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Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes. Proc Natl Acad Sci U S A 2019; 116:17916-17924. [PMID: 31427530 PMCID: PMC6731651 DOI: 10.1073/pnas.1900714116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The sources of human germline mutations are poorly understood. Part of the difficulty is that mutations occur very rarely, and so direct pedigree-based approaches remain limited in the numbers that they can examine. To address this problem, we consider the spectrum of low-frequency variants in a dataset (Genome Aggregation Database, gnomAD) of 13,860 human X chromosomes and autosomes. X-autosome differences are reflective of germline sex differences and have been used extensively to learn about male versus female mutational processes; what is less appreciated is that they also reflect chromosome-level biochemical features that differ between the X and autosomes. We tease these components apart by comparing the mutation spectrum in multiple genomic compartments on the autosomes and between the X and autosomes. In so doing, we are able to ascribe specific mutation patterns to replication timing and recombination and to identify differences in the types of mutations that accrue in males and females. In particular, we identify C > G as a mutagenic signature of male meiotic double-strand breaks on the X, which may result from late repair. Our results show how biochemical processes of damage and repair in the germline interact with sex-specific life history traits to shape mutation patterns on both the X chromosome and autosomes.
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Brien FD, Cloete SWP, Fogarty NM, Greeff JC, Hebart ML, Hiendleder S, Edwards JEH, Kelly JM, Kind KL, Kleemann DO, Plush KL, Miller DR. A review of the genetic and epigenetic factors affecting lamb survival. ANIMAL PRODUCTION SCIENCE 2014. [DOI: 10.1071/an13140] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Poor lamb survival pre-weaning is a major source of reproductive inefficiency in Australian sheep flocks. While nutrition and management options have been extensively researched and promoted to improve lamb survival, the present review focuses on the prospects for obtaining genetic gain and helps identify selection strategies for boosting such gains to improve overall reproductive efficiency in the Australian sheep industry. Estimated heritability for lamb survival using linear model analysis is low, although use of threshold models suggests that heritability could be higher, which, if true, could help explain the substantial genetic gains obtained in long-term selection experiments. Epigenetic mechanisms may hinder selection and quantitative trait-loci identification through confounding and/or masking genetic variances and co-variances. With sufficient information, these effects could be considered in genetic evaluations by identifying those components that are amenable to selection. Regarding indirect selection, finding effective criteria for improving lamb survival has proved elusive. Most measures of maternal behaviour, temperament and lambing difficulty researched are poorly correlated genetically with lamb survival. Of lamb behaviours and thermo-genic indicators studied, latency to bleat following handling by humans is moderately genetically correlated with lamb survival, as is neonatal rectal temperature. Industry application remains to be adequately explored for the more promising of these measures. Finally, in lieu of direct selection for lamb survival, there is merit in selecting for multiple-rearing ability or its equivalent, possibly with additional selection criteria for lamb survival and reproductive efficiency.
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Dynamic changes in paternal X-chromosome activity during imprinted X-chromosome inactivation in mice. Proc Natl Acad Sci U S A 2009; 106:5198-203. [PMID: 19273861 DOI: 10.1073/pnas.0810683106] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In mammals, X-chromosome dosage compensation is achieved by inactivating one of the two X chromosomes in females. In mice, X inactivation is initially imprinted, with inactivation of the paternal X (Xp) chromosome occurring during preimplantation development. One theory is that the Xp is preinactivated in female embryos, because of its previous silence during meiosis in the male germ line. The extent to which the Xp is active after fertilization and the exact time of onset of X-linked gene silencing have been the subject of debate. We performed a systematic, single-cell transcriptional analysis to examine the activity of the Xp chromosome for a panel of X-linked genes throughout early preimplantation development in the mouse. Rather than being preinactivated, we found the Xp to be fully active at the time of zygotic gene activation, with silencing beginning from the 4-cell stage onward. X-inactivation patterns were, however, surprisingly diverse between genes. Some loci showed early onset (4-8-cell stage) of X inactivation, and some showed extremely late onset (postblastocyst stage), whereas others were never fully inactivated. Thus, we show that silencing of some X-chromosomal regions occurs outside of the usual time window and that escape from X inactivation can be highly lineage specific. These results reveal that imprinted X inactivation in mice is far less concerted than previously thought and highlight the epigenetic diversity underlying the dosage compensation process during early mammalian development.
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Chiu RWK, Chim SSC, Wong IHN, Wong CSC, Lee WS, To KF, Tong JHM, Yuen RKC, Shum ASW, Chan JKC, Chan LYS, Yuen JWF, Tong YK, Weier JF, Ferlatte C, Leung TN, Lau TK, Lo KW, Lo YMD. Hypermethylation of RASSF1A in human and rhesus placentas. THE AMERICAN JOURNAL OF PATHOLOGY 2007; 170:941-50. [PMID: 17322379 PMCID: PMC1864885 DOI: 10.2353/ajpath.2007.060641] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The pseudomalignant nature of the placenta prompted us to search for tumor suppressor gene hypermethylation, a phenomenon widely reported in cancer, in the human placenta. Nine tumor suppressor genes were studied. Hypermethylation of the Ras association domain family 1 A (RASSF1A) gene was found in human placentas from all three trimesters of pregnancy but was absent in other fetal tissues. Hypermethylation of Rassf1 was similarly observed in placentas from the rhesus monkey but not the mouse. An inverse relationship between RASSF1A promoter methylation and gene expression was demonstrated by bisulfite sequencing of microdissected placental cells and immunohistochemical staining of placental tissue sections using an anti-RASSF1A antibody. Treatment of choriocarcinoma cell lines, JAR and JEG3, by 5-aza-2'-deoxycytidine and trichostatin A led to reduction in RASSF1A methylation but increased expression. These observations extend the analogy between the primate placenta and malignant tumors to the epigenetic level.
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Affiliation(s)
- Rossa W K Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, China
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Abstract
X chromosome inactivation is most commonly studied in the context of female mammalian development, where it performs an essential role in dosage compensation. However, another form of X-inactivation takes place in the male, during spermatogenesis, as germ cells enter meiosis. This second form of X-inactivation, called meiotic sex chromosome inactivation (MSCI) has emerged as a novel paradigm for studying the epigenetic regulation of gene expression. New studies have revealed that MSCI is a special example of a more general mechanism called meiotic silencing of unsynapsed chromatin (MSUC), which silences chromosomes that fail to pair with their homologous partners and, in doing so, may protect against aneuploidy in subsequent generations. Furthermore, failure in MSCI is emerging as an important etiological factor in meiotic sterility.
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Affiliation(s)
- James M A Turner
- Division of Stem Cell Biology and Developmental Genetics, MRC NIMR, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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Dantzer F, Mark M, Quenet D, Scherthan H, Huber A, Liebe B, Monaco L, Chicheportiche A, Sassone-Corsi P, de Murcia G, Ménissier-de Murcia J. Poly(ADP-ribose) polymerase-2 contributes to the fidelity of male meiosis I and spermiogenesis. Proc Natl Acad Sci U S A 2006; 103:14854-9. [PMID: 17001008 PMCID: PMC1595440 DOI: 10.1073/pnas.0604252103] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Besides the established central role of poly(ADP-ribose) polymerase-1 (Parp-1) and Parp-2 in the maintenance of genomic integrity, accumulating evidence indicates that poly(ADP-ribosyl)ation may modulate epigenetic modifications under physiological conditions. Here, we provide in vivo evidence for the pleiotropic involvement of Parp-2 in both meiotic and postmeiotic processes. We show that Parp-2-deficient mice exhibit severely impaired spermatogenesis, with a defect in prophase of meiosis I characterized by massive apoptosis at pachytene and metaphase I stages. Although Parp-2(-/-) spermatocytes exhibit normal telomere dynamics and normal chromosome synapsis, they display defective meiotic sex chromosome inactivation associated with derailed regulation of histone acetylation and methylation and up-regulated X- and Y-linked gene expression. Furthermore, a drastically reduced number of crossover-associated Mlh1 foci are associated with chromosome missegregation at metaphase I. Moreover, Parp-2(-/-) spermatids are severely compromised in differentiation and exhibit a marked delay in nuclear elongation. Altogether, our findings indicate that, in addition to its well known role in DNA repair, Parp-2 exerts essential functions during meiosis I and haploid gamete differentiation.
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Affiliation(s)
- Françoise Dantzer
- Intégrité du Génome, Unité Mixte de Recherche 7175, Ecole Supérieure de Biotechnologie de Strasbourg, F-67412 Illkirch, France.
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Turner JMA, Mahadevaiah SK, Ellis PJI, Mitchell MJ, Burgoyne PS. Pachytene Asynapsis Drives Meiotic Sex Chromosome Inactivation and Leads to Substantial Postmeiotic Repression in Spermatids. Dev Cell 2006; 10:521-9. [PMID: 16580996 DOI: 10.1016/j.devcel.2006.02.009] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Revised: 02/02/2006] [Accepted: 02/02/2006] [Indexed: 11/27/2022]
Abstract
Transcriptional silencing of the sex chromosomes during male meiosis (MSCI) is conserved among organisms with limited sex chromosome synapsis, including mammals. Since the 1990s the prevailing view has been that MSCI in mammals is transient, with sex chromosome reactivation occurring as cells exit meiosis. Recently, we found that any chromosome region unsynapsed during pachytene of male and female mouse meiosis is subject to transcriptional silencing (MSUC), and we hypothesized that MSCI is an inevitable consequence of this more general meiotic silencing mechanism. Here, we provide direct evidence that asynapsis does indeed drive MSCI. We also show that a substantial degree of transcriptional repression of the sex chromosomes is retained postmeiotically, and we provide evidence that this postmeiotic repression is a downstream consequence of MSCI/MSUC. While this postmeiotic repression occurs after the loss of MSUC-related proteins at the end of prophase, other histone modifications associated with transcriptional repression have by then become established.
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Affiliation(s)
- James M A Turner
- Division of Developmental Genetics and Stem Cell Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom.
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Abstract
The 3.5-day-old blastocyst-stage mouse embryo consists of two tissues and contains approximately 60 cells. This tiny structure has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome.
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Affiliation(s)
- Guy S Eakin
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA
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