetric binding of PRDM9 to heterosubspecific homologs of Mus m. musculus x Mus m. domesticus F1 hybrids and increase of PRDM9-independent DNA double-strand break (DSB) hotspots results in difficult to repair DSBs, incomplete synapsis of homologous chromosomes and meiotic arrest at the first meiotic prophase. Here we show that Prdm9 behaves as a major HMS gene in mice outside the Mus m. musculus x Mus m. domesticus F1 hybrids, in the genomes composed of Mus m. castaneus and Mus m. musculus chromosomes segregating on the Mus m. domesticus background. The Prdm9cst/dom2 (castaneus/domesticus) allelic combination secures meiotic synapsis, testes weight and sperm count within physiological limits, while the Prdm9msc1/dom2 (musculus/domesticus) males show a range of fertility impairment. Out of five quantitative trait loci contributing to the Prdm9msc1/dom2-related infertility, four control either meiotic synapsis or fertility phenotypes and one controls both, synapsis and fertility. Whole-genome genotyping of individual chromosomes showed preferential involvement of nonrecombinant musculus chromosomes in asynapsis in accordance with the chromosomal character of HMS. Moreover, we show that the overall asynapsis rate can be estimated solely from the genotype of individual males by scoring the effect of nonrecombinant musculus chromosomes. Prdm9-controlled HMS represents an example of genetic architecture of HMS consisting of genic and chromosomal components.
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Affiliation(s)
- Barbora Valiskova
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Sona Gregorova
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Diana Lustyk
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Petr Šimeček
- Central Laboratory of Bioinformatics, CEITEC—Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Petr Jansa
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Jiří Forejt
- Corresponding author: Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Průmyslová 595, Vestec 25250, Czech Republic.
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26
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Li Y, Chen S, Rapakoulia T, Kuwahara H, Yip KY, Gao X. Deep learning identifies and quantifies recombination hotspot determinants. Bioinformatics 2022; 38:2683-2691. [PMID: 35561158 PMCID: PMC9113300 DOI: 10.1093/bioinformatics/btac234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/08/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Recombination is one of the essential genetic processes for sexually reproducing organisms, which can happen more frequently in some regions, called recombination hotspots. Although several factors, such as PRDM9 binding motifs, are known to be related to the hotspots, their contributions to the recombination hotspots have not been quantified, and other determinants are yet to be elucidated. Here, we propose a computational method, RHSNet, based on deep learning and signal processing, to identify and quantify the hotspot determinants in a purely data-driven manner, utilizing datasets from various studies, populations, sexes and species. RESULTS RHSNet can significantly outperform other sequence-based methods on multiple datasets across different species, sexes and studies. In addition to being able to identify hotspot regions and the well-known determinants accurately, more importantly, RHSNet can quantify the determinants that contribute significantly to the recombination hotspot formation in the relation between PRDM9 binding motif, histone modification and GC content. Further cross-sex, cross-population and cross-species studies suggest that the proposed method has the generalization power and potential to identify and quantify the evolutionary determinant motifs. AVAILABILITY AND IMPLEMENTATION https://github.com/frankchen121212/RHSNet. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yu Li
- To whom correspondence should be addressed. or
| | | | | | - Hiroyuki Kuwahara
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Kevin Y Yip
- Department of Computer Science and Engineering (CSE), The Chinese University of Hong Kong (CUHK), 999077, Hong Kong SAR, China
| | - Xin Gao
- To whom correspondence should be addressed. or
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27
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Li J, Llorente B, Liti G, Yue JX. RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis. PLoS Genet 2022; 18:e1010047. [PMID: 35533184 PMCID: PMC9119626 DOI: 10.1371/journal.pgen.1010047] [Citation(s) in RCA: 2] [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: 01/23/2022] [Revised: 05/19/2022] [Accepted: 04/14/2022] [Indexed: 01/09/2023] Open
Abstract
Meiotic recombination is an essential biological process that ensures faithful chromosome segregation and promotes parental allele shuffling. Tetrad analysis is a powerful approach to quantify the genetic makeups and recombination landscapes of meiotic products. Here we present RecombineX (https://github.com/yjx1217/RecombineX), a generalized computational framework that automates the full workflow of marker identification, gamete genotyping, and tetrad-based recombination profiling based on any organism or genetic background with batch processing capability. Aside from conventional reference-based analysis, RecombineX can also perform analysis based on parental genome assemblies, which facilitates analyzing meiotic recombination landscapes in their native genomic contexts. Additional features such as copy number variation profiling and missing genotype inference further enhance downstream analysis. RecombineX also includes a dedicate module for simulating the genomes and reads of recombinant tetrads, which enables fine-tuned simulation-based hypothesis testing. This simulation module revealed the power and accuracy of RecombineX even when analyzing tetrads with very low sequencing depths (e.g., 1-2X). Tetrad sequencing data from the budding yeast Saccharomyces cerevisiae and green alga Chlamydomonas reinhardtii were further used to demonstrate the accuracy and robustness of RecombineX for organisms with both small and large genomes, manifesting RecombineX as an all-around one stop solution for future tetrad analysis. Interestingly, our re-analysis of the budding yeast tetrad sequencing data with RecombineX and Oxford Nanopore sequencing revealed two unusual structural rearrangement events that were not noticed before, which exemplify the occasional genome instability triggered by meiosis.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Bertrand Llorente
- Aix-Marseille Université, CNRS, INSERM, CRCM, Institut Paoli-Calmettes, Marseille, France
| | - Gianni Liti
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
- * E-mail: (GL); (JXY)
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
- * E-mail: (GL); (JXY)
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28
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Yang L, Gao Y, Li M, Park KE, Liu S, Kang X, Liu M, Oswalt A, Fang L, Telugu BP, Sattler CG, Li CJ, Cole JB, Seroussi E, Xu L, Yang L, Zhou Y, Li L, Zhang H, Rosen BD, Van Tassell CP, Ma L, Liu GE. Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics 2022; 23:181. [PMID: 35247961 PMCID: PMC8898482 DOI: 10.1186/s12864-022-08415-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, it is not well studied in livestock, including cattle. RESULTS To investigate their distributions in the cattle sperm genome, we sequenced 143 single sperms from two Holstein bulls. We mapped meiotic recombination events at high resolution based on phased heterozygous single nucleotide polymorphism (SNP). In the absence of evolutionary selection pressure in fertilization and survival, recombination events in sperm are enriched near distal chromosomal ends, revealing that such a pattern is intrinsic to the molecular mechanism of meiosis. Furthermore, we further validated these findings in single sperms with results derived from sequencing its family trio of diploid genomes and our previous studies of recombination in cattle. CONCLUSIONS To our knowledge, this is the first large-scale single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of recombination, genome instability, and male infertility.
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Affiliation(s)
- Liu Yang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Mingxun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 China
| | - Ki-Eun Park
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xiaolong Kang
- College of Agriculture, Ningxia University, Yinchuan, 750021 China
| | - Mei Liu
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Adam Oswalt
- Select Sires Inc, 11740 U.S. 42 North, Plain City, OH 43064 USA
| | - Lingzhao Fang
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - Bhanu P. Telugu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
- Division of Animal Sciences, University of Missouri, Columbia, MO 65201 USA
| | | | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, P.O.B 15159, HaMaccabim Road, 7528809 Rishon LeTsiyon, Israel
| | - Lingyang Xu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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29
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PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2. Proc Natl Acad Sci U S A 2022; 119:2114401119. [PMID: 35217607 PMCID: PMC8892340 DOI: 10.1073/pnas.2114401119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2022] [Indexed: 01/12/2023] Open
Abstract
We take a phylogenetic approach to search for molecular partners of PRDM9, a key meiotic recombination gene, by leveraging the fact that the complete PRDM9 gene has been lost at least 13 times independently in vertebrates. We identify two genes, ZCWPW1 and its paralog ZCWPW2, whose presence or absence across vertebrates is coupled to that of PRDM9. ZCWPW1 was recently shown to be recruited to sites of PRDM9 binding and to aid in the repair of double strand breaks. ZCWPW2 is likely recruited to sites of PRDM9 binding as well; its tight coevolution with PRDM9 across vertebrates suggests that it too plays an important role in mammals and beyond, either in double strand break formation or repair. In most mammals and likely throughout vertebrates, the gene PRDM9 specifies the locations of meiotic double strand breaks; in mice and humans at least, it also aids in their repair. For both roles, many of the molecular partners remain unknown. Here, we take a phylogenetic approach to identify genes that may be interacting with PRDM9 by leveraging the fact that PRDM9 arose before the origin of vertebrates but was lost many times, either partially or entirely—and with it, its role in recombination. As a first step, we characterize PRDM9 domain composition across 446 vertebrate species, inferring at least 13 independent losses. We then use the interdigitation of PRDM9 orthologs across vertebrates to test whether it coevolved with any of 241 candidate genes coexpressed with PRDM9 in mice or associated with recombination phenotypes in mammals. Accounting for the phylogenetic relationship among a subsample of 189 species, we find two genes whose presence and absence is unexpectedly coincident with that of PRDM9: ZCWPW1, which was recently shown to facilitate double strand break repair, and its paralog ZCWPW2, as well as, more tentatively, TEX15 and FBXO47. ZCWPW2 is expected to be recruited to sites of PRDM9 binding; its tight coevolution with PRDM9 across vertebrates suggests that it is a key interactor within mammals and beyond, with a role either in recruiting the recombination machinery or in double strand break repair.
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30
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Masset H, Ding J, Dimitriadou E, Debrock S, Tšuiko O, Smits K, Peeraer K, Voet T, Zamani Esteki M, Vermeesch JR. Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing. Nucleic Acids Res 2022; 50:e63. [PMID: 35212381 PMCID: PMC9226495 DOI: 10.1093/nar/gkac134] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 02/07/2023] Open
Abstract
Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. While current methods primarily rely on single-nucleotide polymorphism (SNP) array, we envision sequencing-based methods to become more accessible and cost-efficient. Here, we developed a novel sequencing-based methodology to haplotype and copy-number profile single cells. Following DNA amplification, genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing. This single-cell genotyping-by-sequencing (scGBS) is the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping. We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells. We demonstrate its value in human blastomere and trophectoderm samples as application for PGT for monogenic disorders. Furthermore, we demonstrate the method to work in other species through analyzing blastomeres of bovine embryos. Our scGBS method opens up the path for single-cell haplotyping of any species with diploid genomes and could make its way into the clinic as a PGT application.
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Affiliation(s)
- Heleen Masset
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Jia Ding
- Center of Human Genetics, University Hospitals of Leuven, Leuven, 3000, Belgium
| | | | - Sophie Debrock
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Olga Tšuiko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium.,Center of Human Genetics, University Hospitals of Leuven, Leuven, 3000, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, 9820, Belgium
| | - Karen Peeraer
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Joris R Vermeesch
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium.,Center of Human Genetics, University Hospitals of Leuven, Leuven, 3000, Belgium
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31
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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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32
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Zhai J, Geng W, Zhang T, Wei Y, He H, Chen W. BDE-209 induce spermatocytes arrest at early-pachytene stage during meiotic prophase I in mice. Toxicology 2022; 467:153061. [PMID: 34936917 DOI: 10.1016/j.tox.2021.153061] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 11/03/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022]
Abstract
Deca-brominated diphenyl ether (BDE-209) is a common flame retardant utilized in electronic products, textiles, furniture, and upholstery materials. Environmental BDE-209 exposure results in spermatogenesis disorder, because of the characteristics of bioaccumulation, persistence, and probably toxicity. Meiotic prophase I is a crucial phase during spermatogenesis which is a key influential factor of normal sperm production. However, the effects of BDE-209 on meiotic prophase I during spermatogenesis are poorly understood. The present study aimed to evaluate whether BDE-209 exposure impairs meiotic prophase I during spermatogenesis of spermatocytes. We validated the effects of BDE-209 on alternations of meiotic prophase I in Balb/c male mice. Firstly, we analyzed sperm quality in cauda epididymis with decreasing sperm count, increasing abnormal sperm, and male reproductive dysfunction after exposure to BDE-209. Then, reactive oxygen species (ROS) and malondialdehyde (MDA) levels in testis and GC-2spd cells were significant increased after treated with BDE-209. Furthermore, we found that meiotic prophase I arrest at early-pachytene stage during spermatogenesis with increasing of DSBs damage and trimethylated histone H3 at lysine-4 (H3K4me3) in spermatocytes exposed to BDE-209. Finally, we conducted homologous recombination (HR) analyses to identify the progression of meiosis. The recombination markers, including DMC1 and RAD51, and crossover marker MLH1 were decreased during spermatogenesis after exposure to BDE-209. Collectively, our data indicated that BDE-209 has detrimental impacts on meiotic prophase I of spermatocytes in mice.
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Affiliation(s)
- Jinxia Zhai
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Meishan Rd 81, Hefei, 230032, China.
| | - Wenfeng Geng
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Meishan Rd 81, Hefei, 230032, China.
| | - Taifa Zhang
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Meishan Rd 81, Hefei, 230032, China.
| | - Yu Wei
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Meishan Rd 81, Hefei, 230032, China.
| | - Huan He
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Meishan Rd 81, Hefei, 230032, China.
| | - Wenjing Chen
- Department of Occupational and Environmental Health, School of Public Health, Anhui Medical University, Meishan Rd 81, Hefei, 230032, China.
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33
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Qu W, Liu C, Xu YT, Xu YM, Luo MC. The formation and repair of DNA double-strand breaks in mammalian meiosis. Asian J Androl 2021; 23:572-579. [PMID: 34708719 PMCID: PMC8577251 DOI: 10.4103/aja202191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) are necessary for meiosis in mammals. A sufficient number of DSBs ensure the normal pairing/synapsis of homologous chromosomes. Abnormal DSB repair undermines meiosis, leading to sterility in mammals. The DSBs that initiate recombination are repaired as crossovers and noncrossovers, and crossovers are required for correct chromosome separation. Thus, the placement, timing, and frequency of crossover formation must be tightly controlled. Importantly, mutations in many genes related to the formation and repair of DSB result in infertility in humans. These mutations cause nonobstructive azoospermia in men, premature ovarian insufficiency and ovarian dysgenesis in women. Here, we have illustrated the formation and repair of DSB in mammals, summarized major factors influencing the formation of DSB and the theories of crossover regulation.
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Affiliation(s)
- Wei Qu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Cong Liu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Ya-Ting Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Yu-Min Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Meng-Cheng Luo
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
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34
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Zuo W, Chen G, Gao Z, Li S, Chen Y, Huang C, Chen J, Chen Z, Lei M, Bian Q. Stage-resolved Hi-C analyses reveal meiotic chromosome organizational features influencing homolog alignment. Nat Commun 2021; 12:5827. [PMID: 34625553 PMCID: PMC8501046 DOI: 10.1038/s41467-021-26033-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
During meiosis, chromosomes exhibit dramatic changes in morphology and intranuclear positioning. How these changes influence homolog pairing, alignment, and recombination remain elusive. Using Hi-C, we systematically mapped 3D genome architecture throughout all meiotic prophase substages during mouse spermatogenesis. Our data uncover two major chromosome organizational features varying along the chromosome axis during early meiotic prophase, when homolog alignment occurs. First, transcriptionally active and inactive genomic regions form alternating domains consisting of shorter and longer chromatin loops, respectively. Second, the force-transmitting LINC complex promotes the alignment of ends of different chromosomes over a range of up to 20% of chromosome length. Both features correlate with the pattern of homolog interactions and the distribution of recombination events. Collectively, our data reveal the influences of transcription and force on meiotic chromosome structure and suggest chromosome organization may provide an infrastructure for the modulation of meiotic recombination in higher eukaryotes.
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Affiliation(s)
- Wu Zuo
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guangming Chen
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, 313000, Huzhou, China
| | - Zhimei Gao
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China
| | - Shuai Li
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China
| | - Yanyan Chen
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China
| | - Chenhui Huang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China
| | - Juan Chen
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China
| | - Zhengjun Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China.
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
| | - Qian Bian
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China.
- Shanghai Institute of Precision Medicine, 200125, Shanghai, China.
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35
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Breuss MW, Yang X, Gleeson JG. Sperm mosaicism: implications for genomic diversity and disease. Trends Genet 2021; 37:890-902. [PMID: 34158173 PMCID: PMC9484299 DOI: 10.1016/j.tig.2021.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022]
Abstract
While sperm mosaicism has few consequences for men, the offspring and future generations are unwitting recipients of gonadal cell mutations, often yielding severe disease. Recent studies, fueled by emergent technologies, show that sperm mosaicism is a common source of de novo mutations (DNMs) that underlie severe pediatric disease as well as human genetic diversity. Sperm mosaicism can be divided into three types: Type I arises during sperm meiosis and is non-age dependent; Type II arises in spermatogonia and increases as men age; and Type III arises during paternal embryogenesis, spreads throughout the body, and contributes stably to sperm throughout life. Where Types I and II confer little risk of recurrence, Type III may confer identifiable risk to future offspring. These mutations are likely to be the single largest contributor to human genetic diversity. New sequencing approaches may leverage this framework to evaluate and reduce disease risk for future generations.
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Affiliation(s)
- Martin W Breuss
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiaoxu Yang
- Rady Children's Institute for Genomic Medicine, Department of Neurosciences, University of California, San Diego, CA, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Department of Neurosciences, University of California, San Diego, CA, USA.
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36
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Neupane S, Xu S. Adaptive Divergence of Meiotic Recombination Rate in Ecological Speciation. Genome Biol Evol 2021; 12:1869-1881. [PMID: 32857858 PMCID: PMC7594247 DOI: 10.1093/gbe/evaa182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Theories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here, we examine the population-level recombination rate variation in two incipient ecological species, the microcrustacean Daphnia pulex (an ephemeral-pond species) and Daphnia pulicaria (a permanent-lake species). The divergence of D. pulicaria from D. pulex involved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate in D. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution.
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Affiliation(s)
| | - Sen Xu
- Department of Biology, University of Texas at Arlington
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37
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Davies B, Hinch AG, Cebrian-Serrano A, Alghadban S, Becker PW, Biggs D, Hernandez-Pliego P, Preece C, Moralli D, Zhang G, Myers S, Donnelly P. Altering the binding properties of PRDM9 partially restores fertility across the species boundary. Mol Biol Evol 2021; 38:5555-5562. [PMID: 34491357 PMCID: PMC8662609 DOI: 10.1093/molbev/msab269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sterility or subfertility of male hybrid offspring is commonly observed. This phenomenon contributes to reproductive barriers between the parental populations, an early step in the process of speciation. One frequent cause of such infertility is a failure of proper chromosome pairing during male meiosis. In subspecies of the house mouse, the likelihood of successful chromosome synapsis is improved by the binding of the histone methyltransferase PRDM9 to both chromosome homologues at matching positions. Using genetic manipulation, we altered PRDM9 binding to occur more often at matched sites, and find that chromosome pairing defects can be rescued, not only in an inter-subspecific cross, but also between distinct species. Using different engineered variants, we demonstrate a quantitative link between the degree of matched homologue binding, chromosome synapsis and rescue of fertility in hybrids between Mus musculus and Mus spretus. The resulting partial restoration of fertility reveals additional mechanisms at play that act to lock-in the reproductive isolation between these two species.
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Affiliation(s)
- Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | | | | | - Samy Alghadban
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Philipp W Becker
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | | | - Chris Preece
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Gang Zhang
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Simon Myers
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK.,Dept. of Statistics, University of Oxford, OX1 3LB, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, UK.,Dept. of Statistics, University of Oxford, OX1 3LB, UK
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Abstract
Over the past decade, genomic analyses of single cells-the fundamental units of life-have become possible. Single-cell DNA sequencing has shed light on biological questions that were previously inaccessible across diverse fields of research, including somatic mutagenesis, organismal development, genome function, and microbiology. Single-cell DNA sequencing also promises significant future biomedical and clinical impact, spanning oncology, fertility, and beyond. While single-cell approaches that profile RNA and protein have greatly expanded our understanding of cellular diversity, many fundamental questions in biology and important biomedical applications require analysis of the DNA of single cells. Here, we review the applications and biological questions for which single-cell DNA sequencing is uniquely suited or required. We include a discussion of the fields that will be impacted by single-cell DNA sequencing as the technology continues to advance.
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Affiliation(s)
- Gilad D Evrony
- Center for Human Genetics and Genomics, Grossman School of Medicine, New York University, New York, NY 10016, USA;
| | - Anjali Gupta Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, California 90095, USA;
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39
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Natural variation identifies SNI1, the SMC5/6 component, as a modifier of meiotic crossover in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021970118. [PMID: 34385313 PMCID: PMC8379953 DOI: 10.1073/pnas.2021970118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination plays a fundamental role in shaping genetic diversity in eukaryotes. Extensive variation in crossover rate exists between populations and species. The identity of modifier loci and their roles in genome evolution remain incompletely understood. We explored natural variation in Arabidopsis crossover and identified SNI1 as the causal gene underlying a major modifier locus. To date, SNI1 had no known role in crossover. SNI1 is a component of the SMC5/6 complex that is closely related to cohesin and condensin. Arabidopsis sni1 and other SMC5/6 mutants show similar effects on the interference-independent crossover pathway. Hence, our findings demonstrate that the SMC5/6 complex, which is known for its role in DNA damage repair, is also important for control of meiotic crossover. The frequency and distribution of meiotic crossovers are tightly controlled; however, variation in this process can be observed both within and between species. Using crosses of two natural Arabidopsis thaliana accessions, Col and Ler, we mapped a crossover modifier locus to semidominant polymorphisms in SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), which encodes a component of the SMC5/6 complex. The sni1 mutant exhibits a modified pattern of recombination across the genome with crossovers elevated in chromosome distal regions but reduced in pericentromeres. Mutations in SNI1 result in reduced crossover interference and can partially restore the fertility of a Class I crossover pathway mutant, which suggests that the protein affects noninterfering crossover repair. Therefore, we tested genetic interactions between SNI1 and both RECQ4 and FANCM DNA helicases, which showed that additional Class II crossovers observed in the sni1 mutant are FANCM independent. Furthermore, genetic analysis of other SMC5/6 mutants confirms the observations of crossover redistribution made for SNI1. The study reveals the importance of the SMC5/6 complex in ensuring the proper progress of meiotic recombination in plants.
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40
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Gergelits V, Parvanov E, Simecek P, Forejt J. Chromosome-wide characterization of meiotic noncrossovers (gene conversions) in mouse hybrids. Genetics 2021; 217:1-14. [PMID: 33683354 DOI: 10.1093/genetics/iyaa013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/13/2020] [Indexed: 01/16/2023] Open
Abstract
During meiosis, the recombination-initiating DNA double-strand breaks (DSBs) are repaired by crossovers or noncrossovers (gene conversions). While crossovers are easily detectable, noncrossover identification is hampered by the small size of their converted tracts and the necessity of sequence polymorphism. We report identification and characterization of a mouse chromosome-wide set of noncrossovers by next-generation sequencing of 10 mouse intersubspecific chromosome substitution strains. Based on 94 identified noncrossovers, we determined the mean length of a conversion tract to be 32 bp. The spatial chromosome-wide distribution of noncrossovers and crossovers significantly differed, although both sets overlapped the known hotspots of PRDM9-directed histone methylation and DNA DSBs, thus supporting their origin in the standard DSB repair pathway. A significant deficit of noncrossovers descending from asymmetric DSBs proved their proposed adverse effect on meiotic recombination and pointed to sister chromatids as an alternative template for their repair. The finding has implications for the molecular mechanism of hybrid sterility in mice from crosses between closely related Mus musculus musculus and Mus musculus domesticus subspecies.
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Affiliation(s)
- Vaclav Gergelits
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, CZ-25250 Vestec, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, CZ-12000 Prague, Czech Republic
| | - Emil Parvanov
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, CZ-25250 Vestec, Czech Republic
| | - Petr Simecek
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, CZ-25250 Vestec, Czech Republic
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, CZ-25250 Vestec, Czech Republic
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41
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Molinaro C, Martoriati A, Cailliau K. Proteins from the DNA Damage Response: Regulation, Dysfunction, and Anticancer Strategies. Cancers (Basel) 2021; 13:3819. [PMID: 34359720 PMCID: PMC8345162 DOI: 10.3390/cancers13153819] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Cells respond to genotoxic stress through a series of complex protein pathways called DNA damage response (DDR). These monitoring mechanisms ensure the maintenance and the transfer of a correct genome to daughter cells through a selection of DNA repair, cell cycle regulation, and programmed cell death processes. Canonical or non-canonical DDRs are highly organized and controlled to play crucial roles in genome stability and diversity. When altered or mutated, the proteins in these complex networks lead to many diseases that share common features, and to tumor formation. In recent years, technological advances have made it possible to benefit from the principles and mechanisms of DDR to target and eliminate cancer cells. These new types of treatments are adapted to the different types of tumor sensitivity and could benefit from a combination of therapies to ensure maximal efficiency.
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Affiliation(s)
| | | | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; (C.M.); (A.M.)
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42
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Jin X, Fudenberg G, Pollard KS. Genome-wide variability in recombination activity is associated with meiotic chromatin organization. Genome Res 2021; 31:1561-1572. [PMID: 34301629 PMCID: PMC8415379 DOI: 10.1101/gr.275358.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/22/2021] [Indexed: 11/24/2022]
Abstract
Recombination enables reciprocal exchange of genomic information between parental chromosomes and successful segregation of homologous chromosomes during meiosis. Errors in this process lead to negative health outcomes, whereas variability in recombination rate affects genome evolution. In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, although PRDM9 binding peaks are not all equally hot. We hypothesize that dynamic patterns of meiotic genome folding are linked to recombination activity. We apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strand-break (DSB) and crossover (CO) formation at PRDM9 binding peaks. We show that active, spatially accessible genomic regions during meiotic prophase are associated with DSB-favored loci, which further adopt a transient locally active configuration in early prophase. Conversely, crossover formation is depleted among DSBs in spatially accessible regions during meiotic prophase, particularly within gene bodies. We also find evidence that active chromatin regions have smaller average loop sizes in mammalian meiosis. Collectively, these findings establish that differences in chromatin architecture along chromosomal axes are associated with variable recombination activity. We propose an updated framework describing how 3D organization of brush-loop chromosomes during meiosis may modulate recombination.
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Affiliation(s)
- Xiaofan Jin
- Gladstone Institutes, San Francisco, California 94158, USA
| | - Geoff Fudenberg
- Gladstone Institutes, San Francisco, California 94158, USA.,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, California 94158, USA.,University of California San Francisco, San Francisco, California 94143, USA.,Chan-Zuckerberg Biohub, San Francisco, California 94158, USA
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43
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Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 2021; 184:4251-4267.e20. [PMID: 34260899 DOI: 10.1016/j.cell.2021.06.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/02/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Genetic recombination generates novel trait combinations, and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots; however, megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns; therefore, we devised an approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis, and a distinctive replication pattern in human males underlies the subtelomeric increase in recombination. We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.
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44
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Forejt J, Jansa P, Parvanov E. Hybrid sterility genes in mice (Mus musculus): a peculiar case of PRDM9 incompatibility. Trends Genet 2021; 37:1095-1108. [PMID: 34238593 DOI: 10.1016/j.tig.2021.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/14/2022]
Abstract
Hybrid sterility is a critical step in the evolution of reproductive barriers between diverging taxa during the process of speciation. Recent studies of young subspecies of the house mouse revealed a multigenic nature and frequent polymorphism of hybrid sterility genes as well as the recurrent engagement of the meiosis-specific gene PR domain-containing 9 (Prdm9) and X-linked loci. Prdm9-controlled hybrid sterility is essentially chromosomal in nature, conditioned by the sequence divergence between subspecies. Depending on the Prdm9 interallelic interactions and the X-linked Hstx2 locus, the same homologs either regularly recombine and synapse, or show impaired DNA DSB repair, asynapsis, and early meiotic arrest. Thus, Prdm9-dependent hybrid sterility points to incompatibilities affecting meiotic recombination as a possible mechanism of reproductive isolation between (sub)species.
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Affiliation(s)
- Jiri Forejt
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic.
| | - Petr Jansa
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Emil Parvanov
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
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45
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Mhaskar AN, Koornneef L, Zelensky AN, Houtsmuller AB, Baarends WM. High Resolution View on the Regulation of Recombinase Accumulation in Mammalian Meiosis. Front Cell Dev Biol 2021; 9:672191. [PMID: 34109178 PMCID: PMC8181746 DOI: 10.3389/fcell.2021.672191] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 11/19/2022] Open
Abstract
A distinguishing feature of meiotic DNA double-strand breaks (DSBs), compared to DSBs in somatic cells, is the fact that they are induced in a programmed and specifically orchestrated manner, which includes chromatin remodeling prior to DSB induction. In addition, the meiotic homologous recombination (HR) repair process that follows, is different from HR repair of accidental DSBs in somatic cells. For instance, meiotic HR involves preferred use of the homolog instead of the sister chromatid as a repair template and subsequent formation of crossovers and non-crossovers in a tightly regulated manner. An important outcome of this distinct repair pathway is the pairing of homologous chromosomes. Central to the initial steps in homology recognition during meiotic HR is the cooperation between the strand exchange proteins (recombinases) RAD51 and its meiosis-specific paralog DMC1. Despite our understanding of their enzymatic activity, details on the regulation of their assembly and subsequent molecular organization at meiotic DSBs in mammals have remained largely enigmatic. In this review, we summarize recent mouse data on recombinase regulation via meiosis-specific factors. Also, we reflect on bulk “omics” studies of initial meiotic DSB processing, compare these with studies using super-resolution microscopy in single cells, at single DSB sites, and explore the implications of these findings for our understanding of the molecular mechanisms underlying meiotic HR regulation.
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Affiliation(s)
- Aditya N Mhaskar
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
| | - Lieke Koornneef
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Alex N Zelensky
- Department of Molecular Genetics, Erasmus MC, Rotterdam, Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, Rotterdam, Netherlands.,Department of Pathology, Erasmus MC, Rotterdam, Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
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46
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Li R, Qu H, Chen J, Wang S, Chater JM, Zhang L, Wei J, Zhang YM, Xu C, Zhong WD, Zhu J, Lu J, Feng Y, Chen W, Ma R, Ferrante SP, Roose ML, Jia Z. Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes. Mol Biol Evol 2021; 37:3684-3698. [PMID: 32668004 PMCID: PMC7743722 DOI: 10.1093/molbev/msaa176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.
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Affiliation(s)
- Ruidong Li
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Han Qu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Jinfeng Chen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Shibo Wang
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - John M Chater
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Le Zhang
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Julong Wei
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI
| | - Yuan-Ming Zhang
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chenwu Xu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jianguo Zhu
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Jianming Lu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuanfa Feng
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Weiming Chen
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Renyuan Ma
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Department of Mathematics, Bowdoin College, Brunswick, ME
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA
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47
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Lyu R, Tsui V, McCarthy DJ, Crismani W. Personalized genome structure via single gamete sequencing. Genome Biol 2021; 22:112. [PMID: 33874978 PMCID: PMC8054432 DOI: 10.1186/s13059-021-02327-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromosome-scale assembly of an individual's genome, which historically has been performed with populations and pedigrees. Here, we discuss how single-cell gamete sequencing offers the potential to merge the advantages of short-read sequencing with the ability to build personalized genetic maps and open up an entirely new space in personalized genetics.
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Affiliation(s)
- Ruqian Lyu
- Bioinformatics and Cellular Genomics, St. Vincent's Institute of Medical Research, Melbourne, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Melbourne, Australia
| | - Vanessa Tsui
- DNA Repair and Recombination Laboratory, St. Vincent's Institute of Medical Research, Melbourne, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, Australia
| | - Davis J McCarthy
- Bioinformatics and Cellular Genomics, St. Vincent's Institute of Medical Research, Melbourne, Australia.
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Melbourne, Australia.
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St. Vincent's Institute of Medical Research, Melbourne, Australia.
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Melbourne, Australia.
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48
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Mukaj A, Piálek J, Fotopulosova V, Morgan AP, Odenthal-Hesse L, Parvanov ED, Forejt J. Prdm9 Intersubspecific Interactions in Hybrid Male Sterility of House Mouse. Mol Biol Evol 2020; 37:3423-3438. [PMID: 32642764 PMCID: PMC7743643 DOI: 10.1093/molbev/msaa167] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
The classical definition posits hybrid sterility as a phenomenon when two parental taxa each of which is fertile produce a hybrid that is sterile. The first hybrid sterility gene in vertebrates, Prdm9, coding for a histone methyltransferase, was identified in crosses between two laboratory mouse strains derived from Mus mus musculus and M. m. domesticus subspecies. The unique function of PRDM9 protein in the initiation of meiotic recombination led to the discovery of the basic molecular mechanism of hybrid sterility in laboratory crosses. However, the role of this protein as a component of reproductive barrier outside the laboratory model remained unclear. Here, we show that the Prdm9 allelic incompatibilities represent the primary cause of reduced fertility in intersubspecific hybrids between M. m. musculus and M. m. domesticus including 16 musculus and domesticus wild-derived strains. Disruption of fertility phenotypes correlated with the rate of failure of synapsis between homologous chromosomes in meiosis I and with early meiotic arrest. All phenotypes were restored to normal when the domesticus Prdm9dom2 allele was substituted with the Prdm9dom2H humanized variant. To conclude, our data show for the first time the male infertility of wild-derived musculus and domesticus subspecies F1 hybrids controlled by Prdm9 as the major hybrid sterility gene. The impairment of fertility surrogates, testes weight and sperm count, correlated with increasing difficulties of meiotic synapsis of homologous chromosomes and with meiotic arrest, which we suppose reflect the increasing asymmetry of PRDM9-dependent DNA double-strand breaks.
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Affiliation(s)
- Amisa Mukaj
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vladana Fotopulosova
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | | | - Linda Odenthal-Hesse
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Emil D Parvanov
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jiri Forejt
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
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49
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Wei KHC, Mantha A, Bachtrog D. The Theory and Applications of Measuring Broad-Range and Chromosome-Wide Recombination Rate from Allele Frequency Decay around a Selected Locus. Mol Biol Evol 2020; 37:3654-3671. [PMID: 32658965 PMCID: PMC7743735 DOI: 10.1093/molbev/msaa171] [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] [Indexed: 12/22/2022] Open
Abstract
Recombination is the exchange of genetic material between homologous chromosomes via physical crossovers. High-throughput sequencing approaches detect crossovers genome wide to produce recombination rate maps but are difficult to scale as they require large numbers of recombinants individually sequenced. We present a simple and scalable pooled-sequencing approach to experimentally infer near chromosome-wide recombination rates by taking advantage of non-Mendelian allele frequency generated from a fitness differential at a locus under selection. As more crossovers decouple the selected locus from distal loci, the distorted allele frequency attenuates distally toward Mendelian and can be used to estimate the genetic distance. Here, we use marker selection to generate distorted allele frequency and theoretically derive the mathematical relationships between allele frequency attenuation, genetic distance, and recombination rate in marker-selected pools. We implemented nonlinear curve-fitting methods that robustly estimate the allele frequency decay from batch sequencing of pooled individuals and derive chromosome-wide genetic distance and recombination rates. Empirically, we show that marker-selected pools closely recapitulate genetic distances inferred from scoring recombinants. Using this method, we generated novel recombination rate maps of three wild-derived strains of Drosophila melanogaster, which strongly correlate with previous measurements. Moreover, we show that this approach can be extended to estimate chromosome-wide crossover interference with reciprocal marker selection and discuss how it can be applied in the absence of visible markers. Altogether, we find that our method is a simple and cost-effective approach to generate chromosome-wide recombination rate maps requiring only one or two libraries.
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Affiliation(s)
- Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Aditya Mantha
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
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50
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Imai Y, Biot M, Clément JA, Teragaki M, Urbach S, Robert T, Baudat F, Grey C, de Massy B. PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment. eLife 2020; 9:57117. [PMID: 33047671 PMCID: PMC7599071 DOI: 10.7554/elife.57117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) at specific genomic locations that correspond to PRDM9-binding sites. The molecular steps occurring from PRDM9 binding to DSB formation are unknown. Using proteomic approaches to find PRDM9 partners, we identified HELLS, a member of the SNF2-like family of chromatin remodelers. Upon functional analyses during mouse male meiosis, we demonstrated that HELLS is required for PRDM9 binding and DSB activity at PRDM9 sites. However, HELLS is not required for DSB activity at PRDM9-independent sites. HELLS is also essential for 5-hydroxymethylcytosine (5hmC) enrichment at PRDM9 sites. Analyses of 5hmC in mice deficient for SPO11, which catalyzes DSB formation, and in PRDM9 methyltransferase deficient mice reveal that 5hmC is triggered at DSB-prone sites upon PRDM9 binding and histone modification, but independent of DSB activity. These findings highlight the complex regulation of the chromatin and epigenetic environments at PRDM9-specified hotspots.
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Affiliation(s)
- Yukiko Imai
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Mathilde Biot
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Julie Aj Clément
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Mariko Teragaki
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Thomas Robert
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Frédéric Baudat
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Corinne Grey
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
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