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Single-Cell RNA Sequencing of the Cynomolgus Macaque Testis Reveals Conserved Transcriptional Profiles during Mammalian Spermatogenesis. Dev Cell 2020; 54:548-566.e7. [PMID: 32795394 DOI: 10.1016/j.devcel.2020.07.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/23/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022]
Abstract
Spermatogenesis is highly orchestrated and involves the differentiation of diploid spermatogonia into haploid sperm. The process is driven by spermatogonial stem cells (SSCs). SSCs undergo mitotic self-renewal, whereas sub-populations undergo differentiation and later gain competence to initiate meiosis. Here, we describe a high-resolution single-cell RNA-seq atlas of cells derived from Cynomolgus macaque testis. We identify gene signatures that define spermatogonial populations and explore self-renewal versus differentiation dynamics. We detail transcriptional changes occurring over the entire process of spermatogenesis and highlight the concerted activity of DNA damage response (DDR) pathway genes, which have dual roles in maintaining genomic integrity and effecting meiotic sex chromosome inactivation (MSCI). We show remarkable similarities and differences in gene expression during spermatogenesis with two other eutherian mammals, i.e., mouse and humans. Sex chromosome expression in the male germline in all three species demonstrates conserved features of MSCI but divergent multicopy and ampliconic gene content.
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52
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Fortes MRS, Porto-Neto LR, Satake N, Nguyen LT, Freitas AC, Melo TP, Scalez DCB, Hayes B, Raidan FSS, Reverter A, Boe-Hansen GB. X chromosome variants are associated with male fertility traits in two bovine populations. Genet Sel Evol 2020; 52:46. [PMID: 32787790 PMCID: PMC7425018 DOI: 10.1186/s12711-020-00563-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 07/22/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Twenty-five phenotypes were measured as indicators of bull fertility (1099 Brahman and 1719 Tropical Composite bulls). Measurements included sperm morphology, scrotal circumference, and sperm chromatin phenotypes such as DNA fragmentation and protamine deficiency. We estimated the heritability of these phenotypes and carried out genome-wide association studies (GWAS) within breed, using the bovine high-density chip, to detect quantitative trait loci (QTL). RESULTS Our analyses suggested that both sperm DNA fragmentation and sperm protamine deficiency are heritable (h2 from 0.10 to 0.22). To confirm these first estimates of heritability, further studies on sperm chromatin traits, with larger datasets are necessary. Our GWAS identified 12 QTL for bull fertility traits, based on at least five polymorphisms (P < 10-8) for each QTL. Five QTL were identified in Brahman and another seven in Tropical Composite bulls. Most of the significant polymorphisms detected in both breeds and nine of the 12 QTL were on chromosome X. The QTL were breed-specific, but for some traits, a closer inspection of the GWAS results revealed suggestive single nucleotide polymorphism (SNP) associations (P < 10-7) in both breeds. For example, the QTL for inhibin level in Braham could be relevant to Tropical Composites too (many polymorphisms reached P < 10-7 in the same region). The QTL for sperm midpiece morphological abnormalities on chromosome X (QTL peak at 4.92 Mb, P < 10-17) is an example of a breed-specific QTL, supported by 143 significant SNPs (P < 10-8) in Brahman, but absent in Tropical Composites. Our GWAS results add evidence to the mammalian specialization of the X chromosome, which during evolution has accumulated genes linked to spermatogenesis. Some of the polymorphisms on chromosome X were associated to more than one genetically correlated trait (correlations ranged from 0.33 to 0.51). Correlations and shared polymorphism associations support the hypothesis that these phenotypes share the same underlying cause, i.e. defective spermatogenesis. CONCLUSIONS Genetic improvement for bull fertility is possible through genomic selection, which is likely more accurate if the QTL on chromosome X are considered in the predictions. Polymorphisms associated with male fertility accumulate on this chromosome in cattle, as in humans and mice, suggesting its specialization.
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Affiliation(s)
- Marina R. S. Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Saint Lucia Campus, Brisbane, QLD 4072 Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Saint Lucia Campus, Brisbane, QLD 4072 Australia
| | | | - Nana Satake
- School of Veterinary Science, The University of Queensland, Gatton Campus, Gatton, QLD 4343 Australia
| | - Loan T. Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Saint Lucia Campus, Brisbane, QLD 4072 Australia
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Ana Claudia Freitas
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Thaise P. Melo
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Daiane Cristina Becker Scalez
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Ben Hayes
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Saint Lucia Campus, Brisbane, QLD 4072 Australia
| | | | | | - Gry B. Boe-Hansen
- School of Veterinary Science, The University of Queensland, Gatton Campus, Gatton, QLD 4343 Australia
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53
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Bachtrog D. The Y Chromosome as a Battleground for Intragenomic Conflict. Trends Genet 2020; 36:510-522. [PMID: 32448494 DOI: 10.1016/j.tig.2020.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
Abstract
Y chromosomes are typically viewed as genetic wastelands with few intact genes. Recent genomic analyses in Drosophila, however, show that gene gain is prominent on young Y chromosomes. Meiosis- and RNAi-related genes often coamplify on recently formed X and Y chromosomes, are testis-expressed, and produce antisense transcripts and short RNAs. RNAi pathways are also involved in suppressing sex ratio drive in Drosophila. These observations paint a dynamic picture of sex chromosome differentiation, suggesting that rapidly evolving genomic battles over segregation are rampant on young sex chromosomes and utilize RNAi to defend the genome against selfish elements that manipulate fair meiosis. Recurrent sex chromosome drive can have profound ecological, evolutionary, and cellular impacts and account for unique features of sex chromosomes.
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Affiliation(s)
- Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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54
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Kosugi M, Otani M, Kikkawa Y, Itakura Y, Sakai K, Ito T, Toyoda M, Sekita Y, Kimura T. Mutations of histone demethylase genes encoded by X and Y chromosomes, Kdm5c and Kdm5d, lead to noncompaction cardiomyopathy in mice. Biochem Biophys Res Commun 2020; 525:S0006-291X(20)30311-9. [PMID: 32081420 DOI: 10.1016/j.bbrc.2020.02.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
Mammalian X and Y chromosomes evolved from a pair of autosomes. Although most ancestral genes have been lost from the Y chromosome, a small number of ancestral X-Y gene pairs are still present on the sex chromosomes. The KDM5C and KDM5D genes, which encode H3K4 histone demethylases, are a surviving ancestral gene pair located on the X and Y chromosomes, respectively. Mutations in KDM5C cause X-linked intellectual disability in human males, suggesting functional divergence between KDM5C and KDM5D in the nervous system. In this study, to explore the functional conservation and divergence between these two genes in other organs, we generated female mice lacking Kdm5c (homozygous X5c- X5c- females) and male mice lacking both Kdm5c and Kdm5d (compound hemizygous X5c- Y5d- males). Both X5c- X5c- females and X5c- Y5d- males showed lower body weights and postnatal lethality. Histological examination of the hearts showed prominent trabecular extension and a thin layer of compacted myocardium in the left and right ventricles, indicating noncompaction cardiomyopathy. However, hemizygous males lacking either Kdm5c or Kdm5d showed no signs of noncompaction cardiomyopathy. These results clearly demonstrate that the function of Kdm5c and Kdm5d in heart development is conserved.
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Affiliation(s)
- Mayuko Kosugi
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Mai Otani
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Yurika Kikkawa
- Research Team for Geriatric Medicine (Vascular Medicine), Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Yoko Itakura
- Research Team for Geriatric Medicine (Vascular Medicine), Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Kohei Sakai
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Toshiaki Ito
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Masashi Toyoda
- Research Team for Geriatric Medicine (Vascular Medicine), Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Yoichi Sekita
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.
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55
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Wilson J, Staley JM, Wyckoff GJ. Extinction of chromosomes due to specialization is a universal occurrence. Sci Rep 2020; 10:2170. [PMID: 32034231 PMCID: PMC7005762 DOI: 10.1038/s41598-020-58997-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022] Open
Abstract
The human X and Y chromosomes evolved from a pair of autosomes approximately 180 million years ago. Despite their shared evolutionary origin, extensive genetic decay has resulted in the human Y chromosome losing 97% of its ancestral genes while gene content and order remain highly conserved on the X chromosome. Five 'stratification' events, most likely inversions, reduced the Y chromosome's ability to recombine with the X chromosome across the majority of its length and subjected its genes to the erosive forces associated with reduced recombination. The remaining functional genes are ubiquitously expressed, functionally coherent, dosage-sensitive genes, or have evolved male-specific functionality. It is unknown, however, whether functional specialization is a degenerative phenomenon unique to sex chromosomes, or if it conveys a potential selective advantage aside from sexual antagonism. We examined the evolution of mammalian orthologs to determine if the selective forces that led to the degeneration of the Y chromosome are unique in the genome. The results of our study suggest these forces are not exclusive to the Y chromosome, and chromosomal degeneration may have occurred throughout our evolutionary history. The reduction of recombination could additionally result in rapid fixation through isolation of specialized functions resulting in a cost-benefit relationship during times of intense selective pressure.
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Affiliation(s)
- Jason Wilson
- University of Missouri-Kansas City School of Medicine, Department of Biomedical and Health Informatics, Kansas City, 64108, Missouri, USA.
| | - Joshua M Staley
- Kansas State University College of Veterinary Medicine, Department of Diagnostic Medicine/Pathobiology, Olathe, 66061, Kansas, USA
| | - Gerald J Wyckoff
- University of Missouri-Kansas City School of Medicine, Department of Biomedical and Health Informatics, Kansas City, 64108, Missouri, USA.,Kansas State University College of Veterinary Medicine, Department of Diagnostic Medicine/Pathobiology, Olathe, 66061, Kansas, USA.,University of Missouri-Kansas City School of Biological and Chemical Sciences, Department of Molecular Biology and Biochemistry, Kansas City, 64108, Missouri, USA
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56
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Webster TH, Couse M, Grande BM, Karlins E, Phung TN, Richmond PA, Whitford W, Wilson MA. Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data. Gigascience 2020; 8:5530326. [PMID: 31289836 PMCID: PMC6615978 DOI: 10.1093/gigascience/giz074] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/04/2018] [Accepted: 06/03/2019] [Indexed: 11/25/2022] Open
Abstract
Background Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. Similar sequence content can confound the mapping of short next-generation sequencing reads to a reference genome. It is therefore possible that the presence of both sex chromosomes in a reference genome can cause technical artifacts in genomic data and affect downstream analyses and applications. Understanding this problem is critical for medical genomics and population genomic inference. Results Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We find that sequence homology affects read mapping on the sex chromosomes and this has downstream effects on variant calling. However, we show that XYalign can correct mismapping, resulting in more accurate variant calling. We also show how metrics output by XYalign can be used to identify XX and XY individuals across diverse sequencing experiments, including low- and high-coverage whole-genome sequencing, and exome sequencing. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other uses including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3). Conclusions Sex chromsome sequence homology causes the mismapping of short reads, which in turn affects downstream analyses. XYalign provides a reproducible framework to correct mismapping and improve variant calling on the sex chromsomes.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Department of Anthropology, University of Utah, 260 S Central Drive, Carolyn and Kem Gardner Commons, Suite 4625, Salt Lake City, UT 84112, USA
| | - Madeline Couse
- University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.,BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, MSC 9776, Bethesda, MD 20892, USA
| | - Tanya N Phung
- Interdepartmental Program in Bioinformatics, UCLA, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Phillip A Richmond
- BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V52 4H4, Canada
| | - Whitney Whitford
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
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57
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Li G, Figueiró HV, Eizirik E, Murphy WJ. Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species. Mol Biol Evol 2020; 36:2111-2126. [PMID: 31198971 PMCID: PMC6759079 DOI: 10.1093/molbev/msz139] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.
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Affiliation(s)
- Gang Li
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Henrique V Figueiró
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - Eduardo Eizirik
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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58
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Vockel M, Riera-Escamilla A, Tüttelmann F, Krausz C. The X chromosome and male infertility. Hum Genet 2019; 140:203-215. [PMID: 31875237 PMCID: PMC7864851 DOI: 10.1007/s00439-019-02101-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023]
Abstract
The X chromosome is a key player in germ cell development, as has been highlighted for males in previous studies revealing that the mammalian X chromosome is enriched in genes expressed in early spermatogenesis. In this review, we focus on the X chromosome’s unique biology as associated with human male infertility. Male infertility is most commonly caused by spermatogenic defects to which X chromosome dosage is closely linked; for example, any supernumerary X chromosome as in Klinefelter syndrome will lead to male infertility. Furthermore, because males normally only have a single X chromosome and because X-linked genetic anomalies are generally only present in a single copy in males, any loss-of-function mutations in single-copy X-chromosomal genes cannot be compensated by a normal allele. These features make X-linked genes particularly attractive for studying male spermatogenic failure. However, to date, only very few genetic causes have been identified as being definitively responsible for male infertility in humans. Although genetic studies of germ cell-enriched X-chromosomal genes in mice suggest a role of certain human orthologs in infertile men, these genes in mice and humans have striking evolutionary differences. Furthermore, the complexity and highly repetitive structure of the X chromosome hinder the mutational analysis of X-linked genes in humans. Therefore, we conclude that additional methodological approaches are urgently warranted to advance our understanding of the genetics of X-linked male infertility.
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Affiliation(s)
- Matthias Vockel
- Institute of Human Genetics, University of Münster, Vesaliusweg 12-14, 48149, Münster, Germany
| | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB- Sant Pau), Barcelona, Catalonia, Spain
| | - Frank Tüttelmann
- Institute of Human Genetics, University of Münster, Vesaliusweg 12-14, 48149, Münster, Germany.
| | - Csilla Krausz
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB- Sant Pau), Barcelona, Catalonia, Spain. .,Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Viale PIeraccini, 6, 50139, Florence, Italy.
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59
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Antagonistic coevolution of Y and X. Nat Ecol Evol 2019; 3:1505-1506. [DOI: 10.1038/s41559-019-1006-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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60
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Massive gene amplification on a recently formed Drosophila Y chromosome. Nat Ecol Evol 2019; 3:1587-1597. [PMID: 31666742 PMCID: PMC7217032 DOI: 10.1038/s41559-019-1009-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022]
Abstract
Widespread loss of genes on the Y is considered a hallmark of sex chromosome differentiation. Here we show that the initial stages of Y evolution are driven by massive amplification of distinct classes of genes. The neo-Y chromosome of Drosophila miranda initially contained about 3000 protein-coding genes, but has gained over 3200 genes since its formation about 1.5 MY ago, primarily by tandem amplification of protein-coding genes ancestrally present on this chromosome. We show that distinct evolutionary processes may account for this drastic increase in gene number on the Y. Testis-specific and dosage sensitive genes appear to have amplified on the Y to increase male fitness. A distinct class of meiosis-related multi-copy Y genes independently co-amplified on the X, and their expansion is likely driven by conflicts over segregation. Co-amplified X/Y genes are highly expressed in testis, enriched for meiosis and RNAi functions, and are frequently targeted by small RNAs in testis. This suggests that their amplification is driven by X vs. Y antagonism for increased transmission, where sex chromosome drive suppression is likely mediated by sequence homology between the suppressor and distorter, through RNAi mechanism. Thus, our analysis suggests that newly emerged sex chromosomes are a battleground for sexual and meiotic conflict.
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61
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Kruger AN, Brogley MA, Huizinga JL, Kidd JM, de Rooij DG, Hu YC, Mueller JL. A Neofunctionalized X-Linked Ampliconic Gene Family Is Essential for Male Fertility and Equal Sex Ratio in Mice. Curr Biol 2019; 29:3699-3706.e5. [PMID: 31630956 DOI: 10.1016/j.cub.2019.08.057] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/25/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022]
Abstract
The mammalian sex chromosomes harbor an abundance of newly acquired ampliconic genes, although their functions require elucidation [1-9]. Here, we demonstrate that the X-linked Slx and Slxl1 ampliconic gene families represent mouse-specific neofunctionalized copies of a meiotic synaptonemal complex protein, Sycp3. In contrast to the meiotic role of Sycp3, CRISPR-loxP-mediated multi-megabase deletions of the Slx (5 Mb) and Slxl1 (2.3Mb) ampliconic regions result in post-meiotic defects, abnormal sperm, and male infertility. Males carrying Slxl1 deletions sire more male offspring, whereas males carrying Slx and Slxl1 duplications sire more female offspring, which directly correlates with Slxl1 gene dosage and gene expression levels. SLX and SLXL1 proteins interact with spindlin protein family members (SPIN1 and SSTY1/2) and males carrying Slxl1 deletions downregulate a sex chromatin modifier, Scml2, leading us to speculate that Slx and Slxl1 function in chromatin regulation. Our study demonstrates how newly acquired X-linked genes can rapidly evolve new and essential functions and how gene amplification can increase sex chromosome transmission.
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Affiliation(s)
- Alyssa N Kruger
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Michele A Brogley
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Jamie L Huizinga
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Dirk G de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands; Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Jacob L Mueller
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA.
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62
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Shi W, Massaia A, Louzada S, Handsaker J, Chow W, McCarthy S, Collins J, Hallast P, Howe K, Church DM, Yang F, Xue Y, Tyler-Smith C. Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome. Genome Biol 2019; 20:207. [PMID: 31610793 PMCID: PMC6790999 DOI: 10.1186/s13059-019-1816-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a result, they underlie many genomic disorders. Maintenance of the palindromic structure by gene conversion between the arms has been documented, but over longer time periods, palindromes are remarkably labile. Mechanisms of origin and loss of palindromes have, however, received little attention. RESULTS Here, we use fiber-FISH, 10x Genomics Linked-Read sequencing, and breakpoint PCR sequencing to characterize the structural variation of the P8 palindrome on the human Y chromosome, which contains two copies of the VCY (Variable Charge Y) gene. We find a deletion of almost an entire arm of the palindrome, leading to death of the palindrome, a size increase by recruitment of adjacent sequence, and other complex changes including the formation of an entire new palindrome nearby. Together, these changes are found in ~ 1% of men, and we can assign likely molecular mechanisms to these mutational events. As a result, healthy men can have 1-4 copies of VCY. CONCLUSIONS Gross changes, especially duplications, in palindrome structure can be relatively frequent and facilitate the evolution of sex chromosomes in humans, and potentially also in other mammalian species.
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Affiliation(s)
- Wentao Shi
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Andrea Massaia
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Present address: National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Sandra Louzada
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Juliet Handsaker
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - William Chow
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Shane McCarthy
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Present address: Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Joanna Collins
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Pille Hallast
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Institute of Biomedicine and Translational Medicine, University of Tartu, 51011, Tartu, Estonia
| | - Kerstin Howe
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Deanna M Church
- 10x Genomics, 7068 Koll Center Parkway, Suite 401, Pleasanton, CA, 94566, USA
- Present address: Inscripta Inc., 5500 Central Avenue #220, Boulder, CO, 80301, USA
| | - Fengtang Yang
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Yali Xue
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
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63
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Ellison C, Bachtrog D. Recurrent gene co-amplification on Drosophila X and Y chromosomes. PLoS Genet 2019; 15:e1008251. [PMID: 31329593 PMCID: PMC6690552 DOI: 10.1371/journal.pgen.1008251] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 08/12/2019] [Accepted: 06/18/2019] [Indexed: 12/19/2022] Open
Abstract
Y chromosomes often contain amplified genes which can increase dosage of male fertility genes and counteract degeneration via gene conversion. Here we identify genes with increased copy number on both X and Y chromosomes in various species of Drosophila, a pattern that has previously been associated with sex chromosome drive involving the Slx and Sly gene families in mice. We show that recurrent X/Y co-amplification appears to be an important evolutionary force that has shaped gene content evolution of sex chromosomes in Drosophila. We demonstrate that convergent acquisition and amplification of testis expressed gene families are common on Drosophila sex chromosomes, and especially on recently formed ones, and we carefully characterize one putative novel X/Y co-amplification system. We find that co-amplification of the S-Lap1/GAPsec gene pair on both the X and the Y chromosome occurred independently several times in members of the D. obscura group, where this normally autosomal gene pair is sex-linked due to a sex chromosome-autosome fusion. We explore several evolutionary scenarios that would explain this pattern of co-amplification. Investigation of gene expression and short RNA profiles at the S-Lap1/GAPsec system suggest that, like Slx/Sly in mice, these genes may be remnants of a cryptic sex chromosome drive system, however additional transgenic experiments will be necessary to validate this model. Regardless of whether sex chromosome drive is responsible for this co-amplification, our findings suggest that recurrent gene duplications between X and Y sex chromosomes could have a widespread effect on genomic and evolutionary patterns, including the epigenetic regulation of sex chromosomes, the distribution of sex-biased genes, and the evolution of hybrid sterility.
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Affiliation(s)
- Christopher Ellison
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
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64
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Baiz MD, Tucker PK, Cortés-Ortiz L. Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Mol Ecol 2019; 28:1056-1069. [PMID: 30582763 PMCID: PMC6888905 DOI: 10.1111/mec.14966] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 10/22/2018] [Indexed: 01/02/2023]
Abstract
Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by-product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analysing reduced-representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus-specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by-product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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65
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Abstract
Mammalian sex chromosomes evolved from an ordinary pair of autosomes. The X chromosome is highly conserved, whereas the Y chromosome varies among species in size, structure, and gene content. Unlike autosomes that contain randomly mixed collections of genes, the sex chromosomes are enriched in testis-biased genes related to sexual development and reproduction, particularly in spermatogenesis and male fertility. This review focuses on how sex chromosome dosage compensation takes place and why meiotic sex chromosome inactivation occurs during spermatogenesis. Furthermore, the review also emphasizes how testis-biased genes are enriched on the sex chromosomes and their functions in male fertility. It is concluded that sex chromosomes are critical to sexual development and male fertility; however, our understanding of how sex chromosome genes direct sexual development and fertility has been hampered by the structural complexities of the sex chromosomes and by the multicopy nature of the testis gene families that also play a role in immunity, cancer development, and brain function.
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Affiliation(s)
- Wan-Sheng Liu
- Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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66
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Maezawa S, Alavattam KG, Tatara M, Nagai R, Barski A, Namekawa SH. A rapidly evolved domain, the SCML2 DNA-binding repeats, contributes to chromatin binding of mouse SCML2†. Biol Reprod 2019; 100:409-419. [PMID: 30137219 DOI: 10.1093/biolre/ioy181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/20/2018] [Accepted: 08/16/2018] [Indexed: 11/14/2022] Open
Abstract
Genes involved in sexual reproduction diverge rapidly as a result of reproductive fitness. Here, we identify a novel protein domain in the germline-specific Polycomb protein SCML2 that is required for the establishment of unique gene expression programs after the mitosis-to-meiosis transition in spermatogenesis. We term this novel domain, which is comprised of rapidly evolved, DNA-binding repeat units of 28 amino acids, the SCML2 DNA-binding (SDB) repeats. These repeats are acquired in a specific subgroup of the rodent lineage, having been subjected to positive selection in the course of evolution. Mouse SCML2 has two DNA-binding domains: one is the SDB repeats and the other is an RNA-binding region, which is conserved in human SCML2. For the recruitment of SCML2 to target loci, the SDB repeats cooperate with the other functional domains of SCML2 to bind chromatin. The cooperative action of these domains enables SCML2 to sense DNA hypomethylation in an in vivo chromatin environment, thereby enabling SCML2 to bind to hypomethylated chromatin. We propose that the rapid evolution of SCML2 is due to reproductive adaptation, which has promoted species-specific gene expression programs in spermatogenesis.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mayu Tatara
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Rika Nagai
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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67
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Dumont BL, Williams CL, Ng BL, Horncastle V, Chambers CL, McGraw LA, Adams D, Mackay TFC, Breen M. Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American Voles. Genetics 2018; 210:83-97. [PMID: 30002081 PMCID: PMC6116968 DOI: 10.1534/genetics.118.301182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/07/2018] [Indexed: 11/18/2022] Open
Abstract
In most mammals, the X and Y chromosomes synapse and recombine along a conserved region of homology known as the pseudoautosomal region (PAR). These homology-driven interactions are required for meiotic progression and are essential for male fertility. Although the PAR fulfills key meiotic functions in most mammals, several exceptional species lack PAR-mediated sex chromosome associations at meiosis. Here, we leveraged the natural variation in meiotic sex chromosome programs present in North American voles (Microtus) to investigate the relationship between meiotic sex chromosome dynamics and X/Y sequence homology. To this end, we developed a novel, reference-blind computational method to analyze sparse sequencing data from flow-sorted X and Y chromosomes isolated from vole species with sex chromosomes that always (Microtus montanus), never (Microtus mogollonensis), and occasionally synapse (Microtus ochrogaster) at meiosis. Unexpectedly, we find more shared X/Y homology in the two vole species with no and sporadic X/Y synapsis compared to the species with obligate synapsis. Sex chromosome homology in the asynaptic and occasionally synaptic species is interspersed along chromosomes and largely restricted to low-complexity sequences, including a striking enrichment for the telomeric repeat sequence, TTAGGG. In contrast, homology is concentrated in high complexity, and presumably euchromatic, sequence on the X and Y chromosomes of the synaptic vole species, M. montanus Taken together, our findings suggest key conditions required to sustain the standard program of X/Y synapsis at meiosis and reveal an intriguing connection between heterochromatic repeat architecture and noncanonical, asynaptic mechanisms of sex chromosome segregation in voles.
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Affiliation(s)
- Beth L Dumont
- Initiative in Biological Complexity, North Carolina State University, Raleigh, North Carolina 04609
| | - Christina L Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 04609
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, United Kingdom, CB10 1SA
| | - Valerie Horncastle
- School of Forestry, Northern Arizona University, Flagstaff, Arizona 86011
| | - Carol L Chambers
- School of Forestry, Northern Arizona University, Flagstaff, Arizona 86011
| | - Lisa A McGraw
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 04609
| | - David Adams
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, United Kingdom, CB10 1SA
| | - Trudy F C Mackay
- Initiative in Biological Complexity, North Carolina State University, Raleigh, North Carolina 04609
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 04609
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 04609
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 04609
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 04609
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68
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Larson EL, Kopania EEK, Good JM. Spermatogenesis and the Evolution of Mammalian Sex Chromosomes. Trends Genet 2018; 34:722-732. [PMID: 30077434 PMCID: PMC6161750 DOI: 10.1016/j.tig.2018.06.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/23/2022]
Abstract
Developmental constraint and sexual conflict shape the evolution of heteromorphic sex chromosomes. These contrasting forces are perhaps strongest during spermatogenesis in species with XY males. In this review, we consider how the unique regulatory environment and selective pressures of spermatogenesis interact to impact sex chromosome evolution in mammals. We explore how each developmental phase of spermatogenesis influences sex chromosome gene content, structure, and rate of molecular evolution, and how these attributes may contribute to speciation. We argue that a developmental context is fundamental to understanding sex chromosome evolution and that an evolutionary perspective can shed new light on our understanding of sperm development.
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Affiliation(s)
- Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA.
| | - Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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69
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Iwamori T, Iwamori N, Matsumoto M, Ono E, Matzuk MM. Identification of KIAA1210 as a novel X-chromosome-linked protein that localizes to the acrosome and associates with the ectoplasmic specialization in testes. Biol Reprod 2018; 96:469-477. [PMID: 28203736 DOI: 10.1095/biolreprod.116.145458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/21/2016] [Accepted: 12/15/2016] [Indexed: 11/01/2022] Open
Abstract
Cell junctions are necessary for spermatogenesis, and there are numerous types of junctions in testis, such as blood–testis barrier, intercellular bridge, and ectoplasmic specialization (ES). The details of their functions and construction are still unknown. To identify a novel protein essential to the function of a cell junction, we enriched testis membrane protein and analyzed it using a proteomics approach. Here, we report a novel ES protein, which is encoded on the X chromosome and an ortholog of hypothetical human protein KIAA1210. KIAA1210 is expressed in testis predominantly, localized to the sex body in spermatocyte, acrosome, and near ES. Moreover, KIAA1210 possesses a topoisomerase 2 (TOP2)-associated protein PAT1 domain, a herpes simplex virus 1 (HSV-1) large tegument protein UL36 hypothetical domain, and a provisional DNA translocase FtsK domain. Using IP-proteomics with specific antibody to KIAA1210, we identified proteins including TOP2 isoforms as components of a complex with KIAA1210, in cell junctions in testis. The interaction between KIAA1210 and TOP2 was confirmed by two different proteomic analyses. Furthermore, immunofluorescence showed that KIAA1210 and TOP2B co-localize around the sex body in spermatocyte, apical ES, and residual bodies in elongated spermatids. Our findings suggest that KIAA1210 may be essential cell junction protein that interacts with TOP2B to regulate the dynamic change of chromatin structures during spermiogenesis.
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Affiliation(s)
- Tokuko Iwamori
- Department of Biomedicine, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Iwamori
- Department of Biomedicine, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Matsumoto
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Etsuro Ono
- Department of Biomedicine, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Martin M Matzuk
- Departments of Pathology and Immunology, Molecular and Cellular Biology, Molecular and Human Genetics, and Pharmacology, Center for Drug Discovery, and Center for Reproductive Medicine, Baylor College of Medicine, Houston, Texas, USA
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70
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Kruger AN, Ellison Q, Brogley MA, Gerlinger ER, Mueller JL. Male mice with large inversions or deletions of X-chromosome palindrome arms are fertile and express their associated genes during post-meiosis. Sci Rep 2018; 8:8985. [PMID: 29895860 PMCID: PMC5997626 DOI: 10.1038/s41598-018-27360-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/01/2018] [Indexed: 11/09/2022] Open
Abstract
Large (>10 kb) palindromic sequences are enriched on mammalian sex chromosomes. In mice, these palindromes harbor gene families (≥2 gene copies) expressed exclusively in post-meiotic testicular germ cells, a time when most single-copy sex-linked genes are transcriptionally repressed. This observation led to the hypothesis that palindromic structures or having ≥2 gene copies enable post-meiotic gene expression. We tested these hypotheses by using CRISPR to precisely engineer large (10’s of kb) inversions and deletions of X-chromosome palindrome arms for two regions that carry the mouse 4930567H17Rik and Mageb5 palindrome gene families. We found that 4930567H17Rik and Mageb5 gene expression is unaffected in mice carrying palindrome arm inversions and halved in mice carrying palindrome arm deletions. We assessed whether palindrome-associated genes were sensitive to reduced expression in mice carrying palindrome arm deletions. Male mice carrying palindrome arm deletions are fertile and show no defects in post-meiotic spermatogenesis. Together, these findings suggest palindromic structures on the sex chromosomes are not necessary for their associated genes to evade post-meiotic transcriptional repression and that these genes are not sensitive to reduced expression levels. Large sex chromosome palindromes may be important for other reasons, such as promoting gene conversion between palindrome arms.
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Affiliation(s)
- Alyssa N Kruger
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Quinn Ellison
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Michele A Brogley
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emma R Gerlinger
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jacob L Mueller
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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71
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Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations. Genetics 2018; 209:907-920. [PMID: 29769284 PMCID: PMC6028258 DOI: 10.1534/genetics.118.300826] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/15/2018] [Indexed: 11/18/2022] Open
Abstract
Ampliconic genes are multicopy genes often located on sex chromosomes and enriched for testis-expressed genes. Here, Lucotte et al. developed new bioinformatic approaches to investigate the ampliconic gene copy number and their coding... Ampliconic genes are multicopy, with the majority found on sex chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here, we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene. Our results reveal extensive standing variation in copy number both within and between human populations for several ampliconic genes. For the Y chromosome, we can infer multiple independent amplifications and losses of these gene copies even within closely related Y haplogroups, that diversified < 50,000 years ago. Moreover, X- and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that X- and Y-linked ampliconic genes with extensive CNV are significantly more expressed than genes with no CNV during meiotic sex chromosome inactivation (for both X and Y) and postmeiotic sex chromosome repression (for the Y chromosome only). While we cannot rule out that the XY-linked ampliconic genes are evolving neutrally, this study gives insights into the distribution of copy number within human populations and demonstrates an extremely fast turnover in copy number of these regions.
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72
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Sangrithi MN, Turner JMA. Mammalian X Chromosome Dosage Compensation: Perspectives From the Germ Line. Bioessays 2018; 40:e1800024. [PMID: 29756331 DOI: 10.1002/bies.201800024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/15/2018] [Indexed: 01/04/2023]
Abstract
Sex chromosomes are advantageous to mammals, allowing them to adopt a genetic rather than environmental sex determination system. However, sex chromosome evolution also carries a burden, because it results in an imbalance in gene dosage between females (XX) and males (XY). This imbalance is resolved by X dosage compensation, which comprises both X chromosome inactivation and X chromosome upregulation. X dosage compensation has been well characterized in the soma, but not in the germ line. Germ cells face a special challenge, because genome wide reprogramming erases epigenetic marks responsible for maintaining the X dosage compensated state. Here we explain how evolution has influenced the gene content and germ line specialization of the mammalian sex chromosomes. We discuss new research uncovering unusual X dosage compensation states in germ cells, which we postulate influence sexual dimorphisms in germ line development and cause infertility in individuals with sex chromosome aneuploidy.
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Affiliation(s)
- Mahesh N Sangrithi
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore.,Duke-NUS Graduate Medical School, Singapore, 119077, Singapore
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
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73
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Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, Decker JE, Dodman NH, Ginns EI, Grahn JC, Grahn RA, Haase B, Haggstrom J, Hamilton MJ, Helps CR, Kurushima JD, Lohi H, Longeri M, Malik R, Meurs KM, Montague MJ, Mullikin JC, Murphy WJ, Nilson SM, Pedersen NC, Peterson CB, Rusbridge C, Saif R, Shelton GD, Warren WC, Wasim M, Lyons LA. Applications and efficiencies of the first cat 63K DNA array. Sci Rep 2018; 8:7024. [PMID: 29728693 PMCID: PMC5935720 DOI: 10.1038/s41598-018-25438-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/16/2018] [Indexed: 12/02/2022] Open
Abstract
The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.
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Affiliation(s)
- Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Hasan Alhaddad
- Department of Biological Sciences, Kuwait University, Safat, Kuwait.
| | - Mona Abdi
- Department of Biological Sciences, Kuwait University, Safat, Kuwait
| | - Leslie H Bach
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,University of San Francisco, San Francisco, CA, USA
| | - Erica K Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Nicholas H Dodman
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Edward I Ginns
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennifer C Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Bianca Haase
- Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Jens Haggstrom
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michael J Hamilton
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Department of Biochemistry, University of California - Riverside, Riverside, CA, USA
| | | | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA.,Foothill College, Los Altos Hills, CA, USA
| | - Hannes Lohi
- Department of Veterinary Biosciences, Research Programs Unit, Molecular Neurology, University of Helsinki, and The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Richard Malik
- Centre for Veterinary Education, University of Sydney, New South Wales, Australia
| | - Kathryn M Meurs
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Michael J Montague
- Department of Neuroscience, Parelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA
| | - Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Carlyn B Peterson
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA, USA
| | - Clare Rusbridge
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Rashid Saif
- Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
| | - G Diane Shelton
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Muhammad Wasim
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO, USA.
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74
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Mršić G, Ozretić P, Crnjac J, Merkaš S, Sukser V, Račić I, Rožić S, Barbarić L, Popović M, Korolija M. Expanded Croatian 12 X-STR loci database with an overview of anomalous profiles. Forensic Sci Int Genet 2018; 34:249-256. [PMID: 29573605 DOI: 10.1016/j.fsigen.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/16/2018] [Accepted: 03/02/2018] [Indexed: 02/08/2023]
Abstract
In order to implement X-chromosome short tandem repeat (X-STR) typing into routine forensic practice, reference database of a given population should be established. Therefore we extended already published data with additional 397 blood samples from unrelated Croatian citizens, and analyzed the total of 995 samples (549 male and 446 female) typed by Investigator® Argus X-12 Kit. To test genetic homogeneity of consecutively processed five historic-cultural regions covering the entire national territory, we calculated pairwise Fst genetic distances between regions based on allele and full haplotype frequencies. Since the comparison did not yield any statistically significant difference, we integrated STR profile information from all regions and used the whole data set to calculate forensic parameters. The most informative marker is DXS10135 (polymorphism information content (PIC = 0.929) and the most informative linkage group (LG) is LG1 (PIC = 0.996). We confirmed linkage disequilibrium (LD) for seven marker pairs belonging to LG2, LG3 and LG4. By including LD information, we calculated cumulative power of discrimination that amounted to 0.999999999997 in females and 0.999999005 in males. We also compared Croatia with 13 European populations based on haplotype frequencies and detected no statistically significant Fst values after Bonferroni correction in any LG. Multi-dimensional scaling plot revealed tight grouping of four Croatian regions amongst populations of southern, central and northern Europe, with the exception of northern Croatia. In this study we gave the first extensive overview of aberrant profiles encountered during Investigator® Argus X-12 typing. We found ten profiles consistent with single locus duplication followed by tetranucleotide tract length polymorphism. Locus DXS10079 is by far the most frequently affected one, presumably mutated in eight samples. We also found four profiles consistent with X-chromosome aneuploidy (three profiles with XXX pattern and one profile with XXY pattern). In conclusion, we established integral forensic Croatian X-chromosome database, proved forensic pertinence of Investigator® Argus X-12 Kit for the entire Croatian population and identified locus DXS10079 as a potential duplication hotspot.
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Affiliation(s)
- Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Petar Ozretić
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Josip Crnjac
- University Department for Forensic Sciences, University of Split, Ruđera Boškovića 31, 21000 Split, Croatia
| | - Siniša Merkaš
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Viktorija Sukser
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Ivana Račić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Sara Rožić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Lucija Barbarić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova ulica 55, 10000 Zagreb, Croatia
| | - Marina Korolija
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia.
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75
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Krausz C, Cioppi F, Riera-Escamilla A. Testing for genetic contributions to infertility: potential clinical impact. Expert Rev Mol Diagn 2018. [PMID: 29540081 DOI: 10.1080/14737159.2018.1453358] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Male infertility affects about 7% of the general male population, and it is a multifactorial, polygenic pathological condition. Known genetic factors, accounting for about 20-25% of male factor infertility, are present in each etiological category: i) hypothalamic-pituitary axis dysfunction; ii) quantitative and qualitative alterations of spermatogenesis; iii) ductal obstruction/dysfunction. Areas covered: All routinely available genetic tests are described. Indication for testing for chromosomal anomalies and Y chromosome microdeletions is based on sperm count (severe oligozoospermia/azoospermia). Mutation screening in candidate genes is indicated in specific semen/testis phenotypes. In about 40% of infertile patients, the aetiology remains unknown ('idiopathic cases') and whole exome sequencing may reveal novel genetic causes. Expert commentary: Genetic testing is essential for its relevance in clinical decision-making. For instance, it helps to avoid unnecessary surgical or medical treatments and it may provide prediction for testicular sperm retrieval. The highest frequency of genetic anomalies is observed in severe spermatogenic impairment, which can be treated with in vitro fertilization (IVF). Given the risk of transmitting genetic disorders to the future offspring through IVF, the diagnosis of known and the discovery of novel genetic factors in idiopathic infertility is of outmost clinical importance.
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Affiliation(s)
- Csilla Krausz
- a Department of Experimental, Clinical and Biomedical Sciences Mario Serio, Sexual Medicine and Andrology Unit , University of Florence , Florence , Italy
| | - Francesca Cioppi
- a Department of Experimental, Clinical and Biomedical Sciences Mario Serio, Sexual Medicine and Andrology Unit , University of Florence , Florence , Italy
| | - Antoni Riera-Escamilla
- b Andrology Department , Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau) , Barcelona , Spain
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76
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Cost-effective high-throughput single-haplotype iterative mapping and sequencing for complex genomic structures. Nat Protoc 2018; 13:787-809. [PMID: 29565902 DOI: 10.1038/nprot.2018.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The reference sequences of structurally complex regions can be obtained only through highly accurate clone-based approaches. We and others have successfully used single-haplotype iterative mapping and sequencing (SHIMS) 1.0 to assemble structurally complex regions across the sex chromosomes of several vertebrate species and to allow for targeted improvements to the reference sequences of human autosomes. However, SHIMS 1.0 is expensive and time consuming, requiring resources that only a genome center can provide. Here we introduce SHIMS 2.0, an improved SHIMS protocol that allows even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library-preparation protocol, and taking advantage of inexpensive high-throughput short-read-sequencing technologies, a small laboratory with both molecular biology and bioinformatics experience can sequence and assemble 192 large-insert bacterial artificial chromosome (BAC) or fosmid clones in 1 week. In SHIMS 2.0, in contrast to other pooling strategies, each clone is sequenced with a unique barcode, thus enabling clones containing nearly identical sequences to be multiplexed in a single sequencing run and assembled separately. Relative to SHIMS 1.0, SHIMS 2.0 decreases the required cost and time by two orders of magnitude while preserving high sequencing accuracy.
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77
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Naqvi S, Bellott DW, Lin KS, Page DC. Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Genome Res 2018; 28:474-483. [PMID: 29449410 PMCID: PMC5880238 DOI: 10.1101/gr.230433.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/06/2018] [Indexed: 02/02/2023]
Abstract
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals. Preexisting heterogeneities in dosage sensitivity, manifesting as differences in the extent of miRNA-mediated repression, predicted either the retention of a Y homolog or the acquisition of XCI following Y gene decay. Analogous heterogeneities among avian Z-linked genes predicted either the retention of a W homolog or gene-specific dosage compensation following W gene decay. Genome-wide analyses of human copy number variation indicate that these heterogeneities consisted of sensitivity to both increases and decreases in dosage. We propose a model of XY/ZW evolution incorporating such preexisting dosage sensitivities in determining the evolutionary fates of individual genes. Our findings thus provide a more complete view of the role of dosage sensitivity in shaping the mammalian and avian sex chromosomes and reveal an important role for post-transcriptional regulatory sequences (miRNA target sites) in sex chromosome evolution.
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Affiliation(s)
- Sahin Naqvi
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Kathy S Lin
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
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78
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Abstract
Over the 180 My since their origin, the sex chromosomes of mammals have evolved a gene repertoire highly specialized for function in the male germline. The mouse Y chromosome is unique among mammalian Y chromosomes characterized to date in that it is large, gene-rich and euchromatic. Yet, little is known about its diversity in natural populations. Here, we take advantage of published whole-genome sequencing data to survey the diversity of sequence and copy number of sex-linked genes in three subspecies of house mice. Copy number of genes on the repetitive long arm of both sex chromosomes is highly variable, but sequence diversity in nonrepetitive regions is decreased relative to expectations based on autosomes. We use simulations and theory to show that this reduction in sex-linked diversity is incompatible with neutral demographic processes alone, but is consistent with recent positive selection on genes active during spermatogenesis. Our results support the hypothesis that the mouse sex chromosomes are engaged in ongoing intragenomic conflict.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
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79
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Shen Y, Xu J, Yang X, Liu Y, Ma Y, Yang D, Dong Q, Yang Y. Evidence for the involvement of the proximal copy of the MAGEA9 gene in Xq28-linked CNV67 specific to spermatogenic failure. Biol Reprod 2017; 96:610-616. [PMID: 28339631 DOI: 10.1093/biolre/iox006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/03/2017] [Indexed: 02/05/2023] Open
Abstract
Spermatogenic failure characterized by impaired sperm production is a common multifactorial disease with molecular and cytogenetic causes for its extreme phenotype that include azoospermia and severe oliogzoospermia. Recently, a high-resolution array-comparative genomic hybridization analysis of the X chromosome and a subsequent cohort study revealed three X-linked microdeletions (CNV64, CNV67, and CNV69) that were associated with decreased sperm production in a mixed group that included Spanish and Italian males. To confirm their spermatogenic effect, we examined the hemizygous deletions and copy dosage of the MAGE family member A9 (MAGEA9) gene, which is a potential X-linked candidate for the CNV67-related spermatogenic phenotype, to investigate their association with spermatogenic failure in 1722 Han males from southwest China. The individuals in this group consisted of 884 patients with idiopathic azoospermia/oliogzoospermia and 838 controls with normozoospermia. Our results showed that both CNV64 and CNV69 were more common in patients than in controls. Similar to that reported previously, the CNV67 was also identified as being specific to spermatogenic failure in our population, although it was rare. More importantly, the paralog ratio tests and sequence family variant analyses provided evidence that the CNV67 might cause a partial deletion of the proximal copy of the MAGEA9 and suggests that CNV67-related spermatogenic failure may be attributed to the functional defect of the Cancer/Testis gene. Our findings highlight the potential of the Xq-linked CNV67 to serve as a novel detection target in the etiological diagnosis of spermatogenic failure and male infertility, although its pathogenic mechanism remains to be elucidated.
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Affiliation(s)
- Ying Shen
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinyan Xu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiling Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongyi Ma
- Department of Jinxin Genetic Research, Jinjiang Maternal and Child Health Hospital, Chengdu, Sichuan, China
| | - Dong Yang
- Chengdu Reproductive Medicine Institute, Chengdu Women's and Children's Central Hospital, Chengdu, Sichuan, China
| | - Qiang Dong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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80
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Röpke A, Tüttelmann F. MECHANISMS IN ENDOCRINOLOGY: Aberrations of the X chromosome as cause of male infertility. Eur J Endocrinol 2017; 177:R249-R259. [PMID: 28611019 DOI: 10.1530/eje-17-0246] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/22/2017] [Accepted: 06/13/2017] [Indexed: 11/08/2022]
Abstract
Male infertility is most commonly caused by spermatogenetic failure, clinically noted as oligo- or a-zoospermia. Today, in approximately 20% of azoospermic patients, a causal genetic defect can be identified. The most frequent genetic causes of azoospermia (or severe oligozoospermia) are Klinefelter syndrome (47,XXY), structural chromosomal abnormalities and Y-chromosomal microdeletions. Consistent with Ohno's law, the human X chromosome is the most stable of all the chromosomes, but contrary to Ohno's law, the X chromosome is loaded with regions of acquired, rapidly evolving genes, which are of special interest because they are predominantly expressed in the testis. Therefore, it is not surprising that the X chromosome, considered as the female counterpart of the male-associated Y chromosome, may actually play an essential role in male infertility and sperm production. This is supported by the recent description of a significantly increased copy number variation (CNV) burden on both sex chromosomes in infertile men and point mutations in X-chromosomal genes responsible for male infertility. Thus, the X chromosome seems to be frequently affected in infertile male patients. Four principal X-chromosomal aberrations have been identified so far: (1) aneuploidy of the X chromosome as found in Klinefelter syndrome (47,XXY or mosaicism for additional X chromosomes). (2) Translocations involving the X chromosome, e.g. nonsyndromic 46,XX testicular disorders of sex development (XX-male syndrome) or X-autosome translocations. (3) CNVs affecting the X chromosome. (4) Point mutations disrupting X-chromosomal genes. All these are reviewed herein and assessed concerning their importance for the clinical routine diagnostic workup of the infertile male as well as their potential to shape research on spermatogenic failure in the next years.
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81
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Meyfour A, Pooyan P, Pahlavan S, Rezaei-Tavirani M, Gourabi H, Baharvand H, Salekdeh GH. Chromosome-Centric Human Proteome Project Allies with Developmental Biology: A Case Study of the Role of Y Chromosome Genes in Organ Development. J Proteome Res 2017; 16:4259-4272. [PMID: 28914051 DOI: 10.1021/acs.jproteome.7b00446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination. From an evolutionary perspective, Y chromosome has preserved 3% of ancestral genes compared to 98% preservation of the X chromosome based on Ohno's law. Male specific region of Y chromosome (MSY) contains genes that contribute to central dogma and govern the expression of various targets throughout the genome. One of the most well-known functions of MSY genes is to decide the male-specific characteristics including sex, testis formation, and spermatogenesis, which are majorly formed by ampliconic gene families. Beyond its role in sex-specific gonad development, MSY genes in coexpression with their X counterparts, as single copy and broadly expressed genes, inhibit haplolethality and play a key role in embryogenesis. The role of X-Y related gene mutations in the development of hereditary syndromes suggests an essential contribution of sex chromosome genes to development. MSY genes, solely and independent of their X counterparts and/or in association with sex hormones, have a considerable impact on organ development. In this Review, we present major recent findings on the contribution of MSY genes to gonad formation, spermatogenesis, and the brain, heart, and kidney development and discuss how Y chromosome proteome project may exploit developmental biology to find missing proteins.
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Affiliation(s)
- Anna Meyfour
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | - Paria Pooyan
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute , 19395-4644 Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Department of Developmental Biology, University of Science and Culture , 19395-4644 Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , 31535-1897 Karaj, Iran
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82
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Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res 2017; 27:849-864. [PMID: 28396521 PMCID: PMC5411779 DOI: 10.1101/gr.213611.116] [Citation(s) in RCA: 569] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/14/2017] [Indexed: 11/24/2022]
Abstract
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.
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Affiliation(s)
- Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Tina Graves-Lindsay
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Kerstin Howe
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Nathan Bouk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Hsiu-Chuan Chen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Paul A Kitts
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Derek Albracht
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Robert S Fulton
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Milinn Kremitzki
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Vincent Magrini
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Chris Markovic
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Sean McGrath
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | | | - Kate Auger
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - William Chow
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Joanna Collins
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Glenn Harden
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Timothy Hubbard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sarah Pelan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jared T Simpson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Glen Threadgold
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - James Torrance
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jonathan M Wood
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Paul Peluso
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Heng Li
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | | | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Richard K Wilson
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Deanna M Church
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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83
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Chen ZX, Oliver B, Zhang YE, Gao G, Long M. Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biol Evol 2017; 9:981-992. [PMID: 28338961 PMCID: PMC5398296 DOI: 10.1093/gbe/evx054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2017] [Indexed: 12/24/2022] Open
Abstract
Inverted duplicates are a type of repetitive DNA motifs consist of two copies of reverse complementary sequences separated by a spacer sequence. They can lead to genome instability and many may have no function, but some functional small RNAs are processed from hairpins transcribed from these elements. It is not clear whether the pervasive numbers of such elements in genomes, especially those of mammals, is the result of high generation rates of neutral or slightly deleterious duplication events or positive selection for functionality. To test the functionality of intergenic inverted duplicates without known functions, we used mirror duplicates, a type of repetitive DNA motifs with few reported functions and little potential to form hairpins when transcribed, as a nonfunctional control. We identified large numbers of inverted duplicates within intergenic regions of human and mouse genomes, as well as 19 other vertebrate genomes. Structure characterization of these inverted duplicates revealed higher proportion to form stable hairpins compared with converted mirror duplicates, suggesting that inverted duplicates may produce hairpin RNAs. Expression profiling across tissues demonstrated that 7.8% of human and 5.7% of mouse inverted duplicates were expressed even under strict criteria. We found that expressed inverted duplicates were more likely to be structurally stable than both unexpressed inverted duplicates and expressed converted mirror duplicates. By dating inverted duplicates in the vertebrate phylogenetic tree, we observed higher conservation of inverted duplicates than mirror duplicates. These observations support the notion that expressed inverted duplicates may be functional through forming hairpin RNAs.
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Affiliation(s)
- Zhen-Xia Chen
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, P.R. China.,National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.,Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, P.R. China
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China.,University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Ge Gao
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, P.R. China
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago
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84
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Abstract
X chromosome inactivation (XCI) is a dosage compensation process that was adopted by female mammals to balance gene dosage between XX females and XY males. XCI starts with the upregulation of the non-coding RNA Xist, after which most X-linked genes are silenced and acquire a repressive chromatin state. Even though the chromatin marks of the inactive X have been fairly well described, the mechanisms responsible for the initiation of XCI remain largely unknown. In this review, we discuss recent developments that revealed unexpected factors playing a role in XCI and that might be of crucial importance to understand the mechanisms responsible for the very first steps of this chromosome-wide gene-silencing event.
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Affiliation(s)
- Ines Pinheiro
- Mammalian Developmental Epigenetics Group (équipe labellisée La Ligue), Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 26 Rue d'Ulm, 11 75248 Paris Cedex 05, France
| | - Edith Heard
- Mammalian Developmental Epigenetics Group (équipe labellisée La Ligue), Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 26 Rue d'Ulm, 11 75248 Paris Cedex 05, France
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85
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Y chromosome palindromes and gene conversion. Hum Genet 2017; 136:605-619. [PMID: 28303348 DOI: 10.1007/s00439-017-1777-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/07/2017] [Indexed: 02/02/2023]
Abstract
The presence of large and near-identical inverted repeat sequences (called palindromes) is a common feature of the constitutively haploid sex chromosomes of different species. Despite the fact palindromes originated in a non-recombining context, they have evolved a strong recombinational activity in the form of abundant arm-to-arm gene conversion. Their independent appearance in different species suggests they can have a profound biological significance that has yet to be fully clarified. It has been theorized that natural selection may have favored palindromic organization of male-specific genes and that the establishment of intra-palindrome gene conversion has strong adaptive significance. Arm-to-arm gene conversion allows the efficient removal of deleterious mutations, increases the fixation rate of beneficial mutations and has played an important role in modulating the equilibrium between gene loss and acquisition during Y chromosome evolution. Additionally, a palindromic organization of duplicates could favor the formation of unusual chromatin structures and could optimize the use of gene conversion as a mechanism to maintain the structural integrity of male-specific genes. In this review, we describe the structural features of palindromes on mammalian sex chromosomes and summarize different hypotheses regarding palindrome evolution and the functional benefits of arm-to-arm gene conversion on the unique haploid portion of the nuclear genome.
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86
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Larson EL, Keeble S, Vanderpool D, Dean MD, Good JM. The Composite Regulatory Basis of the Large X-Effect in Mouse Speciation. Mol Biol Evol 2017; 34:282-295. [PMID: 27999113 PMCID: PMC6200130 DOI: 10.1093/molbev/msw243] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The disruption of meiotic sex chromosome inactivation (MSCI) has been proposed to be a major developmental mechanism underlying the rapid evolution of hybrid male sterility. We tested this idea by analyzing cell-specific gene expression across spermatogenesis in two lineages of house mice and their sterile and fertile reciprocal hybrids. We found pervasive disruption of sex chromosome gene expression in sterile hybrids at every stage of spermatogenesis. Failure of MSCI was developmentally preceded by increased silencing of autosomal genes, supporting the hypothesis that divergence at the hybrid incompatibility gene, Prdm9, results in increased rates of autosomal asynapsis which in turn triggers widespread silencing of unsynapsed chromatin. We also detected opposite patterns of postmeiotic overexpression or hyper-repression of the sex chromosomes in reciprocal hybrids, supporting the hypothesis that genomic conflict has driven functional divergence that leads to deleterious X-Y dosage imbalances in hybrids. Our developmental timeline also exposed more subtle patterns of mitotic misregulation on the X chromosome, a previously undocumented stage of spermatogenic disruption in this cross. These results indicate that multiple hybrid incompatibilities have converged on a common regulatory phenotype, the disrupted expression of the sex chromosomes during spermatogenesis. Collectively, these data reveal a composite regulatory basis to hybrid male sterility in mice that helps resolve the mechanistic underpinnings of the well-documented large X-effect in mice speciation. We propose that the inherent sensitivity of spermatogenesis to X-linked regulatory disruption has the potential to be a major driver of reproductive isolation in species with chromosomal sex determination.
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Affiliation(s)
- Erica L Larson
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT
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87
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Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet 2017; 49:387-394. [PMID: 28135246 PMCID: PMC5359078 DOI: 10.1038/ng.3778] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/29/2016] [Indexed: 12/14/2022]
Abstract
After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males ZZ, but in mammals females are XX and males XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly-expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction related genes on sex chromosomes may be specific to the male germ line.
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88
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Sangrithi MN, Royo H, Mahadevaiah SK, Ojarikre O, Bhaw L, Sesay A, Peters AHFM, Stadler M, Turner JMA. Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline. Dev Cell 2017; 40:289-301.e3. [PMID: 28132849 PMCID: PMC5300051 DOI: 10.1016/j.devcel.2016.12.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 11/01/2016] [Accepted: 12/27/2016] [Indexed: 12/02/2022]
Abstract
Somatic X dosage compensation requires two mechanisms: X inactivation balances X gene output between males (XY) and females (XX), while X upregulation, hypothesized by Ohno and documented in vivo, balances X gene with autosomal gene output. Whether X dosage compensation occurs in germ cells is unclear. We show that mouse and human germ cells exhibit non-canonical X dosage states that differ from the soma and between the sexes. Prior to genome-wide reprogramming, X upregulation is present, consistent with Ohno's hypothesis. Subsequently, however, it is erased. In females, erasure follows loss of X inactivation, causing X dosage excess. Conversely, in males, erasure leads to permanent X dosage decompensation. Sex chromosomally abnormal models exhibit a “sex-reversed” X dosage state: XX males, like XX females, develop X dosage excess, while XO females, like XY males, develop X dosage decompensation. Thus, germline X dosage compensation states are determined by X chromosome number, not phenotypic sex. These unexpected differences in X dosage compensation states between germline and soma offer unique perspectives on sex chromosome infertility. X dosage compensation in germ cells is reset during GWR PGCs exhibit X upregulation before GWR, in keeping with Ohno's hypothesis X upregulation is lost during GWR Mouse and human germ cells exhibit X dosage states that are sexually dimorphic
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Affiliation(s)
- Mahesh N Sangrithi
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK; UCL EGA Institute for Women's Health UCL, Medical School Building, 74 Huntley Street, London WC1E 6AU, UK
| | - Helene Royo
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Shantha K Mahadevaiah
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Obah Ojarikre
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Leena Bhaw
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Abdul Sesay
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Michael Stadler
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - James M A Turner
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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89
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Borgmann J, Tüttelmann F, Dworniczak B, Röpke A, Song HW, Kliesch S, Wilkinson MF, Laurentino S, Gromoll J. The human RHOX gene cluster: target genes and functional analysis of gene variants in infertile men. Hum Mol Genet 2016; 25:4898-4910. [PMID: 28171660 PMCID: PMC6281360 DOI: 10.1093/hmg/ddw313] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/06/2016] [Accepted: 09/08/2016] [Indexed: 12/30/2022] Open
Abstract
The X-linked reproductive homeobox (RHOX) gene cluster encodes transcription factors preferentially expressed in reproductive tissues. This gene cluster has important roles in male fertility based on phenotypic defects of Rhox-mutant mice and the finding that aberrant RHOX promoter methylation is strongly associated with abnormal human sperm parameters. However, little is known about the molecular mechanism of RHOX function in humans. Using gene expression profiling, we identified genes regulated by members of the human RHOX gene cluster. Some genes were uniquely regulated by RHOXF1 or RHOXF2/2B, while others were regulated by both of these transcription factors. Several of these regulated genes encode proteins involved in processes relevant to spermatogenesis; e.g. stress protection and cell survival. One of the target genes of RHOXF2/2B is RHOXF1, suggesting cross-regulation to enhance transcriptional responses. The potential role of RHOX in human infertility was addressed by sequencing all RHOX exons in a group of 250 patients with severe oligozoospermia. This revealed two mutations in RHOXF1 (c.515G > A and c.522C > T) and four in RHOXF2/2B (-73C > G, c.202G > A, c.411C > T and c.679G > A), of which only one (c.202G > A) was found in a control group of men with normal sperm concentration. Functional analysis demonstrated that c.202G > A and c.679G > A significantly impaired the ability of RHOXF2/2B to regulate downstream genes. Molecular modelling suggested that these mutations alter RHOXF2/F2B protein conformation. By combining clinical data with in vitro functional analysis, we demonstrate how the X-linked RHOX gene cluster may function in normal human spermatogenesis and we provide evidence that it is impaired in human male fertility.
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Affiliation(s)
- Jennifer Borgmann
- Centre of Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | | | | | | | - Hye-Won Song
- Department of Reproductive Medicine, University of California San Diego, La Jolla, USA
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | - Miles F. Wilkinson
- Department of Reproductive Medicine, University of California San Diego, La Jolla, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, USA
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and Andrology, University of Münster, Münster, Germany
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90
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Moretti C, Vaiman D, Tores F, Cocquet J. Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells. Epigenetics Chromatin 2016; 9:47. [PMID: 27795737 PMCID: PMC5081929 DOI: 10.1186/s13072-016-0099-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing persists to some extent in spermatids. Considering the many reports of XY-linked genes expressed and needed in the post-meiotic phase of mouse spermatogenesis, it is still unclear whether or not the mouse sex chromatin is a repressive or permissive environment, after meiosis. RESULTS To determine the transcriptional and chromatin state of the sex chromosomes after meiosis, we re-analyzed ten ChIP-Seq datasets performed on mouse round spermatids and four RNA-seq datasets from male germ cells purified at different stages of spermatogenesis. For this, we used the last version of the genome (mm10/GRCm38) and included reads that map to several genomic locations in order to properly interpret the high proportion of sex chromosome-encoded multicopy genes. Our study shows that coverage of active epigenetic marks H3K4me3 and Kcr is similar on the sex chromosomes and on autosomes. The post-meiotic sex chromatin nevertheless differs from autosomal chromatin in its enrichment in H3K9me3 and its depletion in H3K27me3 and H4 acetylation. We also identified a posttranslational modification, H3K27ac, which specifically accumulates on the Y chromosome. In parallel, we found that the X and Y chromosomes are enriched in genes expressed post-meiotically and display a higher proportion of spermatid-specific genes compared to autosomes. Finally, we observed that portions of chromosome 14 and of the sex chromosomes share specific features, such as enrichment in H3K9me3 and the presence of multicopy genes that are specifically expressed in round spermatids, suggesting that parts of chromosome 14 are under the same evolutionary constraints than the sex chromosomes. CONCLUSIONS Based on our expression and epigenomic studies, we conclude that, after meiosis, the mouse sex chromosomes are no longer silenced but are nevertheless regulated differently than autosomes and accumulate different chromatin marks. We propose that post-meiotic selective constraints are at the basis of the enrichment of spermatid-specific genes and of the peculiar chromatin composition of the sex chromosomes and of parts of chromosome 14.
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Affiliation(s)
- Charlotte Moretti
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Daniel Vaiman
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Frederic Tores
- INSERM U1163, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Julie Cocquet
- Institut National de la Sante et de la Recherche Medicale (INSERM) U1016, Institut Cochin, Paris, France ; Centre National de la Recherche Scientifique (CNRS), UMR8104, Paris, France ; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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91
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Carmell MA, Dokshin GA, Skaletsky H, Hu YC, van Wolfswinkel JC, Igarashi KJ, Bellott DW, Nefedov M, Reddien PW, Enders GC, Uversky VN, Mello CC, Page DC. A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes. eLife 2016; 5. [PMID: 27718356 PMCID: PMC5098910 DOI: 10.7554/elife.19993] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/05/2016] [Indexed: 12/17/2022] Open
Abstract
The advent of sexual reproduction and the evolution of a dedicated germline in multicellular organisms are critical landmarks in eukaryotic evolution. We report an ancient family of GCNA (germ cell nuclear antigen) proteins that arose in the earliest eukaryotes, and feature a rapidly evolving intrinsically disordered region (IDR). Phylogenetic analysis reveals that GCNA proteins emerged before the major eukaryotic lineages diverged; GCNA predates the origin of a dedicated germline by a billion years. Gcna gene expression is enriched in reproductive cells across eukarya - either just prior to or during meiosis in single-celled eukaryotes, and in stem cells and germ cells of diverse multicellular animals. Studies of Gcna-mutant C. elegans and mice indicate that GCNA has functioned in reproduction for at least 600 million years. Homology to IDR-containing proteins implicated in DNA damage repair suggests that GCNA proteins may protect the genomic integrity of cells carrying a heritable genome.
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Affiliation(s)
| | - Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | | | | | | | | | - Michael Nefedov
- BACPAC Resources, Children's Hospital Oakland, Oakland, United States
| | - Peter W Reddien
- Whitehead Institute, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - George C Enders
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - David C Page
- Whitehead Institute, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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92
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Widespread DNA hypomethylation and differential gene expression in Turner syndrome. Sci Rep 2016; 6:34220. [PMID: 27687697 PMCID: PMC5043230 DOI: 10.1038/srep34220] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/08/2016] [Indexed: 01/15/2023] Open
Abstract
Adults with 45,X monosomy (Turner syndrome) reflect a surviving minority since more than 99% of fetuses with 45,X monosomy die in utero. In adulthood 45,X monosomy is associated with increased morbidity and mortality, although strikingly heterogeneous with some individuals left untouched while others suffer from cardiovascular disease, autoimmune disease and infertility. The present study investigates the leukocyte DNAmethylation profile by using the 450K-Illumina Infinium assay and the leukocyte RNA-expression profile in 45,X monosomy compared with karyotypically normal female and male controls. We present results illustrating that genome wide X-chromosome RNA-expression profile, autosomal DNA-methylation profile, and the X-chromosome methylation profile clearly distinguish Turner syndrome from controls. Our results reveal genome wide hypomethylation with most differentially methylated positions showing a medium level of methylation. Contrary to previous studies, applying a single loci specific analysis at well-defined DNA loci, our results indicate that the hypomethylation extend to repetitive elements. We describe novel candidate genes that could be involved in comorbidity in TS and explain congenital urinary malformations (PRKX), premature ovarian failure (KDM6A), and aortic aneurysm formation (ZFYVE9 and TIMP1).
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93
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Abstract
Meiosis is essential for reproduction in sexually reproducing organisms. A key stage in meiosis is the synapsis of maternal and paternal homologous chromosomes, accompanied by exchange of genetic material to generate crossovers. A decade ago, studies found that when chromosomes fail to synapse, the many hundreds of genes housed within them are transcriptionally inactivated. This process, meiotic silencing, is conserved in all mammals studied to date, but its purpose is not yet defined. Here, I review the molecular genetics of meiotic silencing and consider the many potential functions that it could serve in the mammalian germ line. In addition, I discuss how meiotic silencing influences sex differences in meiotic infertility and the profound impact that meiotic silencing has had on the evolution of mammalian sex chromosomes.
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94
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Krausz C, Escamilla AR, Chianese C. Genetics of male infertility: from research to clinic. Reproduction 2016; 150:R159-74. [PMID: 26447148 DOI: 10.1530/rep-15-0261] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Male infertility is a multifactorial complex disease with highly heterogeneous phenotypic representation and in at least 15% of cases, this condition is related to known genetic disorders, including both chromosomal and single-gene alterations. In about 40% of primary testicular failure, the etiology remains unknown and a portion of them is likely to be caused by not yet identified genetic anomalies. During the last 10 years, the search for 'hidden' genetic factors was largely unsuccessful in identifying recurrent genetic factors with potential clinical application. The armamentarium of diagnostic tests has been implemented only by the screening for Y chromosome-linked gr/gr deletion in those populations for which consistent data with risk estimate are available. On the other hand, it is clearly demonstrated by both single nucleotide polymorphisms and comparative genomic hybridization arrays, that there is a rare variant burden (especially relevant concerning deletions) in men with impaired spermatogenesis. In the era of next generation sequencing (NGS), we expect to expand our diagnostic skills, since mutations in several hundred genes can potentially lead to infertility and each of them is likely responsible for only a small fraction of cases. In this regard, system biology, which allows revealing possible gene interactions and common biological pathways, will provide an informative tool for NGS data interpretation. Although these novel approaches will certainly help in discovering 'hidden' genetic factors, a more comprehensive picture of the etiopathogenesis of idiopathic male infertility will only be achieved by a parallel investigation of the complex world of gene environmental interaction and epigenetics.
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Affiliation(s)
- Csilla Krausz
- Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Antoni Riera Escamilla
- Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Chiara Chianese
- Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain
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95
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Ka S, Ahn H, Seo M, Kim H, Kim JN, Lee HJ. Status of dosage compensation of X chromosome in bovine genome. Genetica 2016; 144:435-44. [PMID: 27376899 DOI: 10.1007/s10709-016-9912-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 06/27/2016] [Indexed: 01/18/2023]
Abstract
Dosage compensation system with X chromosome upregulation and inactivation have evolved to overcome the genetic imbalance between sex chromosomes in both male and female of mammals. Although recent development of chromosome-wide technologies has allowed us to test X upregulation, discrete data processing and analysis methods draw disparate conclusions. A series of expression studies revealed status of dosage compensation in some species belonging to monotremes, marsupials, rodents and primates. However, X upregulation in the Artiodactyla order including cattle have not been studied yet. In this study, we surveyed the genome-wide transcriptional upregulation in X chromosome in cattle RNA-seq data using different gene filtration methods. Overall examination of RNA-seq data revealed that X chromosome in the pituitary gland expressed more genes than in other peripheral tissues, which was consistent with the previous results observed in human and mouse. When analyzed with globally expressed genes, a median X:A expression ratio was 0.94. The ratio of 1-to-1 ortholog genes between chicken and mammals, however, showed considerable reduction to 0.68. These results indicate that status of dosage compensation for cattle is not deviated from those found in rodents and primate, and this is consistent with the evolutionary history of cattle.
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Affiliation(s)
- Sojeong Ka
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeonju Ahn
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Minseok Seo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- C&K Genomics Inc., Seoul National University Research Park, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin Nam Kim
- C&K Genomics Inc., Seoul National University Research Park, Seoul, 08826, Republic of Korea.
| | - Hyun-Jeong Lee
- Animal Nutritional Physiology Team, National Institute of Animal Science, Jeonju, Jeollabuk-Do, 55365, Republic of Korea.
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96
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Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans. Genetics 2016; 204:355-69. [PMID: 27356611 DOI: 10.1534/genetics.116.190298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/27/2016] [Indexed: 01/31/2023] Open
Abstract
Dosage compensation mechanisms equalize the level of X chromosome expression between sexes. Yet the X chromosome is often enriched for genes exhibiting sex-biased, i.e., imbalanced expression. The relationship between X chromosome dosage compensation and sex-biased gene expression remains largely unexplored. Most studies determine sex-biased gene expression without distinguishing between contributions from X chromosome copy number (dose) and the animal's sex. Here, we uncoupled X chromosome dose from sex-specific gene regulation in Caenorhabditis elegans to determine the effect of each on X expression. In early embryogenesis, when dosage compensation is not yet fully active, X chromosome dose drives the hermaphrodite-biased expression of many X-linked genes, including several genes that were shown to be responsible for hermaphrodite fate. A similar effect is seen in the C. elegans germline, where X chromosome dose contributes to higher hermaphrodite X expression, suggesting that lack of dosage compensation in the germline may have a role in supporting higher expression of X chromosomal genes with female-biased functions in the gonad. In the soma, dosage compensation effectively balances X expression between the sexes. As a result, somatic sex-biased expression is almost entirely due to sex-specific gene regulation. These results suggest that lack of dosage compensation in different tissues and developmental stages allow X chromosome copy number to contribute to sex-biased gene expression and function.
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97
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Contrasting Levels of Molecular Evolution on the Mouse X Chromosome. Genetics 2016; 203:1841-57. [PMID: 27317678 DOI: 10.1534/genetics.116.186825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/08/2016] [Indexed: 11/18/2022] Open
Abstract
The mammalian X chromosome has unusual evolutionary dynamics compared to autosomes. Faster-X evolution of spermatogenic protein-coding genes is known to be most pronounced for genes expressed late in spermatogenesis, but it is unclear if these patterns extend to other forms of molecular divergence. We tested for faster-X evolution in mice spanning three different forms of molecular evolution-divergence in protein sequence, gene expression, and DNA methylation-across different developmental stages of spermatogenesis. We used FACS to isolate individual cell populations and then generated cell-specific transcriptome profiles across different stages of spermatogenesis in two subspecies of house mice (Mus musculus), thereby overcoming a fundamental limitation of previous studies on whole tissues. We found faster-X protein evolution at all stages of spermatogenesis and faster-late protein evolution for both X-linked and autosomal genes. In contrast, there was less expression divergence late in spermatogenesis (slower late) on the X chromosome and for autosomal genes expressed primarily in testis (testis-biased). We argue that slower-late expression divergence reflects strong regulatory constraints imposed during this critical stage of sperm development and that these constraints are particularly acute on the tightly regulated sex chromosomes. We also found slower-X DNA methylation divergence based on genome-wide bisulfite sequencing of sperm from two species of mice (M. musculus and M. spretus), although it is unclear whether slower-X DNA methylation reflects development constraints in sperm or other X-linked phenomena. Our study clarifies key differences in patterns of regulatory and protein evolution across spermatogenesis that are likely to have important consequences for mammalian sex chromosome evolution, male fertility, and speciation.
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Genetic Diversity on the Human X Chromosome Does Not Support a Strict Pseudoautosomal Boundary. Genetics 2016; 203:485-92. [PMID: 27010023 PMCID: PMC4858793 DOI: 10.1534/genetics.114.172692] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/11/2016] [Indexed: 11/18/2022] Open
Abstract
Unlike the autosomes, recombination between the X chromosome and the Y chromosome is often thought to be constrained to two small pseudoautosomal regions (PARs) at the tips of each sex chromosome. PAR1 spans the first 2.7 Mb of the proximal arm of the human sex chromosomes, whereas the much smaller PAR2 encompasses the distal 320 kb of the long arm of each sex chromosome. In addition to PAR1 and PAR2, there is a human-specific X-transposed region that was duplicated from the X to the Y chromosome. The X-transposed region is often not excluded from X-specific analyses, unlike the PARs, because it is not thought to routinely recombine. Genetic diversity is expected to be higher in recombining regions than in nonrecombining regions because recombination reduces the effect of linked selection. In this study, we investigated patterns of genetic diversity in noncoding regions across the entire X chromosome of a global sample of 26 unrelated genetic females. We found that genetic diversity in PAR1 is significantly greater than in the nonrecombining regions (nonPARs). However, rather than an abrupt drop in diversity at the pseudoautosomal boundary, there is a gradual reduction in diversity from the recombining through the nonrecombining regions, suggesting that recombination between the human sex chromosomes spans across the currently defined pseudoautosomal boundary. A consequence of recombination spanning this boundary potentially includes increasing the rate of sex-linked disorders (e.g., de la Chapelle) and sex chromosome aneuploidies. In contrast, diversity in PAR2 is not significantly elevated compared to the nonPARs, suggesting that recombination is not obligatory in PAR2. Finally, diversity in the X-transposed region is higher than in the surrounding nonPARs, providing evidence that recombination may occur with some frequency between the X and Y chromosomes in the X-transposed region.
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Hu YC, Namekawa SH. Functional significance of the sex chromosomes during spermatogenesis. Reproduction 2016; 149:R265-77. [PMID: 25948089 DOI: 10.1530/rep-14-0613] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mammalian sex chromosomes arose from an ordinary pair of autosomes. Over hundreds of millions of years, they have evolved into highly divergent X and Y chromosomes and have become increasingly specialized for male reproduction. Both sex chromosomes have acquired and amplified testis-specific genes, suggestive of roles in spermatogenesis. To understand how the sex chromosome genes participate in the regulation of spermatogenesis, we review genes, including single-copy, multi-copy, and ampliconic genes, whose spermatogenic functions have been demonstrated in mouse genetic studies. Sex chromosomes are subject to chromosome-wide transcriptional silencing in meiotic and postmeiotic stages of spermatogenesis. We also discuss particular sex-linked genes that escape postmeiotic silencing and their evolutionary implications. The unique gene contents and genomic structures of the sex chromosomes reflect their strategies to express genes at various stages of spermatogenesis and reveal the driving forces that shape their evolution.Free Chinese abstract: A Chinese translation of this abstract is freely available at http://www.reproduction-online.org/content/149/6/R265/suppl/DC1.Free Japanese abstract: A Japanese translation of this abstract is freely available at http://www.reproduction-online.org/content/149/6/R265/suppl/DC2.
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Affiliation(s)
- Yueh-Chiang Hu
- Division of Developmental BiologyDivision of Reproductive SciencesCincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Satoshi H Namekawa
- Division of Developmental BiologyDivision of Reproductive SciencesCincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA Division of Developmental BiologyDivision of Reproductive SciencesCincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
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Raudsepp T, Chowdhary BP. The Eutherian Pseudoautosomal Region. Cytogenet Genome Res 2016; 147:81-94. [PMID: 26730606 DOI: 10.1159/000443157] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
The pseudoautosomal region (PAR) is a unique segment of sequence homology between differentiated sex chromosomes where recombination occurs during meiosis. Molecular and functional properties of the PAR are distinctive from the autosomes and the remaining regions of the sex chromosomes. These include a higher rate of recombination than genome average, bias towards GC-substitutions and increased interindividual nucleotide divergence and mutations. As yet, the PAR has been physically demarcated in only 28 eutherian species representing 6 mammalian orders. Murid rodents have the smallest, gene-poorest and most diverged PARs. Other eutherian PARs are largely homologous but differ in size and gene content, being the smallest in equids and human/simian primates and much larger in other eutherians. Because pseudoautosomal genes escape X inactivation, their dosage changes with sex chromosome aneuploidies, whereas phenotypic effects of the latter depend on the size and gene content of the PAR. Thus, X monosomy is more viable in mice, humans and horses than in species with larger PARs. Presently, little is known about the functions of PAR genes in individual species, though human studies suggest their involvement in early embryonic development. The PAR is, thus, of evolutionary, genetic and biomedical significance and a 'research hotspot' in eutherian genomes.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, CVM, Texas A&M University, College Station, Tex., USA
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