1
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Errbii M, Gadau J, Becker K, Schrader L, Oettler J. Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior. Genome Res 2024; 34:863-876. [PMID: 38839375 PMCID: PMC11293551 DOI: 10.1101/gr.278392.123] [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: 08/15/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Eusocial Hymenoptera have the highest recombination rates among all multicellular animals studied so far, but it is unclear why this is and how this affects the biology of individual species. A high-resolution linkage map for the ant Cardiocondyla obscurior corroborates genome-wide high recombination rates reported for ants (8.1 cM/Mb). However, recombination is locally suppressed in regions that are enriched with TEs, that have strong haplotype divergence, or that show signatures of epistatic selection in C. obscurior The results do not support the hypotheses that high recombination rates are linked to phenotypic plasticity or to modulating selection efficiency. Instead, genetic diversity and the frequency of structural variants correlate positively with local recombination rates, potentially compensating for the low levels of genetic variation expected in haplodiploid social Hymenoptera with low effective population size. Ultimately, the data show that recombination contributes to within-population polymorphism and to the divergence of the lineages within C. obscurior.
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Affiliation(s)
- Mohammed Errbii
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Kerstin Becker
- Cologne Center for Genomics (CCG), Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
| | - Jan Oettler
- Lehrstuhl für Zoologie/Evolutionsbiologie, University Regensburg, 93053 Regensburg, Germany
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2
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Ariad D, Madjunkova S, Madjunkov M, Chen S, Abramov R, Librach C, McCoy RC. Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. Genome Res 2024; 34:70-84. [PMID: 38071472 PMCID: PMC10903951 DOI: 10.1101/gr.278168.123] [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: 06/12/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
Meiotic recombination is crucial for human genetic diversity and chromosome segregation accuracy. Understanding its variation across individuals and the processes by which it goes awry are long-standing goals in human genetics. Current approaches for inferring recombination landscapes rely either on population genetic patterns of linkage disequilibrium (LD)-capturing a time-averaged view-or on direct detection of crossovers in gametes or multigeneration pedigrees, which limits data set scale and availability. Here, we introduce an approach for inferring sex-specific recombination landscapes using data from preimplantation genetic testing for aneuploidy (PGT-A). This method relies on low-coverage (<0.05×) whole-genome sequencing of in vitro fertilized (IVF) embryo biopsies. To overcome the data sparsity, our method exploits its inherent relatedness structure, knowledge of haplotypes from external population reference panels, and the frequent occurrence of monosomies in embryos, whereby the remaining chromosome is phased by default. Extensive simulations show our method's high accuracy, even at coverages as low as 0.02×. Applying this method to PGT-A data from 18,967 embryos, we mapped 70,660 recombination events with ∼150 kbp resolution, replicating established sex-specific recombination patterns. We observed a reduced total length of the female genetic map in trisomies compared with disomies, as well as chromosome-specific alterations in crossover distributions. Based on haplotype configurations in pericentromeric regions, our data indicate chromosome-specific propensities for different mechanisms of meiotic error. Our results provide a comprehensive view of the role of aberrant meiotic recombination in the origins of human aneuploidies and offer a versatile tool for mapping crossovers in low-coverage sequencing data from multiple siblings.
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Affiliation(s)
- Daniel Ariad
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Svetlana Madjunkova
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Siwei Chen
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
| | - Rina Abramov
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
| | - Clifford Librach
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario M5G 1E2, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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3
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Liang M, Suresh B, Bareke E, Choufani S, Jagadeesh S, Weksberg R, Majewski J, Slim R. A homozygous stop codon in HORMAD2 in a patient with recurrent digynic triploid miscarriage. Mol Genet Genomic Med 2024; 12:e2402. [PMID: 38400599 PMCID: PMC10891434 DOI: 10.1002/mgg3.2402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Recurrent miscarriage (RM) affects 1% to 5% of couples trying to conceive. Despite extensive clinical and laboratory testing, half of the RM cases remain unexplained. We report the genetic analysis of a couple with eight miscarriages and the search for their potential genetic etiology. METHODS Short tandem repeat (STR) markers, single nucleotide polymorphic (SNP) microarray, and human DNA methylation microarray were used to analyze the genotypes of two miscarriages. Exomes sequencing was performed on DNA from the two partners and identified variants were validated by Sanger sequencing. RESULTS STR marker genotyping demonstrated that the two available miscarriages are triploid digynic and resulted from the failure of Meiosis II. SNP microarray analysis revealed an additional Meiosis I abnormality that is the segregation of the two maternal homologous chromosomes in one triploid miscarriage. Whole-exome sequencing on DNA from the two partners identified candidate variants only in the female partner in two genes with roles in female reproduction, a missense in EIF4ENIF1 (OMIM 607445) and a stop gain in HORMAD2 (OMIM 618842). EIF4ENIF1 is a eukaryotic translation initiation factor 4E nuclear import factor required for the oocyte germinal vesicle breakdown, and HORMAD2 is part of the synaptonemal complex that was hypothesized to act as a checkpoint mechanism to eliminate oocytes with asynapsis during meiotic prophase I in mice. CONCLUSION While both genes may contribute to the phenotype, the Meiosis I abnormalities in the conceptions favor the causal role of HORMAD2 in the etiology of RM in this couple. This report illustrates the importance of comprehensively analyzing the products of conception to guide the search for the genetic causation of RM.
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Affiliation(s)
- Manqi Liang
- Department of Human GeneticsResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Beena Suresh
- Department of Clinical Genetics & Genetic CounsellingMediscan SystemsChennaiIndia
| | - Eric Bareke
- Department of Human GeneticsMcGill UniversityMontrealQuebecCanada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research InstituteThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Sujatha Jagadeesh
- Department of Clinical Genetics & Genetic CounsellingMediscan SystemsChennaiIndia
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research InstituteThe Hospital for Sick ChildrenTorontoOntarioCanada
- Division of Clinical & Metabolic Genetics, Department of PaediatricsThe Hospital for Sick ChildrenTorontoOntarioCanada
- Institute of Medical SciencesUniversity of TorontoTorontoOntarioCanada
| | - Jacek Majewski
- Department of Human GeneticsMcGill UniversityMontrealQuebecCanada
| | - Rima Slim
- Department of Human GeneticsResearch Institute of the McGill University Health CentreMontrealQuebecCanada
- Department of Obstetrics and GynecologyMcGill University Health CentreMontrealQuebecCanada
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4
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Ariad D, Madjunkova S, Madjunkov M, Chen S, Abramov R, Librach C, McCoy RC. Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.543910. [PMID: 37333422 PMCID: PMC10274764 DOI: 10.1101/2023.06.07.543910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Meiotic recombination is crucial for human genetic diversity and chromosome segregation accuracy. Understanding its variation across individuals and the processes by which it goes awry are long-standing goals in human genetics. Current approaches for inferring recombination landscapes either rely on population genetic patterns of linkage disequilibrium (LD)-capturing a time-averaged view-or direct detection of crossovers in gametes or multi-generation pedigrees, which limits dataset scale and availability. Here, we introduce an approach for inferring sex-specific recombination landscapes using data from preimplantation genetic testing for aneuploidy (PGT-A). This method relies on low-coverage (<0.05×) whole-genome sequencing of in vitro fertilized (IVF) embryo biopsies. To overcome the data sparsity, our method exploits its inherent relatedness structure, knowledge of haplotypes from external population reference panels, as well as the frequent occurrence of monosomies in embryos, whereby the remaining chromosome is phased by default. Extensive simulations demonstrate our method's high accuracy, even at coverages as low as 0.02×. Applying this method to PGT-A data from 18,967 embryos, we mapped 70,660 recombination events with ~150 kbp resolution, replicating established sex-specific recombination patterns. We observed a reduced total length of the female genetic map in trisomies compared to disomies, as well as chromosome-specific alterations in crossover distributions. Based on haplotype configurations in pericentromeric regions, our data indicate chromosome-specific propensities for different mechanisms of meiotic error. Our results provide a comprehensive view of the role of aberrant meiotic recombination in the origins of human aneuploidies and offer a versatile tool for mapping crossovers in low-coverage sequencing data from multiple siblings.
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Affiliation(s)
- Daniel Ariad
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Svetlana Madjunkova
- CReATe Fertility Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | - Siwei Chen
- CReATe Fertility Centre, Toronto, Canada
| | | | - Clifford Librach
- CReATe Fertility Centre, Toronto, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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5
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Bruggeman JW, Koster J, van Pelt AMM, Speijer D, Hamer G. How germline genes promote malignancy in cancer cells. Bioessays 2023; 45:e2200112. [PMID: 36300921 DOI: 10.1002/bies.202200112] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 02/01/2023]
Abstract
Cancers often express hundreds of genes otherwise specific to germ cells, the germline/cancer (GC) genes. Here, we present and discuss the hypothesis that activation of a "germline program" promotes cancer cell malignancy. We do so by proposing four hallmark processes of the germline: meiosis, epigenetic plasticity, migration, and metabolic plasticity. Together, these hallmarks enable replicative immortality of germ cells as well as cancer cells. Especially meiotic genes are frequently expressed in cancer, implying that genes unique to meiosis may play a role in oncogenesis. Because GC genes are not expressed in healthy somatic tissues, they form an appealing source of specific treatment targets with limited side effects besides infertility. Although it is still unclear why germ cell specific genes are so abundantly expressed in cancer, from our hypothesis it follows that the germline's reproductive program is intrinsic to cancer development.
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Affiliation(s)
- Jan Willem Bruggeman
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
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6
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Marín-Gual L, González-Rodelas L, M. Garcias M, Kratochvíl L, Valenzuela N, Georges A, Waters PD, Ruiz-Herrera A. Meiotic chromosome dynamics and double strand break formation in reptiles. Front Cell Dev Biol 2022; 10:1009776. [PMID: 36313577 PMCID: PMC9597255 DOI: 10.3389/fcell.2022.1009776] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
During meiotic prophase I, tightly regulated processes take place, from pairing and synapsis of homologous chromosomes to recombination, which are essential for the generation of genetically variable haploid gametes. These processes have canonical meiotic features conserved across different phylogenetic groups. However, the dynamics of meiotic prophase I in non-mammalian vertebrates are poorly known. Here, we compare four species from Sauropsida to understand the regulation of meiotic prophase I in reptiles: the Australian central bearded dragon (Pogona vitticeps), two geckos (Paroedura picta and Coleonyx variegatus) and the painted turtle (Chrysemys picta). We first performed a histological characterization of the spermatogenesis process in both the bearded dragon and the painted turtle. We then analyzed prophase I dynamics, including chromosome pairing, synapsis and the formation of double strand breaks (DSBs). We show that meiosis progression is highly conserved in reptiles with telomeres clustering forming the bouquet, which we propose promotes homologous pairing and synapsis, along with facilitating the early pairing of micro-chromosomes during prophase I (i.e., early zygotene). Moreover, we detected low levels of meiotic DSB formation in all taxa. Our results provide new insights into reptile meiosis.
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Affiliation(s)
- Laia Marín-Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Laura González-Rodelas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Maria M. Garcias
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, NSW, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- *Correspondence: Aurora Ruiz-Herrera,
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7
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Fan C, Yang X, Nie H, Wang S, Zhang L. Per-nucleus crossover covariation is regulated by chromosome organization. iScience 2022; 25:104115. [PMID: 35391833 PMCID: PMC8980760 DOI: 10.1016/j.isci.2022.104115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/15/2022] [Accepted: 03/15/2022] [Indexed: 12/22/2022] Open
Abstract
Meiotic crossover (CO) recombination between homologous chromosomes regulates chromosome segregation and promotes genetic diversity. Human females have different CO patterns than males, and some of these features contribute to the high frequency of chromosome segregation errors. In this study, we show that CO covariation is transmitted to progenies without detectable selection in both human males and females. Further investigations show that chromosome pairs with longer axes tend to have stronger axis length covariation and a stronger correlation between axis length and CO number, and the consequence of these two effects would be the stronger CO covariation as observed in females. These findings reveal a previously unsuspected feature for chromosome organization: long chromosome axes are more coordinately regulated than short ones. Additionally, the stronger CO covariation may work with human female-specific CO maturation inefficiency to confer female germlines the ability to adapt to changing environments on evolution.
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Affiliation(s)
- Cunxian Fan
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014 China
| | - Xiao Yang
- Center for Reproductive Medicine, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Hui Nie
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014 China
| | - Shunxin Wang
- Center for Reproductive Medicine, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 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
| | - Liangran Zhang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014 China.,Center for Reproductive Medicine, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
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8
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Catalano R, Bruckner T, Casey JA, Gemmill A, Margerison C, Hartig T. Twinning during the pandemic: Evidence of selection in utero. Evol Med Public Health 2021; 9:374-382. [PMID: 34858596 PMCID: PMC8634460 DOI: 10.1093/emph/eoab033] [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] [Received: 07/28/2021] [Accepted: 10/10/2021] [Indexed: 11/13/2022] Open
Abstract
Background and objectives The suspicion that a population stressor as profound as the COVID-19 pandemic would increase preterm birth among cohorts in gestation at its outset has not been supported by data collected in 2020. An evolutionary perspective on this circumstance suggests that natural selection in utero, induced by the onset of the pandemic, caused pregnancies that would otherwise have produced a preterm birth to end early in gestation as spontaneous abortions. We test this possibility using the odds of a live-born twin among male births in Norway as an indicator of the depth of selection in birth cohorts. Methodology We apply Box–Jenkins methods to 50 pre-pandemic months to estimate counterfactuals for the nine birth cohorts in gestation in March 2020 when the first deaths attributable to SARS-CoV-2 infection occurred in Norway. We use Alwan and Roberts outlier detection methods to discover any sequence of outlying values in the odds of a live-born twin among male births in exposed birth cohorts. Results We find a downward level shift of 27% in the monthly odds of a twin among male births beginning in May and persisting through the remainder of 2020. Conclusions and implications Consistent with evolutionary theory and selection in utero, birth cohorts exposed in utero to the onset of the COVID-19 pandemic yielded fewer male twins than expected. Lay Summary Our finding of fewer than expected male twin births during the onset of the COVID-19 pandemic provides more evidence that evolution continues to affect the characteristics and health of contemporary populations.
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Affiliation(s)
- Ralph Catalano
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Tim Bruckner
- Program in Public Health and Center for Population, Inequality and Policy, University of California, Irvine, Irvine, CA, USA
| | - Joan A Casey
- Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Alison Gemmill
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Claire Margerison
- Department of Epidemiology & Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Terry Hartig
- Institute for Housing and Urban Research, Uppsala University, Uppsala, Sweden
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9
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The impact of chromosomal fusions on 3D genome folding and recombination in the germ line. Nat Commun 2021; 12:2981. [PMID: 34016985 PMCID: PMC8137915 DOI: 10.1038/s41467-021-23270-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/16/2021] [Indexed: 02/08/2023] Open
Abstract
The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome conformation capture in combination with single-nucleotide polymorphism (SNP) genotyping and analysis of crossover events to study how the higher-order chromatin organization and recombination landscapes are affected by chromosomal fusions in the mammalian germ line. We demonstrate that chromosomal fusions alter the nuclear architecture during meiosis, including an increased rate of heterologous interactions in primary spermatocytes, and alterations in both chromosome synapsis and axis length. These disturbances in topology were associated with changes in genomic landscapes of recombination, resulting in detectable genomic footprints. Overall, we show that chromosomal fusions impact the dynamic genome topology of germ cells in two ways: (i) altering chromosomal nuclear occupancy and synapsis, and (ii) reshaping landscapes of recombination.
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10
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Lozada-Soto EA, Maltecca C, Wackel H, Flowers W, Gray K, He Y, Huang Y, Jiang J, Tiezzi F. Evidence for recombination variability in purebred swine populations. J Anim Breed Genet 2020; 138:259-273. [PMID: 32975329 DOI: 10.1111/jbg.12510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/27/2020] [Accepted: 09/05/2020] [Indexed: 01/04/2023]
Abstract
This study aimed to investigate interpopulation variation due to sex, breed and age, and the intrapopulation variation in the form of genetic variance for recombination in swine. Genome-wide recombination rate and recombination occurrences (RO) were traits studied in Landrace (LR) and Large White (LW) male and female populations. Differences were found for sex, breed, sex-breed interaction, and age effects for genome-wide recombination rate and RO at one or more chromosomes. Dams were found to have a higher genome-wide recombination rate and RO at all chromosomes than sires. LW animals had higher genome-wide recombination rate and RO at seven chromosomes but lower at two chromosomes than LR individuals. The sex-breed interaction effect did not show any pattern not already observable by sex. Recombination increased with increasing parity in females, while in males no effect of age was observed. We estimated heritabilities and repeatabilities for both investigated traits and obtained the genetic correlation between male and female genome-wide recombination rate within each of the two breeds studied. Estimates of heritability and repeatability were low (h2 = 0.01-0.26; r = 0.18-0.42) for both traits in all populations. Genetic correlations were high and positive, with estimates of 0.98 and 0.94 for the LR and LW breeds, respectively. We performed a GWAS for genome-wide recombination rate independently in the four sex/breed populations. The results of the GWAS were inconsistent across the four populations with different significant genomic regions identified. The results of this study provide evidence of variability for recombination in purebred swine populations.
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Affiliation(s)
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Hanna Wackel
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - William Flowers
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Kent Gray
- Smithfield Premium Genetics, Rose Hill, NC, USA
| | - Yuqing He
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | | | - Jicai Jiang
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
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11
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Xu P, Kennell T, Gao M, Kimberly RP, Chong Z. MRLR: unraveling high-resolution meiotic recombination by linked reads. Bioinformatics 2020; 36:10-16. [PMID: 31214684 PMCID: PMC6956785 DOI: 10.1093/bioinformatics/btz503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/30/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Meiotic recombination facilitates the transmission of exchanged genetic material between homologous chromosomes and plays a crucial role in increasing the genetic variations in eukaryotic organisms. In humans, thousands of crossover events have been identified by genotyping related family members. However, most of these crossover regions span tens to hundreds of kb, which is not sufficient resolution to accurately identify the crossover breakpoints in a typical trio family. RESULTS We have developed MRLR, a software using 10X linked reads to identify crossover events at a high resolution. By reconstructing the gamete genome, MRLR only requires a trio family dataset and can efficiently discover the crossover events. Using MRLR, we revealed a fine-scale pattern of crossover regions in six human families. From the two closest heterozygous alleles around the crossovers, we determined that MRLR achieved a median resolution 4.5 kb. This method can delineate a genome-wide landscape of crossover events at a precise scale, which is important for both functional and genomic features analysis of meiotic recombination. AVAILABILITY AND IMPLEMENTATION MRLR is freely available at https://github.com/ChongLab/MRLR, implemented in Perl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peng Xu
- Department of Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Timothy Kennell
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Min Gao
- Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Robert P Kimberly
- Department of Medicine, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zechen Chong
- Department of Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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12
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CENP-A binding domains and recombination patterns in horse spermatocytes. Sci Rep 2019; 9:15800. [PMID: 31676881 PMCID: PMC6825197 DOI: 10.1038/s41598-019-52153-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Centromeres exert an inhibitory effect on meiotic recombination, but the possible contribution of satellite DNA to this "centromere effect" is under debate. In the horse, satellite DNA is present at all centromeres with the exception of the one from chromosome 11. This organization of centromeres allowed us to investigate the role of satellite DNA on recombination suppression in horse spermatocytes at the stage of pachytene. To this aim we analysed the distribution of the MLH1 protein, marker of recombination foci, relative to CENP-A, marker of centromeric function. We demonstrated that the satellite-less centromere of chromosome 11 causes crossover suppression, similarly to satellite-based centromeres. These results suggest that the centromere effect does not depend on satellite DNA. During this analysis, we observed a peculiar phenomenon: while, as expected, the centromere of the majority of meiotic bivalent chromosomes was labelled with a single immunofluorescence centromeric signal, double-spotted or extended signals were also detected. Their number varied from 0 to 7 in different cells. This observation can be explained by positional variation of the centromeric domain on the two homologs and/or misalignment of pericentromeric satellite DNA arrays during homolog pairing confirming the great plasticity of equine centromeres.
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Yang H, Yang W, Dao FY, Lv H, Ding H, Chen W, Lin H. A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae. Brief Bioinform 2019; 21:1568-1580. [PMID: 31633777 DOI: 10.1093/bib/bbz123] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/03/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is one of the most important driving forces of biological evolution, which is initiated by double-strand DNA breaks. Recombination has important roles in genome diversity and evolution. This review firstly provides a comprehensive survey of the 15 computational methods developed for identifying recombination hotspots in Saccharomyces cerevisiae. These computational methods were discussed and compared in terms of underlying algorithms, extracted features, predictive capability and practical utility. Subsequently, a more objective benchmark data set was constructed to develop a new predictor iRSpot-Pse6NC2.0 (http://lin-group.cn/server/iRSpot-Pse6NC2.0). To further demonstrate the generalization ability of these methods, we compared iRSpot-Pse6NC2.0 with existing methods on the chromosome XVI of S. cerevisiae. The results of the independent data set test demonstrated that the new predictor is superior to existing tools in the identification of recombination hotspots. The iRSpot-Pse6NC2.0 will become an important tool for identifying recombination hotspot.
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Affiliation(s)
- Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wuritu Yang
- Development and Planning Department, Inner Mongolia University, Hohhot 010021, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Hao Lin
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
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14
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Bolcun-Filas E, Handel MA. Meiosis: the chromosomal foundation of reproduction. Biol Reprod 2019; 99:112-126. [PMID: 29385397 DOI: 10.1093/biolre/ioy021] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/23/2018] [Indexed: 12/14/2022] Open
Abstract
Meiosis is the chromosomal foundation of reproduction, with errors in this important process leading to aneuploidy and/or infertility. In this review celebrating the 50th anniversary of the founding of the Society for the Study of Reproduction, the important chromosomal structures and dynamics contributing to genomic integrity across generations are highlighted. Critical unsolved biological problems are identified, and the advances that will lead to their ultimate resolution are predicted.
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Wang S, Veller C, Sun F, Ruiz-Herrera A, Shang Y, Liu H, Zickler D, Chen Z, Kleckner N, Zhang L. Per-Nucleus Crossover Covariation and Implications for Evolution. Cell 2019; 177:326-338.e16. [PMID: 30879787 PMCID: PMC6472931 DOI: 10.1016/j.cell.2019.02.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 12/25/2022]
Abstract
Crossing over is a nearly universal feature of sexual reproduction. Here, analysis of crossover numbers on a per-chromosome and per-nucleus basis reveals a fundamental, evolutionarily conserved feature of meiosis: within individual nuclei, crossover frequencies covary across different chromosomes. This effect results from per-nucleus covariation of chromosome axis lengths. Crossovers can promote evolutionary adaptation. However, the benefit of creating favorable new allelic combinations must outweigh the cost of disrupting existing favorable combinations. Covariation concomitantly increases the frequencies of gametes with especially high, or especially low, numbers of crossovers, and thus might concomitantly enhance the benefits of crossing over while reducing its costs. A four-locus population genetic model suggests that such an effect can pertain in situations where the environment fluctuates: hyper-crossover gametes are advantageous when the environment changes while hypo-crossover gametes are advantageous in periods of environmental stasis. These findings reveal a new feature of the basic meiotic program and suggest a possible adaptive advantage.
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Affiliation(s)
- Shunxin Wang
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China.
| | - Carl Veller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
| | - Fei Sun
- School of Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, Jiangsu, China
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Yongliang Shang
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
| | - Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Zijiang Chen
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Liangran Zhang
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China; Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250014, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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16
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Vendrell X, Escribà MJ. The model of "genetic compartments": a new insight into reproductive genetics. J Assist Reprod Genet 2019; 36:363-369. [PMID: 30421342 PMCID: PMC6439105 DOI: 10.1007/s10815-018-1366-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/02/2018] [Indexed: 12/20/2022] Open
Abstract
Currently, we are witnessing revolutionary advances in the analytical power of genetic tools. An enormous quantity of data can now be obtained from samples; however, the translation of genetic findings to the general status of individuals, or their offspring, should be done with caution. This is especially relevant in the reproductive context, where the concepts of "transmission" and "inheritability" of a trait are crucial. Against this background, we offer new insight based on a systemic view of genetic constitution in the compartmentalized organism, that is, the human body. This model considers the coexistence of "different" genomes in the same individual and the repercussion of this on reproductive efficacy and offspring. Herein, we review the major differences between somatic, germinal, embryonic, and fetal/placental genomes and their contribution to the next generation and its reproductive efficacy. The major novelty of our approach is the holistic interaction between microsystems within a macrosystem (i.e., the reproductive system). This panoramic model allows us to sketch the future implications of genetic results in function of the origin (compartment) of the sample: peripheral blood or other somatic tissues, gametes, zygotes, preimplantation embryos, fetus, or placenta. We believe this perspective can be of great use in the context of reproductive genetic counseling.
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Affiliation(s)
- X Vendrell
- Reproductive Genetics Unit, Sistemas Genómicos, Parc Tecnològic de Paterna, G. Marconi 6, 46980, València, Spain.
| | - M J Escribà
- IVF Laboratory, IVIRMA-Valencia, Plaça de la Policia Local, 3, 46015, València, Spain
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17
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Jordan KW, Wang S, He F, Chao S, Lun Y, Paux E, Sourdille P, Sherman J, Akhunova A, Blake NK, Pumphrey MO, Glover K, Dubcovsky J, Talbert L, Akhunov ED. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1039-1054. [PMID: 29952048 PMCID: PMC6174997 DOI: 10.1111/tpj.14009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/21/2018] [Accepted: 06/06/2018] [Indexed: 05/18/2023]
Abstract
Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes.
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Affiliation(s)
| | - Shichen Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Shiaoman Chao
- USDA‐ARS Cereal Crops Research Unit1605 Albrecht Blvd NFargoNDUSA
| | - Yanni Lun
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Etienne Paux
- INRA GDEC Auvergne‐Rhône‐AlpesClermont‐FerrandFrance
| | | | | | - Alina Akhunova
- Integrated Genomics FacilityKansas State UniversityManhattanKSUSA
| | | | | | - Karl Glover
- Department of Agronomy, Horticulture and Plant ScienceSouth Dakota State UniversityBrookingsSDUSA
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavis, DavisCAUSA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
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18
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Abstract
Recombination often differs markedly between males and females. Here we present the first analysis of sex-specific recombination in Gasterosteus sticklebacks. Using whole-genome sequencing of 15 crosses between G. aculeatus and G. nipponicus, we localized 698 crossovers with a median resolution of 2.3 kb. We also used a bioinformatic approach to infer historical sex-averaged recombination patterns for both species. Recombination is greater in females than males on all chromosomes, and overall map length is 1.64 times longer in females. The locations of crossovers differ strikingly between sexes. Crossovers cluster toward chromosome ends in males, but are distributed more evenly across chromosomes in females. Suppression of recombination near the centromeres in males causes crossovers to cluster at the ends of long arms in acrocentric chromosomes, and greatly reduces crossing over on short arms. The effect of centromeres on recombination is much weaker in females. Genomic differentiation between G. aculeatus and G. nipponicus is strongly correlated with recombination rate, and patterns of differentiation along chromosomes are strongly influenced by male-specific telomere and centromere effects. We found no evidence for fine-scale correlations between recombination and local gene content in either sex. We discuss hypotheses for the origin of sexual dimorphism in recombination and its consequences for sexually antagonistic selection and sex chromosome evolution.
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19
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Wang RJ, Gray MM, Parmenter MD, Broman KW, Payseur BA. Recombination rate variation in mice from an isolated island. Mol Ecol 2016; 26:457-470. [PMID: 27864900 DOI: 10.1111/mec.13932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 01/14/2023]
Abstract
Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including subchromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genomewide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbour a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales.
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Affiliation(s)
- Richard J Wang
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Melissa M Gray
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Michelle D Parmenter
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Karl W Broman
- Department of Biostatistics & Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
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20
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Liu B, Liu Y, Jin X, Wang X, Liu B. iRSpot-DACC: a computational predictor for recombination hot/cold spots identification based on dinucleotide-based auto-cross covariance. Sci Rep 2016; 6:33483. [PMID: 27641752 PMCID: PMC5027590 DOI: 10.1038/srep33483] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/25/2016] [Indexed: 01/01/2023] Open
Abstract
Meiotic recombination presents an uneven distribution across the genome. Genomic regions that exhibit at relatively high frequencies of recombination are called hotspots, whereas those with relatively low frequencies of recombination are called coldspots. Therefore, hotspots and coldspots would provide useful information for the study of the mechanism of recombination. In this study, we proposed a computational predictor called iRSpot-DACC to predict hot/cold spots across the yeast genome. It combined Support Vector Machines (SVMs) and a feature called dinucleotide-based auto-cross covariance (DACC), which is able to incorporate the global sequence-order information and fifteen local DNA properties into the predictor. Combined with Principal Component Analysis (PCA), its performance was further improved. Experimental results on a benchmark dataset showed that iRSpot-DACC can achieve an accuracy of 82.7%, outperforming some highly related methods.
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Affiliation(s)
- Bingquan Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150080, China
| | - Yumeng Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Xiaopeng Jin
- School of Computer Science and Technology, Harbin Engineering University, Harbin, Heilongjiang 150001, China
| | - Xiaolong Wang
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.,Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.,Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
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21
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Recombination Hotspot/Coldspot Identification Combining Three Different Pseudocomponents via an Ensemble Learning Approach. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8527435. [PMID: 27648451 PMCID: PMC5015011 DOI: 10.1155/2016/8527435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 11/17/2022]
Abstract
Recombination presents a nonuniform distribution across the genome. Genomic regions that present relatively higher frequencies of recombination are called hotspots while those with relatively lower frequencies of recombination are recombination coldspots. Therefore, the identification of hotspots/coldspots could provide useful information for the study of the mechanism of recombination. In this study, a new computational predictor called SVM-EL was proposed to identify hotspots/coldspots across the yeast genome. It combined Support Vector Machines (SVMs) and Ensemble Learning (EL) based on three features including basic kmer (Kmer), dinucleotide-based auto-cross covariance (DACC), and pseudo dinucleotide composition (PseDNC). These features are able to incorporate the nucleic acid composition and their order information into the predictor. The proposed SVM-EL achieves an accuracy of 82.89% on a widely used benchmark dataset, which outperforms some related methods.
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22
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Battagin M, Gorjanc G, Faux AM, Johnston SE, Hickey JM. Effect of manipulating recombination rates on response to selection in livestock breeding programs. Genet Sel Evol 2016; 48:44. [PMID: 27335010 PMCID: PMC4917950 DOI: 10.1186/s12711-016-0221-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 06/07/2016] [Indexed: 11/10/2022] Open
Abstract
Background In this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs. Methods We carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %. Results Increasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination. Conclusions Higher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in recombination rates are unknown. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0221-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mara Battagin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Anne-Michelle Faux
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
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Abstract
The mangrove killifish Kryptolebias marmoratus, and its close relative Kryptolebias hermaphroditus, are the only vertebrate species known to reproduce by self-fertilization due to functional ovotestis development. To improve our understanding of their genomes, we constructed a genetic map. First, a single F1 fish was made by artificial fertilization between K. marmoratus and K. hermaphroditus strains. F2 progeny were then obtained by self-fertilization of the F1 fish. We used RAD-seq to query genomic DNAs from the two parental strains, the F1 individual and 49 F2 progeny. Results identified 9904 polymorphic RAD-tags (DNA markers) that mapped to 24 linkage groups, corresponding to the haploid chromosome number of these species. The total length of the map was 1248 cM, indicating that about one recombination occurred for each of the 24 homologous chromosome pairs in each meiosis. Markers were not evenly distributed along the chromosomes: in all chromosomes, many markers (> 8% of the total markers for each chromosome) mapped to chromosome tips. Centromeres suppress recombination, and this uneven distribution is probably due to the species’ acrocentric chromosomes. Mapped marker sequences were compared to genomic sequences of medaka and platyfish, the next most closely related species with sequenced genomes that are anchored to genetic maps. Results showed that each mangrove killifish chromosome corresponds to a single chromosome of both platyfish and medaka, suggesting strong conservation of chromosomes over 100 million years of evolution. Our genetic map provides a framework for the K. marmoratus/K. hermaphroditus genome sequence and an important resource for understanding the biology of hermaphroditism.
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24
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Nambiar M, Smith GR. Repression of harmful meiotic recombination in centromeric regions. Semin Cell Dev Biol 2016; 54:188-97. [PMID: 26849908 DOI: 10.1016/j.semcdb.2016.01.042] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/27/2016] [Indexed: 11/16/2022]
Abstract
During the first division of meiosis, segregation of homologous chromosomes reduces the chromosome number by half. In most species, sister chromatid cohesion and reciprocal recombination (crossing-over) between homologous chromosomes are essential to provide tension to signal proper chromosome segregation during the first meiotic division. Crossovers are not distributed uniformly throughout the genome and are repressed at and near the centromeres. Rare crossovers that occur too near or in the centromere interfere with proper segregation and can give rise to aneuploid progeny, which can be severely defective or inviable. We review here how crossing-over occurs and how it is prevented in and around the centromeres. Molecular mechanisms of centromeric repression are only now being elucidated. However, rapid advances in understanding crossing-over, chromosome structure, and centromere functions promise to explain how potentially deleterious crossovers are avoided in certain chromosomal regions while allowing beneficial crossovers in others.
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Affiliation(s)
- Mridula Nambiar
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, United States.
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, United States.
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25
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Gruhn J, Al-Asmar N, Fasnacht R, Maylor-Hagen H, Peinado V, Rubio C, Broman K, Hunt P, Hassold T. Correlations between Synaptic Initiation and Meiotic Recombination: A Study of Humans and Mice. Am J Hum Genet 2016; 98:102-15. [PMID: 26749305 DOI: 10.1016/j.ajhg.2015.11.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022] Open
Abstract
Meiotic recombination is initiated by programmed double strand breaks (DSBs), only a small subset of which are resolved into crossovers (COs). The mechanism determining the location of these COs is not well understood. Studies in plants, fungi, and insects indicate that the same genomic regions are involved in synaptic initiation and COs, suggesting that early homolog alignment is correlated with the eventual resolution of DSBs as COs. It is generally assumed that this relationship extends to mammals, but little effort has been made to test this idea. Accordingly, we conducted an analysis of synaptic initiation sites (SISs) and COs in human and mouse spermatocytes and oocytes. In contrast to our expectation, we observed remarkable sex- and species-specific differences, including pronounced differences between human males and females in both the number and chromosomal location of SISs. Further, the combined data from our studies in mice and humans suggest that the relationship between SISs and COs in mammals is a complex one that is not dictated by the sites of synaptic initiation as reported in other organisms, although it is clearly influenced by them.
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26
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Using weighted features to predict recombination hotspots in Saccharomyces cerevisiae. J Theor Biol 2015; 382:15-22. [DOI: 10.1016/j.jtbi.2015.06.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/04/2015] [Accepted: 06/20/2015] [Indexed: 01/06/2023]
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27
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Fröhlich J, Vozdova M, Kubickova S, Cernohorska H, Sebestova H, Rubes J. Variation of Meiotic Recombination Rates and MLH1 Foci Distribution in Spermatocytes of Cattle, Sheep and Goats. Cytogenet Genome Res 2015; 146:211-21. [PMID: 26406935 DOI: 10.1159/000439452] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
Despite similar genome sizes, a great variability in recombination rates is observed in mammals. We used antibodies against SYCP3, MLH1 and centromeres to compare crossover frequency, position along chromosome arms and the effect of crossover interference in spermatocytes of 4 species from the family Bovidae (Bos taurus, 2n = 60, tribe Bovini; Ovis aries, 2n = 54, Capra hircus, 2n = 60 and Ammotragus lervia, 2n = 58, tribe Caprini). Despite significant individual variability, our results also show significant differences in both recombination rates and the total length of autosomal synaptonemal complexes (SC) between cattle (47.53 MLH1 foci/cell, 244.59 µm) and members of the tribe Caprini (61.83 MLH1 foci, 296.19 µm) which can be explained by the length of time that has passed since their evolutionary divergence. Sheep displayed the highest number of MLH1 foci per cell and recombination density, although they have a lower diploid chromosome number caused by centric fusions corresponding to cattle chromosomes 1;3, 2;8 and 5;11. However, the proportion of MLH1 foci observed on the fused chromosomes in sheep (26.14%) was significantly lower than on the orthologous acrocentrics in cattle (27.6%) and goats (28.2%), and their distribution along the SC arms differed significantly. The reduced recombination rate in metacentrics is probably caused by interference acting across the centromere.
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Affiliation(s)
- Jan Fröhlich
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
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Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6. Chromosoma 2015; 125:15-27. [PMID: 25947290 PMCID: PMC4761004 DOI: 10.1007/s00412-015-0518-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/02/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
Abstract
The Smc5/6 complex, along with cohesin and condensin, is a member of the structural maintenance of chromosome (SMC) family, large ring-like protein complexes that are essential for chromatin structure and function. Thanks to numerous studies of the mitotic cell cycle, Smc5/6 has been implicated to have roles in homologous recombination, restart of stalled replication forks, maintenance of ribosomal DNA (rDNA) and heterochromatin, telomerase-independent telomere elongation, and regulation of chromosome topology. The nature of these functions implies that the Smc5/6 complex also contributes to the profound chromatin changes, including meiotic recombination, that characterize meiosis. Only recently, studies in diverse model organisms have focused on the potential meiotic roles of the Smc5/6 complex. Indeed, Smc5/6 appears to be essential for meiotic recombination. However, due to both the complexity of the process of meiosis and the versatility of the Smc5/6 complex, many additional meiotic functions have been described. In this review, we provide a clear overview of the multiple functions found so far for the Smc5/6 complex in meiosis. Additionally, we compare these meiotic functions with the known mitotic functions in an attempt to find a common denominator and thereby create clarity in the field of Smc5/6 research.
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Capilla L, Medarde N, Alemany-Schmidt A, Oliver-Bonet M, Ventura J, Ruiz-Herrera A. Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background. Proc Biol Sci 2015; 281:rspb.2014.0297. [PMID: 24850922 DOI: 10.1098/rspb.2014.0297] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite the existence of formal models to explain how chromosomal rearrangements can be fixed in a population in the presence of gene flow, few empirical data are available regarding the mechanisms by which genome shuffling contributes to speciation, especially in mammals. In order to shed light on this intriguing evolutionary process, here we present a detailed empirical study that shows how Robertsonian (Rb) fusions alter the chromosomal distribution of recombination events during the formation of the germline in a Rb system of the western house mouse (Mus musculus domesticus). Our results indicate that both the total number of meiotic crossovers and the chromosomal distribution of recombination events are reduced in mice with Rb fusions and that this can be related to alterations in epigenetic signatures for heterochromatinization. Furthermore, we detected novel house mouse Prdm9 allelic variants in the Rb system. Remarkably, mean recombination rates were positively correlated with a decrease in the number of ZnF domains in the Prdm9 gene. The suggestion that recombination can be modulated by both chromosomal reorganizations and genetic determinants that control the formation of double-stranded breaks during meiosis opens new avenues for understanding the role of recombination in chromosomal speciation.
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Affiliation(s)
- Laia Capilla
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | - Nuria Medarde
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | | | - Maria Oliver-Bonet
- Unitat d'Investigació, Hospital Universitari Son Espases, Ctra Valldemossa 79, Palma 07010, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
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Muñoz-Fuentes V, Marcet-Ortega M, Alkorta-Aranburu G, Linde Forsberg C, Morrell JM, Manzano-Piedras E, Söderberg A, Daniel K, Villalba A, Toth A, Di Rienzo A, Roig I, Vilà C. Strong artificial selection in domestic mammals did not result in an increased recombination rate. Mol Biol Evol 2014; 32:510-23. [PMID: 25414125 DOI: 10.1093/molbev/msu322] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recombination rates vary in intensity and location at the species, individual, sex and chromosome levels. Despite the fundamental biological importance of this process, the selective forces that operate to shape recombination rate and patterns are unclear. Domestication offers a unique opportunity to study the interplay between recombination and selection. In domesticates, intense selection for particular traits is imposed on small populations over many generations, resulting in organisms that differ, sometimes dramatically, in morphology and physiology from their wild ancestor. Although earlier studies suggested increased recombination rate in domesticates, a formal comparison of recombination rates between domestic mammals and their wild congeners was missing. In order to determine broad-scale recombination rate, we used immunolabeling detection of MLH1 foci as crossover markers in spermatocytes in three pairs of closely related wild and domestic species (dog and wolf, goat and ibex, and sheep and mouflon). In the three pairs, and contrary to previous suggestions, our data show that contemporary recombination rate is higher in the wild species. Subsequently, we inferred recombination breakpoints in sequence data for 16 genomic regions in dogs and wolves, each containing a locus associated with a dog phenotype potentially under selection during domestication. No difference in the number and distribution of recombination breakpoints was found between dogs and wolves. We conclude that our data indicate that strong directional selection did not result in changes in recombination in domestic mammals, and that both upper and lower bounds for crossover rates may be tightly regulated.
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Affiliation(s)
- Violeta Muñoz-Fuentes
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana EBD-CSIC, Sevilla, Spain Department of Population and Conservation Biology, Uppsala University, Uppsala, Sweden
| | - Marina Marcet-Ortega
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | | | - Jane M Morrell
- Division of Reproduction, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Arne Söderberg
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Katrin Daniel
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Adrian Villalba
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Attila Toth
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Anna Di Rienzo
- Department of Human Genetics, Cummings Life Science Center, University of Chicago
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain Cytology and Histology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana EBD-CSIC, Sevilla, Spain
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Sato-Carlton A, Li X, Crawley O, Testori S, Martinez-Perez E, Sugimoto A, Carlton PM. Protein phosphatase 4 promotes chromosome pairing and synapsis, and contributes to maintaining crossover competence with increasing age. PLoS Genet 2014; 10:e1004638. [PMID: 25340746 PMCID: PMC4207613 DOI: 10.1371/journal.pgen.1004638] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/15/2014] [Indexed: 11/18/2022] Open
Abstract
Prior to the meiotic divisions, dynamic chromosome reorganizations including pairing, synapsis, and recombination of maternal and paternal chromosome pairs must occur in a highly regulated fashion during meiotic prophase. How chromosomes identify each other's homology and exclusively pair and synapse with their homologous partners, while rejecting illegitimate synapsis with non-homologous chromosomes, remains obscure. In addition, how the levels of recombination initiation and crossover formation are regulated so that sufficient, but not deleterious, levels of DNA breaks are made and processed into crossovers is not understood well. We show that in Caenorhabditis elegans, the highly conserved Serine/Threonine protein phosphatase PP4 homolog, PPH-4.1, is required independently to carry out four separate functions involving meiotic chromosome dynamics: (1) synapsis-independent chromosome pairing, (2) restriction of synapsis to homologous chromosomes, (3) programmed DNA double-strand break initiation, and (4) crossover formation. Using quantitative imaging of mutant strains, including super-resolution (3D-SIM) microscopy of chromosomes and the synaptonemal complex, we show that independently-arising defects in each of these processes in the absence of PPH-4.1 activity ultimately lead to meiotic nondisjunction and embryonic lethality. Interestingly, we find that defects in double-strand break initiation and crossover formation, but not pairing or synapsis, become even more severe in the germlines of older mutant animals, indicating an increased dependence on PPH-4.1 with increasing maternal age. Our results demonstrate that PPH-4.1 plays multiple, independent roles in meiotic prophase chromosome dynamics and maintaining meiotic competence in aging germlines. PP4's high degree of conservation suggests it may be a universal regulator of meiotic prophase chromosome dynamics. Meiosis creates gametes by distributing diploid genomes containing homologous chromosome pairs into daughter cells that receive only one of each chromosome. To segregate correctly at the first meiotic division, chromosomes must pair and synapse with their homologous partners, and undergo crossover recombination, which requires breaking and repairing the DNA strands of all chromosomes. How chromosomes recognize their partners, and how a cell controls the amount of DNA breakage and recombination that occurs, are open questions. In this study, we observed meiosis in the nematode Caenorhabditis elegans to examine the role of Protein Phosphatase 4 (PP4). We found that in the absence of PP4, chromosomes often paired and synapsed with non-homologous chromosomes, or synapsed with themselves by folding in half. Additionally, without PP4 activity, the number of DNA breaks and of crossover recombination events were both independently reduced. The latter two defects became even worse with increasing age, indicating that older animals require PP4 to a greater extent. These findings shed light on how protein phosphorylation controls meiotic events, and demonstrate unanticipated, important roles for PP4.
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Affiliation(s)
- Aya Sato-Carlton
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Xuan Li
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Oliver Crawley
- MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, London, United Kingdom
| | - Sarah Testori
- MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, London, United Kingdom
| | - Enrique Martinez-Perez
- MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, London, United Kingdom
| | - Asako Sugimoto
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Peter M. Carlton
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- * E-mail:
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Abstract
Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies.
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Seplyarskiy VB, Logacheva MD, Penin AA, Baranova MA, Leushkin EV, Demidenko NV, Klepikova AV, Kondrashov FA, Kondrashov AS, James TY. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Mol Biol Evol 2014; 31:3016-25. [PMID: 25135947 PMCID: PMC4209137 DOI: 10.1093/molbev/msu242] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0–99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.
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Affiliation(s)
- Vladimir B Seplyarskiy
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksey A Penin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Maria A Baranova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny V Leushkin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Natalia V Demidenko
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Anna V Klepikova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, Barcelona, Spain
| | - Alexey S Kondrashov
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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Verver DE, Langedijk NSM, Jordan PW, Repping S, Hamer G. The SMC5/6 complex is involved in crucial processes during human spermatogenesis. Biol Reprod 2014; 91:22. [PMID: 24855106 PMCID: PMC6058740 DOI: 10.1095/biolreprod.114.118596] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Genome integrity is crucial for safe reproduction. Therefore, chromatin structure and dynamics should be tightly regulated during germ cell development. Chromatin structure and function are in large part determined by the structural maintenance of chromosomes (SMC) protein complexes, of which SMC5/6 recently has been shown to be involved in both spermatogonial differentiation and meiosis during mouse spermatogenesis. We therefore investigated the role of this complex in human spermatogenesis. We found SMC6 to be expressed in the human testis and present in a subset of type Adark and type Apale spermatogonia, all spermatocytes, and round spermatids. During human meiosis, SMC5/6 is located at the synaptonemal complex (SC), the XY body, and at the centromeres during meiotic metaphases. However, in contrast to mouse spermatogenesis, SMC6 is not located at pericentromeric heterochromatin in human spermatogenic cells, indicating subtle but perhaps important differences in not only SMC5/6 function but maybe also in maintenance of genomic integrity at the repetitive pericentromeric regions. Nonetheless, our data clearly indicate that the SMC5/6 complex, as shown in mice, is involved in numerous crucial processes during human spermatogenesis, such as in spermatogonial development, on the SC between synapsed chromosomes, and in DNA double-strand break repair on unsynapsed chromosomes during pachynema.
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Affiliation(s)
- Dideke E Verver
- Center for Reproductive Medicine, Women's and Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Nathalia S M Langedijk
- Center for Reproductive Medicine, Women's and Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Philip W Jordan
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Sjoerd Repping
- Center for Reproductive Medicine, Women's and Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Center for Reproductive Medicine, Women's and Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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35
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Gruhn JR, Rubio C, Broman KW, Hunt PA, Hassold T. Cytological studies of human meiosis: sex-specific differences in recombination originate at, or prior to, establishment of double-strand breaks. PLoS One 2013; 8:e85075. [PMID: 24376867 PMCID: PMC3869931 DOI: 10.1371/journal.pone.0085075] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/21/2013] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination is sexually dimorphic in most mammalian species, including humans, but the basis for the male:female differences remains unclear. In the present study, we used cytological methodology to directly compare recombination levels between human males and females, and to examine possible sex-specific differences in upstream events of double-strand break (DSB) formation and synaptic initiation. Specifically, we utilized the DNA mismatch repair protein MLH1 as a marker of recombination events, the RecA homologue RAD51 as a surrogate for DSBs, and the synaptonemal complex proteins SYCP3 and/or SYCP1 to examine synapsis between homologs. Consistent with linkage studies, genome-wide recombination levels were higher in females than in males, and the placement of exchanges varied between the sexes. Subsequent analyses of DSBs and synaptic initiation sites indicated similar male:female differences, providing strong evidence that sex-specific differences in recombination rates are established at or before the formation of meiotic DSBs. We then asked whether these differences might be linked to variation in the organization of the meiotic axis and/or axis-associated DNA and, indeed, we observed striking male:female differences in synaptonemal complex (SC) length and DNA loop size. Taken together, our observations suggest that sex specific differences in recombination in humans may derive from chromatin differences established prior to the onset of the recombination pathway.
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Affiliation(s)
- Jennifer R. Gruhn
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Carmen Rubio
- Preimplantation Genetic Diagnosis Unit, Iviomics, Paterna, Valencia, Spain
| | - Karl W. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patricia A. Hunt
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Terry Hassold
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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36
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Effects of diethylhexyl phthalate (DEHP) given neonatally on spermatogenesis of mice. Mol Biol Rep 2013; 40:6509-17. [DOI: 10.1007/s11033-013-2769-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 09/14/2013] [Indexed: 11/27/2022]
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37
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Verver DE, van Pelt AMM, Repping S, Hamer G. Role for rodent Smc6 in pericentromeric heterochromatin domains during spermatogonial differentiation and meiosis. Cell Death Dis 2013; 4:e749. [PMID: 23907463 PMCID: PMC3763431 DOI: 10.1038/cddis.2013.269] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/14/2013] [Accepted: 06/19/2013] [Indexed: 01/08/2023]
Abstract
Chromatin structure and function are for a large part determined by the six members of the structural maintenance of chromosomes (SMC) protein family, which form three heterodimeric complexes: Smc1/3 (cohesin), Smc2/4 (condensin) and Smc5/6. Each complex has distinct and important roles in chromatin dynamics, gene expression and differentiation. In yeast and Drosophila, Smc6 is involved in recombinational repair, restarting collapsed replication forks and prevention of recombination in repetitive sequences such as rDNA and pericentromeric heterochromatin. Although such DNA damage control mechanisms, as well as highly dynamic changes in chromatin composition and function, are essential for gametogenesis, knowledge on Smc6 function in mammalian systems is limited. We therefore have investigated the role of Smc6 during mammalian spermatogonial differentiation, meiosis and subsequent spermiogenesis. We found that, during mouse spermatogenesis, Smc6 functions as part of meiotic pericentromeric heterochromatin domains that are initiated when differentiating spermatogonia become irreversibly committed toward meiosis. To our knowledge, we are the first to provide insight into how commitment toward meiosis alters chromatin structure and dynamics, thereby setting apart differentiating spermatogonia from the undifferentiated spermatogonia, including the spermatogonial stem cells. Interestingly, Smc6 is not essential for spermatogonial mitosis, whereas Smc6-negative meiotic cells appear unable to finish their first meiotic division. Importantly, during meiosis, we find that DNA repair or recombination sites, marked by γH2AX or Rad51 respectively, do not co-localize with the pericentromeric heterochromatin domains where Smc6 is located. Considering the repetitive nature of these domains and that Smc6 has been previously shown to prevent recombination in repetitive sequences, we hypothesize that Smc6 has a role in the prevention of aberrant recombination events between pericentromeric regions during the first meiotic prophase that would otherwise cause chromosomal aberrations leading to apoptosis, meiotic arrest or aneuploidies.
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Affiliation(s)
- D E Verver
- Center for Reproductive Medicine, Women's and Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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38
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Jiang L, Chu G, Zhang Q, Wang Z, Wang X, Zhai J, Yu H. A microsatellite genetic linkage map of half smooth tongue sole (Cynoglossus semilaevis). Mar Genomics 2013; 9:17-23. [DOI: 10.1016/j.margen.2012.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/25/2012] [Accepted: 07/26/2012] [Indexed: 10/28/2022]
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39
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Farré M, Micheletti D, Ruiz-Herrera A. Recombination rates and genomic shuffling in human and chimpanzee--a new twist in the chromosomal speciation theory. Mol Biol Evol 2012. [PMID: 23204393 PMCID: PMC3603309 DOI: 10.1093/molbev/mss272] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A long-standing question in evolutionary biology concerns the effect of recombination in shaping the genomic architecture of organisms and, in particular, how this impacts the speciation process. Despite efforts employed in the last decade, the role of chromosomal reorganizations in the human-chimpanzee speciation process remains unresolved. Through whole-genome comparisons, we have analyzed the genome-wide impact of genomic shuffling in the distribution of human recombination rates during the human-chimpanzee speciation process. We have constructed a highly refined map of the reorganizations and evolutionary breakpoint regions in the human and chimpanzee genomes based on orthologous genes and genome sequence alignments. The analysis of the most recent human and chimpanzee recombination maps inferred from genome-wide single-nucleotide polymorphism data revealed that the standardized recombination rate was significantly lower in rearranged than in collinear chromosomes. In fact, rearranged chromosomes presented significantly lower recombination rates than chromosomes that have been maintained since the ancestor of great apes, and this was related with the lineage in which they become fixed. Importantly, inverted regions had lower recombination rates than collinear and noninverted regions, independently of the effect of centromeres. Our observations have implications for the chromosomal speciation theory, providing new evidences for the contribution of inversions in suppressing recombination in mammals.
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Affiliation(s)
- Marta Farré
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
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40
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Maiburg M, Repping S, Giltay J. The genetic origin of Klinefelter syndrome and its effect on spermatogenesis. Fertil Steril 2012; 98:253-60. [PMID: 22749222 DOI: 10.1016/j.fertnstert.2012.06.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 06/10/2012] [Accepted: 06/12/2012] [Indexed: 01/18/2023]
Abstract
Klinefelter syndrome is the most prevalent chromosome abnormality and genetic cause of azoospermia in males. The availability of assisted reproductive technology (ART) has allowed men with Klinefelter syndrome to father their own genetic offspring. When providing ART to men with Klinefelter syndrome, it is important to be able to counsel them properly on both the chance of finding sperm and the potential effects on their offspring. The aim of this review is twofold: [1] to describe the genetic etiology of Klinefelter syndrome and [2] to describe how spermatogenesis occurs in men with Klinefelter syndrome and the consequences this has for children born from men with Klinefelter syndrome.
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Affiliation(s)
- Merel Maiburg
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
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The Growing Rate of The Information Quantity of The Human Genome is Modulated by Recombination*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Nagaoka SI, Hassold TJ, Hunt PA. Human aneuploidy: mechanisms and new insights into an age-old problem. Nat Rev Genet 2012; 13:493-504. [PMID: 22705668 PMCID: PMC3551553 DOI: 10.1038/nrg3245] [Citation(s) in RCA: 648] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Trisomic and monosomic (aneuploid) embryos account for at least 10% of human pregnancies and, for women nearing the end of their reproductive lifespan, the incidence may exceed 50%. The errors that lead to aneuploidy almost always occur in the oocyte but, despite intensive investigation, the underlying molecular basis has remained elusive. Recent studies of humans and model organisms have shed new light on the complexity of meiotic defects, providing evidence that the age-related increase in errors in the human female is not attributable to a single factor but to an interplay between unique features of oogenesis and a host of endogenous and exogenous factors.
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Affiliation(s)
- So I Nagaoka
- School of Molecular Biosciences, Center for Reproductive Biology, Washington State University, Pullman, Washington 99164, USA
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43
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Sequence-dependent prediction of recombination hotspots in Saccharomyces cerevisiae. J Theor Biol 2012; 293:49-54. [DOI: 10.1016/j.jtbi.2011.10.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 10/04/2011] [Accepted: 10/04/2011] [Indexed: 11/18/2022]
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Giraut L, Falque M, Drouaud J, Pereira L, Martin OC, Mézard C. Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS Genet 2011; 7:e1002354. [PMID: 22072983 PMCID: PMC3207851 DOI: 10.1371/journal.pgen.1002354] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 09/08/2011] [Indexed: 11/19/2022] Open
Abstract
In most species, crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in Arabidopsis thaliana, in male and female meiosis. We observed dramatic differences between male and female meiosis which included: (i) genetic map length; 575 cM versus 332 cM respectively; (ii) CO distribution patterns: male CO rates were very high at both ends of each chromosome, whereas female CO rates were very low; (iii) correlations between CO rates and various chromosome features: female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements (TEs) density, whereas male CO rates correlated positively with the CpG ratio. However, except for CpG, the correlations could be explained by the unequal repartition of these sequences along the Arabidopsis chromosome. For both male and female meiosis, the number of COs per chromosome correlates with chromosome size expressed either in base pairs or as synaptonemal complex length. Finally, we show that interference modulates the CO distribution both in male and female meiosis.
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Affiliation(s)
- Laurène Giraut
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Matthieu Falque
- UMR de Génétique Végétale du Moulon, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Gif sur Yvette, France
| | - Jan Drouaud
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Lucie Pereira
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Olivier C. Martin
- UMR de Génétique Végétale du Moulon, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Gif sur Yvette, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- * E-mail:
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Lee YS, Chao A, Chen CH, Chou T, Wang SYM, Wang TH. Analysis of human meiotic recombination events with a parent-sibling tracing approach. BMC Genomics 2011; 12:434. [PMID: 21867557 PMCID: PMC3186786 DOI: 10.1186/1471-2164-12-434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 08/26/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Meiotic recombination ensures that each child inherits distinct genetic materials from each parent, but the distribution of crossovers along meiotic chromosomes remains difficult to identify. In this study, we developed a parent-sibling tracing (PST) approach from previously reported methods to identify meiotic crossover sites of GEO GSE6754 data set. This approach requires only the single nucleotide polymorphism (SNP) data of the pedigrees of both parents and at least two of children. RESULTS Compared to other SNP-based algorithms (identity by descent or pediSNP), fewer uninformative SNPs were derived with the use of PST. Analysis of a GEO GSE6754 data set containing 2,145 maternal and paternal meiotic events revealed that the pattern and distribution of paternal and maternal recombination sites vary along the chromosomes. Lower crossover rates near the centromeres were more prominent in males than in females. Based on analysis of repetitive sequences, we also showed that recombination hotspots are positively correlated with SINE/MIR repetitive elements and negatively correlated with LINE/L1 elements. The number of meiotic recombination events was positively correlated with the number of shorter tandem repeat sequences. CONCLUSIONS The advantages of the PST approach include the ability to use only two-generation pedigrees with two siblings and the ability to perform gender-specific analyses of repetitive elements and tandem repeat sequences while including fewer uninformative SNP regions in the results.
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Affiliation(s)
- Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Tao-Yuan, Taiwan
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Garcia-Cruz R, Pacheco S, Brieño MA, Steinberg ER, Mudry MD, Ruiz-Herrera A, Garcia-Caldés M. A comparative study of the recombination pattern in three species of Platyrrhini monkeys (primates). Chromosoma 2011; 120:521-30. [PMID: 21735165 DOI: 10.1007/s00412-011-0329-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/30/2011] [Accepted: 06/23/2011] [Indexed: 01/26/2023]
Abstract
Homologous chromosomes exchange genetic information through recombination during meiotic synapsis, a process that increases genetic diversity and is fundamental to sexual reproduction. Meiotic studies in mammalian species are scarce and mainly focused on human and mouse. Here, the meiotic recombination events were determined in three species of Platyrrhini monkeys (Cebus libidinosus, Cebus nigritus and Alouatta caraya) by analysing the distribution of MLH1 foci at the stage of pachytene. Moreover, the combination of immunofluorescence and fluorescent in situ hybridisation has enabled us to construct recombination maps of primate chromosomes that are homologous to human chromosomes 13 and 21. Our results show that (a) the overall number of MLH1 foci varies among all three species, (b) the presence of heterochromatin blocks does not have a major influence on the distribution of MLH1 foci and (c) the distribution of crossovers in the homologous chromosomes to human chromosomes 13 and 21 are conserved between species of the same genus (C. libidinosus and C. nigritus) but are significantly different between Cebus and Alouatta. This heterogeneity in recombination behaviour among Ceboidea species may reflect differences in genetic diversity and genome composition.
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Affiliation(s)
- Raquel Garcia-Cruz
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, UAB Campus, Bellaterra, Spain
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Abstract
Recombination, together with mutation, generates the raw material of evolution, is essential for reproduction and lies at the heart of all genetic analysis. Recent advances in our ability to construct genome-scale, high-resolution recombination maps and new molecular techniques for analysing recombination products have substantially furthered our understanding of this important biological phenomenon in humans and mice: from describing the properties of recombination hot spots in male and female meiosis to the recombination landscape along chromosomes. This progress has been accompanied by the identification of trans-acting systems that regulate the location and relative activity of individual hot spots.
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Hultén MA. On the origin of crossover interference: A chromosome oscillatory movement (COM) model. Mol Cytogenet 2011; 4:10. [PMID: 21477316 PMCID: PMC3103480 DOI: 10.1186/1755-8166-4-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/08/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND It is now nearly a century since it was first discovered that crossovers between homologous parental chromosomes, originating at the Prophase stage of Meiosis I, are not randomly placed. In fact, the number and distribution of crossovers are strictly regulated with crossovers/chiasmata formed in optimal positions along the length of individual chromosomes, facilitating regular chromosome segregation at the first meiotic division. In spite of much research addressing this question, the underlying mechanism(s) for the phenomenon called crossover/chiasma interference is/are still unknown; and this constitutes an outstanding biological enigma. RESULTS The Chromosome Oscillatory Movement (COM) model for crossover/chiasma interference implies that, during Prophase of Meiosis I, oscillatory movements of the telomeres (attached to the nuclear membrane) and the kinetochores (within the centromeres) create waves along the length of chromosome pairs (bivalents) so that crossing-over and chiasma formation is facilitated by the proximity of parental homologs induced at the nodal regions of the waves thus created. This model adequately explains the salient features of crossover/chiasma interference, where (1) there is normally at least one crossover/chiasma per bivalent, (2) the number is correlated to bivalent length, (3) the positions are dependent on the number per bivalent, (4) interference distances are on average longer over the centromere than along chromosome arms, and (5) there are significant changes in carriers of structural chromosome rearrangements. CONCLUSIONS The crossover/chiasma frequency distribution in humans and mice with normal karyotypes as well as in carriers of structural chromosome rearrangements are those expected on the COM model. Further studies are underway to analyze mechanical/mathematical aspects of this model for the origin of crossover/chiasma interference, using string replicas of the homologous chromosomes at the Prophase stage of Meiosis I. The parameters to vary in this type of experiment will include: (1) the mitotic karyotype, i.e. ranked length and centromere index of the chromosomes involved, (2) the specific bivalent/multivalent length and flexibility, dependent on the way this structure is positioned within the nucleus and the size of the respective meiocyte nuclei, (3) the frequency characteristics of the oscillatory movements at respectively the telomeres and the kinetochores.
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Affiliation(s)
- Maj A Hultén
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, CMM L8:02, Karolinska Institutet, Karolinska University Hospital, Solna, S-17 1 76 Stockholm, Sweden.
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Abstract
The two alleles at a heterozygous locus segregate during meiosis, sometimes at meiosis I and sometimes at meiosis II. The timing of segregation is determined by the pattern of crossing-over between a locus and its attached centromeres. Genes near centromeres can exploit this process by driving against spores from which the genes separated at meiosis I. Other genes, located distal to centromeres, can benefit from driving against spores from which they separated at meiosis II. Asymmetric female meiosis is particularly susceptible to such forms of drive. Selection on modifiers of recombination favors changes in the location of chiasmata that increase the proportion of tetrads of high average fitness by changing the timing of segregation. Such changes increase the frequency of driving alleles. This source of selection on recombination does not depend on effects on linkage disequilibrium. Recombinational responses to meiotic drive may contribute to sex differences in overall recombination and sex differences in the localization of chiasmata.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome. Genome Biol 2010; 11:R103. [PMID: 20961408 PMCID: PMC3218659 DOI: 10.1186/gb-2010-11-10-r103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/25/2010] [Accepted: 10/20/2010] [Indexed: 12/02/2022] Open
Abstract
Background Meiotic recombination events tend to cluster into narrow spans of a few kilobases long, called recombination hotspots. Such hotspots are not conserved between human and chimpanzee and vary between different human ethnic groups. At the same time, recombination hotspots are heritable. Previous studies showed instances where differences in recombination rate could be associated with sequence polymorphisms. Results In this work we developed a novel computational approach, LDsplit, to perform a large-scale association study of recombination hotspots with genetic polymorphisms. LDsplit was able to correctly predict the association between the FG11 SNP and the DNA2 hotspot observed by sperm typing. Extensive simulation demonstrated the accuracy of LDsplit under various conditions. Applying LDsplit to human chromosome 6, we found that for a significant fraction of hotspots, there is an association between variations in intensity of historical recombination and sequence polymorphisms. From flanking regions of the SNPs output by LDsplit we identified a conserved 11-mer motif GGNGGNAGGGG, whose complement partially matches 13-mer CCNCCNTNNCCNC, a critical motif for the regulation of recombination hotspots. Conclusions Our result suggests that computational approaches based on historical recombination events are likely to be more powerful than previously anticipated. The putative associations we identified may be a promising step toward uncovering the mechanisms of recombination hotspots.
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