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Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. Genetics 2024; 226:iyae013. [PMID: 38298127 PMCID: PMC10990422 DOI: 10.1093/genetics/iyae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/11/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates should not scale with a mother's age at her child's conception, since oocytes spend a mother's reproductive years arrested in meiosis II and undergo a fixed number of cell divisions that are independent of the age at ovulation. Yet, mirroring recent findings, we find that STR mutation rates covary with paternal and maternal age, implying that some STR mutations are caused by DNA damage in quiescent cells rather than polymerase slippage in replicating progenitor cells. These results echo the recent finding that DNA damage in oocytes is a significant source of de novo single nucleotide variants and corroborate evidence of STR expansion in postmitotic cells. However, we find that the maternal age effect is not confined to known hotspots of oocyte mutagenesis, nor are postzygotic mutations likely to contribute significantly. STR nucleotide composition demonstrates divergent effects on de novo mutation (DNM) rates between sexes. Unlike the paternal lineage, maternally derived DNMs at A/T STRs display a significantly greater association with maternal age than DNMs at G/C-containing STRs. These observations may suggest the mechanism and developmental timing of certain STR mutations and contradict prior attribution of replication slippage as the primary mechanism of STR mutagenesis.
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Affiliation(s)
- Michael E Goldberg
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - Michelle D Noyes
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Computational Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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2
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Harris M, Kim BY, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. Genetics 2024; 226:iyae019. [PMID: 38366786 PMCID: PMC10990427 DOI: 10.1093/genetics/iyae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across 6 commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
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Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nandita Garud
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
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3
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de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
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Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
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4
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Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573131. [PMID: 38187618 PMCID: PMC10769404 DOI: 10.1101/2023.12.22.573131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates should not scale with a mother's age at her child's conception, since oocytes spend a mother's reproductive years arrested in meiosis II and undergo a fixed number of cell divisions that are independent of the age at ovulation. Yet, mirroring recent findings, we find that STR mutation rates covary with paternal and maternal age, implying that some STR mutations are caused by DNA damage in quiescent cells rather than the classical mechanism of polymerase slippage in replicating progenitor cells. These results also echo the recent finding that DNA damage in quiescent oocytes is a significant source of de novo SNVs and corroborate evidence of STR expansion in postmitotic cells. However, we find that the maternal age effect is not confined to previously discovered hotspots of oocyte mutagenesis, nor are post-zygotic mutations likely to contribute significantly. STR nucleotide composition demonstrates divergent effects on DNM rates between sexes. Unlike the paternal lineage, maternally derived DNMs at A/T STRs display a significantly greater association with maternal age than DNMs at GC-containing STRs. These observations may suggest the mechanism and developmental timing of certain STR mutations and are especially surprising considering the prior belief in replication slippage as the dominant mechanism of STR mutagenesis.
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Affiliation(s)
- Michael E. Goldberg
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Departments of Human Genetics and Biomedical Informatics, University of Utah, 15 S 2030 E, Salt Lake City, UT, 84112
| | - Michelle D. Noyes
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Howard Hughes Medical Institute, 3720 15 Ave NE, University of Washington, Seattle, WA, 98195
| | - Aaron R. Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, 15 S 2030 E, Salt Lake City, UT, 84112
- These authors contributed equally to this work
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, 3720 15 Ave NE, Seattle, WA, 98195
- Computational Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109
- These authors contributed equally to this work
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5
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Harris M, Kim B, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545888. [PMID: 38106201 PMCID: PMC10723260 DOI: 10.1101/2023.06.21.545888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across six commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps, and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
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Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles California, United States of America
| | - Bernard Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Nandita Garud
- Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles California, United States of America
- Department of Human Genetics, University of California, Los Angeles, California, United States of America
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6
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Back G, Walther D. Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility. NAR Genom Bioinform 2023; 5:lqad097. [PMID: 37954573 PMCID: PMC10632188 DOI: 10.1093/nargab/lqad097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Mechanical properties of DNA have been implied to influence many of its biological functions. Recently, a new high-throughput method, called loop-seq, which allows measuring the intrinsic bendability of DNA fragments, has been developed. Using loop-seq data, we created a deep learning model to explore the biological significance of local DNA flexibility in a range of different species from different kingdoms. Consistently, we observed a characteristic and largely dinucleotide-composition-driven change of local flexibility near transcription start sites. In the presence of a TATA-box, a pronounced peak of high flexibility can be observed. Furthermore, depending on the transcription factor investigated, flanking-sequence-dependent DNA flexibility was identified as a potential factor influencing DNA binding. Compared to randomized genomic sequences, depending on species and taxa, actual genomic sequences were observed both with increased and lowered flexibility. Furthermore, in Arabidopsis thaliana, mutation rates, both de novo and fixed, were found to be associated with relatively rigid sequence regions. Our study presents a range of significant correlations between characteristic DNA mechanical properties and genomic features, the significance of which with regard to detailed molecular relevance awaits further theoretical and experimental exploration.
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Affiliation(s)
- Georg Back
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
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Hahn MW, Peña-Garcia Y, Wang RJ. The 'faulty male' hypothesis for sex-biased mutation and disease. Curr Biol 2023; 33:R1166-R1172. [PMID: 37989088 DOI: 10.1016/j.cub.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Biological differences between males and females lead to many differences in physiology, disease, and overall health. One of the most prominent disparities is in the number of germline mutations passed to offspring: human males transmit three times as many mutations as do females. While the classic explanation for this pattern invokes differences in post-puberty germline replication between the sexes, recent whole-genome evidence in humans and other mammals has cast doubt on this mechanism. Here, we review recent work that is inconsistent with a replication-driven model of male-biased mutation, and propose an alternative, 'faulty male' hypothesis. This model proposes that males are less able to repair and/or protect DNA from damage compared to females. Importantly, we suggest that this new model for male-biased mutation may also help to explain several pronounced differences between the sexes in cancer, aging, and DNA repair. Although the detailed contributions of genetic, epigenetic, and hormonal influences of biological sex on mutation remain to be fully understood, a reconsideration of the mechanisms underlying these differences will lead to a deeper understanding of evolution and disease.
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Affiliation(s)
- Matthew W Hahn
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA.
| | - Yadira Peña-Garcia
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA
| | - Richard J Wang
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA
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8
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Wang Y, Obbard DJ. Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis. Evol Lett 2023; 7:216-226. [PMID: 37475753 PMCID: PMC10355183 DOI: 10.1093/evlett/qrad027] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity-while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages-or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.
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Affiliation(s)
- Yiguan Wang
- Corresponding author: Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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9
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Transcriptional and mutational signatures of the Drosophila ageing germline. Nat Ecol Evol 2023; 7:440-449. [PMID: 36635344 PMCID: PMC10291629 DOI: 10.1038/s41559-022-01958-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/24/2022] [Indexed: 01/14/2023]
Abstract
Ageing is a complex biological process that is accompanied by changes in gene expression and mutational load. In many species, including humans, older fathers pass on more paternally derived de novo mutations; however, the cellular basis and cell types driving this pattern are still unclear. To explore the root causes of this phenomenon, we performed single-cell RNA sequencing on testes from young and old male Drosophila and genomic sequencing (DNA sequencing) on somatic tissues from the same flies. We found that early germ cells from old and young flies enter spermatogenesis with similar mutational loads but older flies are less able to remove mutations during spermatogenesis. Mutations in old cells may also increase during spermatogenesis. Our data reveal that old and young flies have distinct mutational biases. Many classes of genes show increased postmeiotic expression in the germlines of older flies. Late spermatogenesis-biased genes have higher dN/dS (ratio of non-synonymous to synonymous substitutions) than early spermatogenesis-biased genes, supporting the hypothesis that late spermatogenesis is a source of evolutionary innovation. Surprisingly, genes biased in young germ cells show higher dN/dS than genes biased in old germ cells. Our results provide new insights into the role of the germline in de novo mutation.
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10
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Kaltsas A, Moustakli E, Zikopoulos A, Georgiou I, Dimitriadis F, Symeonidis EN, Markou E, Michaelidis TM, Tien DMB, Giannakis I, Ioannidou EM, Papatsoris A, Tsounapi P, Takenaka A, Sofikitis N, Zachariou A. Impact of Advanced Paternal Age on Fertility and Risks of Genetic Disorders in Offspring. Genes (Basel) 2023; 14:486. [PMID: 36833413 PMCID: PMC9957550 DOI: 10.3390/genes14020486] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/01/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
The average age of fathers at first pregnancy has risen significantly over the last decade owing to various variables, including a longer life expectancy, more access to contraception, later marriage, and other factors. As has been proven in several studies, women over 35 years of age have an increased risk of infertility, pregnancy problems, spontaneous abortion, congenital malformations, and postnatal issues. There are varying opinions on whether a father's age affects the quality of his sperm or his ability to father a child. First, there is no single accepted definition of old age in a father. Second, much research has reported contradictory findings in the literature, particularly concerning the most frequently examined criteria. Increasing evidence suggests that the father's age contributes to his offspring's higher vulnerability to inheritable diseases. Our comprehensive literature evaluation shows a direct correlation between paternal age and decreased sperm quality and testicular function. Genetic abnormalities, such as DNA mutations and chromosomal aneuploidies, and epigenetic modifications, such as the silencing of essential genes, have all been linked to the father's advancing years. Paternal age has been shown to affect reproductive and fertility outcomes, such as the success rate of in vitro fertilisation (IVF), intracytoplasmic sperm injection (ICSI), and premature birth rate. Several diseases, including autism, schizophrenia, bipolar disorders, and paediatric leukaemia, have been linked to the father's advanced years. Therefore, informing infertile couples of the alarming correlations between older fathers and a rise in their offspring's diseases is crucial, so that they can be effectively guided through their reproductive years.
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Affiliation(s)
- Aris Kaltsas
- Laboratory of Spermatology, Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Efthalia Moustakli
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Athanasios Zikopoulos
- Laboratory of Spermatology, Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Ioannis Georgiou
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Fotios Dimitriadis
- Department of Urology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Evangelos N. Symeonidis
- Department of Urology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Eleftheria Markou
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Theologos M. Michaelidis
- Department of Biological Applications and Technologies, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45500 Ioannina, Greece
| | - Dung Mai Ba Tien
- Department of Andrology, Binh Dan Hospital, Ho chi Minh City 70000, Vietnam
| | - Ioannis Giannakis
- Laboratory of Spermatology, Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | | | - Athanasios Papatsoris
- 2nd Department of Urology, School of Medicine, Sismanoglio Hospital, National and Kapodistrian Univesity of Athens, 15126 Athens, Greece
| | - Panagiota Tsounapi
- Division of Urology, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Atsushi Takenaka
- Division of Urology, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Nikolaos Sofikitis
- Laboratory of Spermatology, Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Athanasios Zachariou
- Laboratory of Spermatology, Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
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11
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Sultanova Z, Downing PA, Carazo P. Genetic sex determination, sex chromosome size and sex-specific lifespans across tetrapods. J Evol Biol 2023; 36:480-494. [PMID: 36537352 PMCID: PMC10107984 DOI: 10.1111/jeb.14130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
Sex differences in lifespan are ubiquitous across the tree of life and exhibit broad taxonomic patterns that remain a puzzle, such as males living longer than females in birds and vice versa in mammals. The prevailing unguarded X hypothesis explains sex differences in lifespan by differential expression of recessive mutations on the X or Z chromosome of the heterogametic sex, but has only received indirect support to date. An alternative hypothesis is that the accumulation of deleterious mutations and repetitive elements on the Y or W chromosome might lower the survival of the heterogametic sex ('toxic Y' hypothesis). Here, we use a new database to report lower survival of the heterogametic relative to the homogametic sex across 136 species of birds, mammals, reptiles and amphibians, as expected if sex chromosomes shape sex-specific lifespans, and consistent with previous findings. We also found that the relative sizes of both the X and the Y chromosomes in mammals (but not the Z or the W chromosomes in birds) are associated with sex differences in lifespan, as predicted by the unguarded X and the 'toxic Y'. Furthermore, we report that the relative size of the Y is negatively associated with male lifespan in mammals, so that small Y size correlates with increased male lifespan. In theory, toxic Y effects are expected to be particularly strong in mammals, and we did not find similar effects in birds. Our results confirm the role of sex chromosomes in explaining sex differences in lifespan across tetrapods and further suggest that, at least in mammals, 'toxic Y' effects may play an important part in this role.
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Affiliation(s)
- Zahida Sultanova
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Philip A Downing
- Department of Biology, Lund University, Lund, Sweden.,Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Pau Carazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
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12
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Radzvilavicius AL, Johnston IG. Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys. Front Genet 2022; 13:974472. [PMID: 36386853 PMCID: PMC9650085 DOI: 10.3389/fgene.2022.974472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/11/2022] [Indexed: 07/09/2024] Open
Abstract
Bioenergetic organelles-mitochondria and plastids-retain their own genomes (mtDNA and ptDNA), and these organelle DNA (oDNA) molecules are vital for eukaryotic life. Like all genomes, oDNA must be able to evolve to suit new environmental challenges. However, mixed oDNA populations in cells can challenge cellular bioenergetics, providing a penalty to the appearance and adaptation of new mutations. Here we show that organelle "bottlenecks," mechanisms increasing cell-to-cell oDNA variability during development, can overcome this mixture penalty and facilitate the adaptation of beneficial mutations. We show that oDNA heteroplasmy and bottlenecks naturally emerge in evolutionary simulations subjected to fluctuating environments, demonstrating that this evolvability is itself evolvable. Usually thought of as a mechanism to clear damaging mutations, organelle bottlenecks therefore also resolve the tension between intracellular selection for pure cellular oDNA populations and the "bet-hedging" need for evolvability and adaptation to new environments. This general theory suggests a reason for the maintenance of organelle heteroplasmy in cells, and may explain some of the observed diversity in organelle maintenance and inheritance across taxa.
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Affiliation(s)
- Arunas L. Radzvilavicius
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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13
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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14
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de Manuel M, Wu FL, Przeworski M. A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell divisions. eLife 2022; 11:80008. [PMID: 35916372 PMCID: PMC9439683 DOI: 10.7554/elife.80008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
In humans and other mammals, germline mutations are more likely to arise in fathers than in mothers. Although this sex bias has long been attributed to DNA replication errors in spermatogenesis, recent evidence from humans points to the importance of mutagenic processes that do not depend on cell division, calling into question our understanding of this basic phenomenon. Here, we infer the ratio of paternal-to-maternal mutations, α, in 42 species of amniotes, from putatively neutral substitution rates of sex chromosomes and autosomes. Despite marked differences in gametogenesis, physiologies and environments across species, fathers consistently contribute more mutations than mothers in all the species examined, including mammals, birds, and reptiles. In mammals, α is as high as 4 and correlates with generation times; in birds and snakes, α appears more stable around 2. These observations are consistent with a simple model, in which mutations accrue at equal rates in both sexes during early development and at a higher rate in the male germline after sexual differentiation, with a conserved paternal-to-maternal ratio across species. Thus, α may reflect the relative contributions of two or more developmental phases to total germline mutations, and is expected to depend on generation time even if mutations do not track cell divisions.
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Affiliation(s)
- Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, United States
| | - Felix L Wu
- Department of Biological Sciences, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, United States
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15
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Ji YW, Ahn H, Shin KJ, Kim TI, Seo KY, Stulting RD, Kim EK. De Novo L509P Mutation of the TGFBI Gene Associated with Slit-Lamp Findings of Lattice Corneal Dystrophy Type IIIA. J Clin Med 2022; 11:jcm11113055. [PMID: 35683443 PMCID: PMC9181583 DOI: 10.3390/jcm11113055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Mutations of the transforming growth factor-β-induced (TGFBI) gene produce various types of corneal dystrophy. Here, we report a novel de novo L509P mutation not located in a known hot spot of the transforming growth factor-β-induced (TGFBI) gene and its clinical phenotype, which resembles that of lattice corneal dystrophy type IIIA (LCD IIIA). Case presentation: A 36-year-old man (proband) visited our clinic due to decreased visual acuity with intermittent ocular irritation in conjunction with painful recurrent erosions in both eyes for 10 years. Molecular genetic analyses revealed a TGFBI L509P mutation (c.1526T>C) in the proband and one of his sons. Interestingly, neither TGFBI mutations nor corneal abnormalities were detected in either of the proband’s biological parents, indicating the occurrence of a de novo L509P mutation. Clinical examinations, including slit-lamp retro-illumination and Fourier-domain anterior segment optical coherence tomography (FD-OCT), revealed gray deposits in the anterior stroma and deeper refractile lines extending from limbus to limbus in both corneas of the proband, consistent with a diagnosis of LCD IIIA. Superficial diffuse haze and surface irregularity were observed in conjunction with corneal erosions and visual impairment, necessitating phototherapeutic keratectomy (PTK). A 60 μm PTK of the Bowman layer and anterior stroma of the proband’s left eye was performed following the removal of the epithelium in order to remove superficial corneal opacities. His BCVA improved from 20/400 to 20/50 at postoperative week 8 and was maintained for 45 months. Pinhole-corrected VA was 20/20 at the last visit, and corneal opacities had not recurred. Conclusions: An inheritable de novo mutation of L509P in the TGFBI gene can produce severe LCD IIIA, which can be successfully treated with OCT-guided PRK.
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Affiliation(s)
- Yong Woo Ji
- Department of Ophthalmology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin 16995, Korea;
| | - Hyunmin Ahn
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (H.A.); (T.-i.K.); (K.Y.S.)
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Tae-im Kim
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (H.A.); (T.-i.K.); (K.Y.S.)
- Corneal Dystrophy Research Institute, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyoung Yul Seo
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Korea; (H.A.); (T.-i.K.); (K.Y.S.)
| | | | - Eung Kweon Kim
- Corneal Dystrophy Research Institute, Yonsei University College of Medicine, Seoul 03722, Korea
- Saevit Eye Hospital, Goyang 10447, Korea
- Correspondence:
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16
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Cavin L, Alvarez N. Why Coelacanths Are Almost “Living Fossils”? Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.896111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Gebert D, Neubert LK, Lloyd C, Gui J, Lehmann R, Teixeira FK. Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation. Mol Cell 2021; 81:3965-3978.e5. [PMID: 34352205 PMCID: PMC8516431 DOI: 10.1016/j.molcel.2021.07.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/23/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022]
Abstract
PIWI proteins and their guiding Piwi-interacting small RNAs (piRNAs) are crucial for fertility and transposon defense in the animal germline. In most species, the majority of piRNAs are produced from distinct large genomic loci, called piRNA clusters. It is assumed that germline-expressed piRNA clusters, particularly in Drosophila, act as principal regulators to control transposons dispersed across the genome. Here, using synteny analysis, we show that large clusters are evolutionarily labile, arise at loci characterized by recurrent chromosomal rearrangements, and are mostly species-specific across the Drosophila genus. By engineering chromosomal deletions in D. melanogaster, we demonstrate that the three largest germline clusters, which account for the accumulation of >40% of all transposon-targeting piRNAs in ovaries, are neither required for fertility nor for transposon regulation in trans. We provide further evidence that dispersed elements, rather than the regulatory action of large Drosophila germline clusters in trans, may be central for transposon defense.
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Affiliation(s)
- Daniel Gebert
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Lena K Neubert
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Catrin Lloyd
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Jinghua Gui
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ruth Lehmann
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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18
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Bergeron LA, Besenbacher S, Bakker J, Zheng J, Li P, Pacheco G, Sinding MHS, Kamilari M, Gilbert MTP, Schierup MH, Zhang G. The germline mutational process in rhesus macaque and its implications for phylogenetic dating. Gigascience 2021; 10:giab029. [PMID: 33954793 PMCID: PMC8099771 DOI: 10.1093/gigascience/giab029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/05/2021] [Accepted: 03/29/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. RESULTS Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ∼76× per individual and estimated a mean rate of 0.77 × 10-8de novo mutations per site per generation (95% CI: 0.69 × 10-8 to 0.85 × 10-8). By phasing 50% of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed a mean of 81% of the de novo mutations, with a trend of an increasing male contribution for older fathers. Approximately 3.5% of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated on the basis of the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecoidea/Hominoidea molecular divergence dated at 58 Mya using our new estimate of the yearly mutation rate. CONCLUSIONS When compared to the traditional molecular clock methods, new estimated rates from pedigree samples can provide insights into the evolution of well-studied groups such as primates.
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Affiliation(s)
- Lucie A Bergeron
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Brendstrupgårdsvej 21A, 8200 Aarhus N, Denmark
| | - Jaco Bakker
- Animal Science Department, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, Netherlands
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
| | - Panyi Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Mikkel-Holger S Sinding
- Department of genetics, Trinity College Dublin, 2 college green, D02 VF25, Dublin, Ireland
- Greenland Institute of Natural Resources, Kivioq 2, 3900 Nuuk, Greenland
| | - Maria Kamilari
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen K, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, C.F.Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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19
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Abstract
Genetic diseases cause numerous complex and intractable pathologies. DNA sequences encoding each human's complexity and many disease risks are contained in the mitochondrial genome, nuclear genome, and microbial metagenome. Diagnosis of these diseases has unified around applications of next-generation DNA sequencing. However, translating specific genetic diagnoses into targeted genetic therapies remains a central goal. To date, genetic therapies have fallen into three broad categories: bulk replacement of affected genetic compartments with a new exogenous genome, nontargeted addition of exogenous genetic material to compensate for genetic errors, and most recently, direct correction of causative genetic alterations using gene editing. Generalized methods of diagnosis, therapy, and reagent delivery into each genetic compartment will accelerate the next generations of curative genetic therapies. We discuss the structure and variability of the mitochondrial, nuclear, and microbial metagenomic compartments, as well as the historical development and current practice of genetic diagnostics and gene therapies targeting each compartment.
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Affiliation(s)
- Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, California 94143, USA; .,Department of Microbiology and Immunology and Diabetes Center, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.,Gladstone Institutes, San Francisco, California 94158, USA
| | - Alexander Marson
- Department of Microbiology and Immunology and Diabetes Center, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.,Gladstone Institutes, San Francisco, California 94158, USA.,Department of Medicine, University of California, San Francisco, California 94143, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, California 94129, USA.,Chan Zuckerberg Biohub, San Francisco, California 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
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20
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Jia X, Zhang Q, Jiang M, Huang J, Yu L, Traw MB, Tian D, Hurst LD, Yang S. Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation. PLoS Biol 2021; 19:e3001164. [PMID: 33750968 PMCID: PMC8016264 DOI: 10.1371/journal.pbio.3001164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 04/01/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
In contrast to common meiotic gene conversion, mitotic gene conversion, because it is so rare, is often ignored as a process influencing allelic diversity. We show that if there is a large enough number of premeiotic cell divisions, as seen in many organisms without early germline sequestration, such as plants, this is an unsafe position. From examination of 1.1 million rice plants, we determined that the rate of mitotic gene conversion events, per mitosis, is 2 orders of magnitude lower than the meiotic rate. However, owing to the large number of mitoses between zygote and gamete and because of long mitotic tract lengths, meiotic and mitotic gene conversion can be of approximately equivalent importance in terms of numbers of markers converted from zygote to gamete. This holds even if we assume a low number of premeiotic cell divisions (approximately 40) as witnessed in Arabidopsis. A low mitotic rate associated with long tracts is also seen in yeast, suggesting generality of results. For species with many mitoses between each meiotic event, mitotic gene conversion should not be overlooked. Gene conversion associated with meiosis has long been a focus of attention in population genomics, but mitotic conversion has been relatively overlooked as it was thought to be rare. Analysis in plants suggests that this could be a mistake; long tract lengths and multiple mitoses in species lacking germline sequestration suggest that mitotic conversion, although rare per mitosis, should not be ignored.
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Affiliation(s)
- Xianqing Jia
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Qijun Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Milton Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Dacheng Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sihai Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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21
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Singh RS, Singh KK, Singh SM. Origin of Sex-Biased Mental Disorders: An Evolutionary Perspective. J Mol Evol 2021; 89:195-213. [PMID: 33630117 PMCID: PMC8116267 DOI: 10.1007/s00239-021-09999-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/06/2021] [Indexed: 12/12/2022]
Abstract
Sexual dimorphism or sex bias in diseases and mental disorders have two biological causes: sexual selection and sex hormones. We review the role of sexual selection theory and bring together decades of molecular studies on the variation and evolution of sex-biased genes and provide a theoretical basis for the causes of sex bias in disease and health. We present a Sexual Selection-Sex Hormone theory and show that male-driven evolution, including sexual selection, leads to: (1) increased male vulnerability due to negative pleiotropic effects associated with male-driven sexual selection and evolution; (2) increased rates of male-driven mutations and epimutations in response to early fitness gains and at the cost of late fitness; and (3) enhanced female immunity due to antagonistic responses to mutations that are beneficial to males but harmful to females, reducing female vulnerability to diseases and increasing the thresholds for disorders such as autism. Female-driven evolution, such as reproduction-related fluctuation in female sex hormones in association with stress and social condition, has been shown to be associated with increased risk of certain mental disorders such as major depression disorder in women. Bodies have history, cells have memories. An evolutionary framework, such as the Sexual Selection–Sex Hormone theory, provides a historical perspective for understanding how the differences in the sex-biased diseases and mental disorders have evolved over time. It has the potential to direct the development of novel preventive and treatment strategies.
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Affiliation(s)
- Rama S Singh
- Department of Biology, McMaster University, Hamilton, Canada.
| | - Karun K Singh
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Canada.,Krembil Research Institute, University Health Network, Toronto, Canada
| | - Shiva M Singh
- Department of Biology, University of Western Ontario, London, Canada
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22
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Burian A. Does Shoot Apical Meristem Function as the Germline in Safeguarding Against Excess of Mutations? FRONTIERS IN PLANT SCIENCE 2021; 12:707740. [PMID: 34421954 PMCID: PMC8374955 DOI: 10.3389/fpls.2021.707740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/19/2021] [Indexed: 05/04/2023]
Abstract
A genetic continuity of living organisms relies on the germline which is a specialized cell lineage producing gametes. Essential in the germline functioning is the protection of genetic information that is subjected to spontaneous mutations. Due to indeterminate growth, late specification of the germline, and unique longevity, plants are expected to accumulate somatic mutations during their lifetime that leads to decrease in individual and population fitness. However, protective mechanisms, similar to those in animals, exist in plant shoot apical meristem (SAM) allowing plants to reduce the accumulation and transmission of mutations. This review describes cellular- and tissue-level mechanisms related to spatio-temporal distribution of cell divisions, organization of stem cell lineages, and cell fate specification to argue that the SAM functions analogous to animal germline.
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23
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Cai L, Xi Z, Lemmon EM, Lemmon AR, Mast A, Buddenhagen CE, Liu L, Davis CC. The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales. Syst Biol 2020; 70:491-507. [PMID: 33169797 DOI: 10.1093/sysbio/syaa083] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022] Open
Abstract
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0$\%$, 34.8$\%$, and 21.4$\%$ of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution. [Coalescent; concatenation; flanking region; hybrid enrichment, introgression; phylogenomics; rapid radiation, triplet frequency.].
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Affiliation(s)
- Liming Cai
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Austin Mast
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher E Buddenhagen
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
- AgResearch, 10 Bisley Road, Hamilton 3214, New Zealand
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
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24
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Wu FL, Strand AI, Cox LA, Ober C, Wall JD, Moorjani P, Przeworski M. A comparison of humans and baboons suggests germline mutation rates do not track cell divisions. PLoS Biol 2020; 18:e3000838. [PMID: 32804933 PMCID: PMC7467331 DOI: 10.1371/journal.pbio.3000838] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 09/02/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
In humans, most germline mutations are inherited from the father. This observation has been widely interpreted as reflecting the replication errors that accrue during spermatogenesis. If so, the male bias in mutation should be substantially lower in a closely related species with similar rates of spermatogonial stem cell divisions but a shorter mean age of reproduction. To test this hypothesis, we resequenced two 3-4 generation nuclear families (totaling 29 individuals) of olive baboons (Papio anubis), who reproduce at approximately 10 years of age on average, and analyzed the data in parallel with three 3-generation human pedigrees (26 individuals). We estimated a mutation rate per generation in baboons of 0.57×10-8 per base pair, approximately half that of humans. Strikingly, however, the degree of male bias in germline mutations is approximately 4:1, similar to that of humans-indeed, a similar male bias is seen across mammals that reproduce months, years, or decades after birth. These results mirror the finding in humans that the male mutation bias is stable with parental ages and cast further doubt on the assumption that germline mutations track cell divisions. Our mutation rate estimates for baboons raise a further puzzle, suggesting a divergence time between apes and Old World monkeys of 65 million years, too old to be consistent with the fossil record; reconciling them now requires not only a slowdown of the mutation rate per generation in humans but also in baboons.
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Affiliation(s)
- Felix L. Wu
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, New York, United States of America
| | - Alva I. Strand
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jeffrey D. Wall
- Institute for Human Genetics, Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
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25
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Wang RJ, Thomas GWC, Raveendran M, Harris RA, Doddapaneni H, Muzny DM, Capitanio JP, Radivojac P, Rogers J, Hahn MW. Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Res 2020; 30:826-834. [PMID: 32461224 PMCID: PMC7370888 DOI: 10.1101/gr.255174.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Mutation is the ultimate source of all genetic novelty and the cause of heritable genetic disorders. Mutational burden has been linked to complex disease, including neurodevelopmental disorders such as schizophrenia and autism. The rate of mutation is a fundamental genomic parameter and direct estimates of this parameter have been enabled by accurate comparisons of whole-genome sequences between parents and offspring. Studies in humans have revealed that the paternal age at conception explains most of the variation in mutation rate: Each additional year of paternal age in humans leads to approximately 1.5 additional inherited mutations. Here, we present an estimate of the de novo mutation rate in the rhesus macaque (Macaca mulatta) using whole-genome sequence data from 32 individuals in four large pedigrees. We estimated an average mutation rate of 0.58 × 10−8 per base pair per generation (at an average parental age of 7.5 yr), much lower than found in direct estimates from great apes. As in humans, older macaque fathers transmit more mutations to their offspring, increasing the per generation mutation rate by 4.27 × 10−10 per base pair per year. We found that the rate of mutation accumulation after puberty is similar between macaques and humans, but that a smaller number of mutations accumulate before puberty in macaques. We additionally investigated the role of paternal age on offspring sociability, a proxy for normal neurodevelopment, by studying 203 male macaques in large social groups.
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Affiliation(s)
- Richard J Wang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - John P Capitanio
- California National Primate Research Center, University of California-Davis, Davis, California 95616, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA.,Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
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26
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Acosta A, Martínez-Pacheco ML, Díaz-Barba K, Porras N, Gutiérrez-Mariscal M, Cortez D. Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias. Genome Biol Evol 2020; 11:3054-3067. [PMID: 31605487 PMCID: PMC6823514 DOI: 10.1093/gbe/evz221] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2019] [Indexed: 12/13/2022] Open
Abstract
The age of sex chromosomes is commonly obtained by comparing the substitution rates of XY gametologs. Coupled with phylogenetic reconstructions, one can refine the origin of a sex chromosome system relative to specific speciation events. However, these approaches are insufficient to determine the presence and duration of ancestral sex chromosome systems that were lost in some species. In this study, we worked with genomic and transcriptomic data from mammals and squamates and analyzed the effect of male mutation bias on X-linked sequences in these groups. We searched for signatures indicating whether monotremes shared the same sex chromosomes with placental mammals or whether pleurodonts and acrodonts had a common ancestral sex chromosome system. Our analyses indicate that platypus did not share the XY chromosomes with placental mammals, in agreement with previous work. In contrast, analyses of agamids showed that this lineage maintained the pleurodont XY chromosomes for several million years. We performed multiple simulations using different strengths of male mutation bias to confirm the results. Overall, our work shows that variations in substitution rates due to male mutation bias could be applied to uncover signatures of ancestral sex chromosome systems.
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Affiliation(s)
| | | | | | | | | | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
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27
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Barth NKH, Li L, Taher L. Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome. Genome Biol Evol 2020; 12:1-17. [PMID: 31950992 PMCID: PMC7093719 DOI: 10.1093/gbe/evaa004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: Redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become nonfunctional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue specificity as compared with other genes. Finally, we found that although enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.
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Affiliation(s)
- Nicolai K H Barth
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Lifei Li
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Leila Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
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28
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Evans JJ, Alkaisi MM, Sykes PH. Tumour Initiation: a Discussion on Evidence for a "Load-Trigger" Mechanism. Cell Biochem Biophys 2019; 77:293-308. [PMID: 31598831 PMCID: PMC6841748 DOI: 10.1007/s12013-019-00888-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/23/2019] [Indexed: 12/18/2022]
Abstract
Appropriate mechanical forces on cells are vital for normal cell behaviour and this review discusses the possibility that tumour initiation depends partly on the disruption of the normal physical architecture of the extracellular matrix (ECM) around a cell. The alterations that occur thence promote oncogene expression. Some questions, that are not answered with certainty by current consensus mechanisms of tumourigenesis, are elegantly explained by the triggering of tumours being a property of the physical characteristics of the ECM, which is operative following loading of the tumour initiation process with a relevant gene variant. Clinical observations are consistent with this alternative hypothesis which is derived from studies that have, together, accumulated an extensive variety of data incorporating biochemical, genetic and clinical findings. Thus, this review provides support for the view that the ECM may have an executive function in induction of a tumour. Overall, reported observations suggest that either restoring an ECM associated with homeostasis or targeting the related signal transduction mechanisms may possibly be utilised to modify or control the early progression of cancers. The review provides a coherent template for discussing the notion, in the context of contemporary knowledge, that tumourigenesis is an alliance of biochemistry, genetics and biophysics, in which the physical architecture of the ECM may be a fundamental component. For more definitive clarification of the concept there needs to be a phalanx of experiments conceived around direct questions that are raised by this paper.
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Affiliation(s)
- John J Evans
- Department of Obstetrics and Gynaecology, University of Otago Christchurch, Christchurch, New Zealand.
- MacDiarmid Institute of Advanced Materials and Nanotechnology, Christchurch, New Zealand.
| | - Maan M Alkaisi
- MacDiarmid Institute of Advanced Materials and Nanotechnology, Christchurch, New Zealand
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Peter H Sykes
- Department of Obstetrics and Gynaecology, University of Otago Christchurch, Christchurch, New Zealand
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29
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Álvarez-Escribano I, Sasse C, Bok JW, Na H, Amirebrahimi M, Lipzen A, Schackwitz W, Martin J, Barry K, Gutiérrez G, Cea-Sánchez S, Marcos AT, Grigoriev IV, Keller NP, Braus GH, Cánovas D. Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. BMC Biol 2019; 17:88. [PMID: 31711484 PMCID: PMC6844060 DOI: 10.1186/s12915-019-0702-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/19/2019] [Indexed: 01/19/2023] Open
Abstract
Background Aspergillus spp. comprises a very diverse group of lower eukaryotes with a high relevance for industrial applications and clinical implications. These multinucleate species are often cultured for many generations in the laboratory, which can unknowingly propagate hidden genetic mutations. To assess the likelihood of such events, we studied the genome stability of aspergilli by using a combination of mutation accumulation (MA) lines and whole genome sequencing. Results We sequenced the whole genomes of 30 asexual and 10 sexual MA lines of three Aspergillus species (A. flavus, A. fumigatus and A. nidulans) and estimated that each MA line accumulated mutations for over 4000 mitoses during asexual cycles. We estimated mutation rates of 4.2 × 10−11 (A. flavus), 1.1 × 10−11 (A. fumigatus) and 4.1 × 10−11 (A. nidulans) per site per mitosis, suggesting that the genomes are very robust. Unexpectedly, we found a very high rate of GC → TA transversions only in A. flavus. In parallel, 30 asexual lines of the non-homologous end-joining (NHEJ) mutants of the three species were also allowed to accumulate mutations for the same number of mitoses. Sequencing of these NHEJ MA lines gave an estimated mutation rate of 5.1 × 10−11 (A. flavus), 2.2 × 10−11 (A. fumigatus) and 4.5 × 10−11 (A. nidulans) per base per mitosis, which is slightly higher than in the wild-type strains and some ~ 5–6 times lower than in the yeasts. Additionally, in A. nidulans, we found a NHEJ-dependent interference of the sexual cycle that is independent of the accumulation of mutations. Conclusions We present for the first time direct counts of the mutation rate of filamentous fungal species and find that Aspergillus genomes are very robust. Deletion of the NHEJ machinery results in a slight increase in the mutation rate, but at a rate we suggest is still safe to use for biotechnology purposes. Unexpectedly, we found GC→TA transversions predominated only in the species A. flavus, which could be generated by the hepatocarcinogen secondary metabolite aflatoxin. Lastly, a strong effect of the NHEJ mutation in self-crossing was observed and an increase in the mutations of the asexual lines was quantified.
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Affiliation(s)
- Isidro Álvarez-Escribano
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - Christoph Sasse
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Gabriel Gutiérrez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Sara Cea-Sánchez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Ana T Marcos
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto para el Estudio de la Reproducción Humana (Inebir), Avda de la Cruz Roja 1, 41009, Sevilla, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.
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30
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Goldmann JM, Veltman JA, Gilissen C. De Novo Mutations Reflect Development and Aging of the Human Germline. Trends Genet 2019; 35:828-839. [PMID: 31610893 DOI: 10.1016/j.tig.2019.08.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 01/19/2023]
Abstract
Human germline de novo mutations (DNMs) are both a driver of evolution and an important cause of genetic diseases. In the past few years, whole-genome sequencing (WGS) of parent-offspring trios has facilitated the large-scale detection and study of human DNMs, which has led to exciting discoveries. The overarching theme of all of these studies is that the DNMs of an individual are a complex mixture of mutations that arise through different biological processes acting at different times during human development and life.
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Affiliation(s)
- J M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - J A Veltman
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK; Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands.
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31
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Lindsay SJ, Rahbari R, Kaplanis J, Keane T, Hurles ME. Similarities and differences in patterns of germline mutation between mice and humans. Nat Commun 2019; 10:4053. [PMID: 31492841 PMCID: PMC6731245 DOI: 10.1038/s41467-019-12023-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Whole genome sequencing (WGS) studies have estimated the human germline mutation rate per basepair per generation (~1.2 × 10−8) to be higher than in mice (3.5–5.4 × 10−9). In humans, most germline mutations are paternal in origin and numbers of mutations per offspring increase with paternal and maternal age. Here we estimate germline mutation rates and spectra in six multi-sibling mouse pedigrees and compare to three multi-sibling human pedigrees. In both species we observe a paternal mutation bias, a parental age effect, and a highly mutagenic first cell division contributing to the embryo. We also observe differences between species in mutation spectra, in mutation rates per cell division, and in the parental bias of mutations in early embryogenesis. These differences between species likely result from both species-specific differences in cellular genealogies of the germline, as well as biological differences within the same stage of embryogenesis or gametogenesis. Estimates of mutation rates differ between species. Here, Lindsay et al. perform side-by-side analyses of germline mutation rates using multi-sibling mouse and human pedigrees and find different mutation rates between species, also stratified by sex and temporal stage of mutation acquisition.
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Affiliation(s)
| | | | | | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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32
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Yehuda Y, Blumenfeld B, Mayorek N, Makedonski K, Vardi O, Cohen-Daniel L, Mansour Y, Baror-Sebban S, Masika H, Farago M, Berger M, Carmi S, Buganim Y, Koren A, Simon I. Germline DNA replication timing shapes mammalian genome composition. Nucleic Acids Res 2019; 46:8299-8310. [PMID: 29986092 PMCID: PMC6144785 DOI: 10.1093/nar/gky610] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/26/2018] [Indexed: 12/13/2022] Open
Abstract
Mammalian DNA replication is a highly organized and regulated process. Large, Mb-sized regions are replicated at defined times along S-phase. Replication Timing (RT) is thought to play a role in shaping the mammalian genome by affecting mutation rates. Previous analyses relied on somatic RT profiles. However, only germline mutations are passed on to offspring and affect genomic composition. Therefore, germ cell RT information is necessary to evaluate the influences of RT on the mammalian genome. We adapted the RT mapping technique for limited amounts of cells, and measured RT from two stages in the mouse germline - primordial germ cells (PGCs) and spermatogonial stem cells (SSCs). RT in germline cells exhibited stronger correlations to both mutation rate and recombination hotspots density than those of RT in somatic tissues, emphasizing the importance of using correct tissues-of-origin for RT profiling. Germline RT maps exhibited stronger correlations to additional genetic features including GC-content, transposable elements (SINEs and LINEs), and gene density. GC content stratification and multiple regression analysis revealed independent contributions of RT to SINE, gene, mutation, and recombination hotspot densities. Together, our results establish a central role for RT in shaping multiple levels of mammalian genome composition.
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Affiliation(s)
- Yishai Yehuda
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Bioinformatics, Jerusalem College of Technology, Jerusalem, Israel
| | - Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nina Mayorek
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Kirill Makedonski
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oriya Vardi
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Leonor Cohen-Daniel
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Yousef Mansour
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Shulamit Baror-Sebban
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hagit Masika
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marganit Farago
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Berger
- The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Koren
- Deptartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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33
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Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M. Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proc Natl Acad Sci U S A 2019; 116:9491-9500. [PMID: 31019089 PMCID: PMC6511033 DOI: 10.1073/pnas.1901259116] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The textbook view that most germline mutations in mammals arise from replication errors is indirectly supported by the fact that there are both more mutations and more cell divisions in the male than in the female germline. When analyzing large de novo mutation datasets in humans, we find multiple lines of evidence that call that view into question. Notably, despite the drastic increase in the ratio of male to female germ cell divisions after the onset of spermatogenesis, even young fathers contribute three times more mutations than young mothers, and this ratio barely increases with parental age. This surprising finding points to a substantial contribution of damage-induced mutations. Indeed, C-to-G transversions and CpG transitions, which together constitute over one-fourth of all base substitution mutations, show genomic distributions and sex-specific age dependencies indicative of double-strand break repair and methylation-associated damage, respectively. Moreover, we find evidence that maternal age at conception influences the mutation rate both because of the accumulation of damage in oocytes and potentially through an influence on the number of postzygotic mutations in the embryo. These findings reveal underappreciated roles of DNA damage and maternal age in the genesis of human germline mutations.
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Affiliation(s)
- Ziyue Gao
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305;
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Center for Computational Biology, University of California, Berkeley, CA 94720
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Guy Amster
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY 10027;
- Department of Systems Biology, Columbia University, New York, NY 10027
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34
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Repeat Instability in the Fragile X-Related Disorders: Lessons from a Mouse Model. Brain Sci 2019; 9:brainsci9030052. [PMID: 30832215 PMCID: PMC6468611 DOI: 10.3390/brainsci9030052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 12/21/2022] Open
Abstract
The fragile X-related disorders (FXDs) are a group of clinical conditions that result primarily from an unusual mutation, the expansion of a CGG-repeat tract in exon 1 of the FMR1 gene. Mouse models are proving useful for understanding many aspects of disease pathology in these disorders. There is also reason to think that such models may be useful for understanding the molecular basis of the unusual mutation responsible for these disorders. This review will discuss what has been learnt to date about mechanisms of repeat instability from a knock-in FXD mouse model and what the implications of these findings may be for humans carrying expansion-prone FMR1 alleles.
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35
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Ohno M. Spontaneous de novo germline mutations in humans and mice: rates, spectra, causes and consequences. Genes Genet Syst 2019; 94:13-22. [DOI: 10.1266/ggs.18-00015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Mizuki Ohno
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Science, Kyushu University
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36
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Abe H, Alavattam KG, Kato Y, Castrillon DH, Pang Q, Andreassen PR, Namekawa SH. CHEK1 coordinates DNA damage signaling and meiotic progression in the male germline of mice. Hum Mol Genet 2019; 27:1136-1149. [PMID: 29360988 DOI: 10.1093/hmg/ddy022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/09/2018] [Indexed: 12/22/2022] Open
Abstract
The continuity of life depends on mechanisms in the germline that ensure the integrity of the genome. The DNA damage response/checkpoint kinases ATM and ATR are essential signaling factors in the germline. However, it remains unknown how a downstream transducer, Checkpoint Kinase 1 (CHEK1 or CHK1), mediates signaling in the male germline. Here, we show that CHEK1 has distinct functions in both the mitotic and meiotic phases of the male germline in mice. In the mitotic phase, CHEK1 is required for the resumption of prospermatogonia proliferation after birth and the maintenance of spermatogonia. In the meiotic phase, we uncovered two functions for CHEK1: one is the stage-specific attenuation of DNA damage signaling on autosomes, and the other is coordination of meiotic stage progression. On autosomes, the loss of CHEK1 delays the removal of DNA damage signaling that manifests as phosphorylation of histone variant H2AX at serine 139 (γH2AX). Importantly, CHEK1 does not have a direct function in meiotic sex chromosome inactivation (MSCI), an essential event in male meiosis, in which ATR is a key regulator. Thus, the functions of ATR and CHEK1 are uncoupled in MSCI, in contrast to their roles in DNA damage signaling in somatic cells. Our study reveals stage-specific functions for CHEK1 that ensure the integrity of the male germline.
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Affiliation(s)
- Hironori Abe
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Yasuko Kato
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Diego H Castrillon
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qishen Pang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.,Division of Experimental Hematology & Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Paul R Andreassen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.,Division of Experimental Hematology & Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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Foldi CJ, Eyles DW, McGrath JJ, Burne THJ. Increasing paternal age alters anxiety-related behaviour in adult mice. GENES BRAIN AND BEHAVIOR 2018; 18:e12522. [DOI: 10.1111/gbb.12522] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Claire J. Foldi
- Queensland Brain Institute; The University of Queensland; St Lucia Queensland Australia
- Department of Physiology; Monash University; Clayton Victoria Australia
| | - Darryl W. Eyles
- Queensland Brain Institute; The University of Queensland; St Lucia Queensland Australia
- Queensland Centre for Mental Health Research; The Park Centre for Mental Health; Richlands Queensland Australia
| | - John J. McGrath
- Queensland Brain Institute; The University of Queensland; St Lucia Queensland Australia
- Queensland Centre for Mental Health Research; The Park Centre for Mental Health; Richlands Queensland Australia
| | - Thomas H. J. Burne
- Queensland Brain Institute; The University of Queensland; St Lucia Queensland Australia
- Queensland Centre for Mental Health Research; The Park Centre for Mental Health; Richlands Queensland Australia
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38
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Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE, Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW. Reproductive Longevity Predicts Mutation Rates in Primates. Curr Biol 2018; 28:3193-3197.e5. [PMID: 30270182 DOI: 10.1016/j.cub.2018.08.050] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Mutation rates vary between species across several orders of magnitude, with larger organisms having the highest per-generation mutation rates. Hypotheses for this pattern typically invoke physiological or population-genetic constraints imposed on the molecular machinery preventing mutations [1]. However, continuing germline cell division in multicellular eukaryotes means that organisms with longer generation times and of larger size will leave more mutations to their offspring simply as a byproduct of their increased lifespan [2, 3]. Here, we deeply sequence the genomes of 30 owl monkeys (Aotus nancymaae) from six multi-generation pedigrees to demonstrate that paternal age is the major factor determining the number of de novo mutations in this species. We find that owl monkeys have an average mutation rate of 0.81 × 10-8 per site per generation, roughly 32% lower than the estimate in humans. Based on a simple model of reproductive longevity that does not require any changes to the mutational machinery, we show that this is the expected mutation rate in owl monkeys. We further demonstrate that our model predicts species-specific mutation rates in other primates, including study-specific mutation rates in humans based on the average paternal age. Our results suggest that variation in life history traits alone can explain variation in the per-generation mutation rate among primates, and perhaps among a wide range of multicellular organisms.
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Affiliation(s)
- Gregg W C Thomas
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
| | - Richard J Wang
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Arthi Puri
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Lawrence E Williams
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christian R Abee
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, 201 Dowman Drive, Atlanta, GA, USA; Division of Infectious Diseases, Department of Medicine, Emory University, 201 Dowman Drive, Atlanta, GA, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
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Zhao XN, Usdin K. Timing of Expansion of Fragile X Premutation Alleles During Intergenerational Transmission in a Mouse Model of the Fragile X-Related Disorders. Front Genet 2018; 9:314. [PMID: 30147707 PMCID: PMC6096447 DOI: 10.3389/fgene.2018.00314] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022] Open
Abstract
Fragile X syndrome (FXS) is caused by the maternal expansion of an unstable CGG-repeat tract located in the first exon of the FMR1 gene. Further changes in repeat number occur during embryogenesis resulting in individuals sometimes being highly mosaic. Here we show in a mouse model that, in males, expansions are already present in primary spermatocytes with no additional expansions occurring in later stages of gametogenesis. We also show that, in females, expansion occurs in the post-natal oocyte. Additional expansions and a high frequency of large contractions are seen in two-cell stage embryos. Expansion in oocytes, which are non-dividing, would be consistent with a mechanism involving aberrant DNA repair or recombination rather than a problem with chromosomal replication. Given the difficulty of replicating large CGG-repeat tracts, we speculate that very large expanded alleles may be prone to contract in the mitotically proliferating spermatagonial stem cells in men. However, expanded alleles may not be under such pressure in the non-dividing oocyte. The high degree of both expansions and contractions seen in early embryos may contribute to the high frequency of somatic mosaicism that is observed in humans. Our data thus suggest an explanation for the fact that FXS is exclusively maternally transmitted and lend support to models for repeat expansion that are based on problems arising during DNA repair.
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Affiliation(s)
- Xiao-Nan Zhao
- Gene Structure and Disease Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Karen Usdin
- Gene Structure and Disease Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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40
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Morgan AP, Pardo-Manuel de Villena F. Sequence and Structural Diversity of Mouse Y Chromosomes. Mol Biol Evol 2018; 34:3186-3204. [PMID: 29029271 DOI: 10.1093/molbev/msx250] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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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41
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Impact of a gestational exposure to diesel exhaust on offspring gonadal development: experimental study in the rabbit. J Dev Orig Health Dis 2018; 9:519-529. [PMID: 29909796 DOI: 10.1017/s2040174418000351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The aim of the present work was to address experimentally the possible impact of exposure to air pollution during gestation on the differentiation and function of the gonads of the offspring using a rabbit model. Rabbits were exposed daily to diluted diesel exhaust gas or filtered air from the 3rd until the 27th day of gestation, during which time germ cells migrate in genital ridges and divide, and fetal sex is determined. Offspring gonads were collected shortly before birth (28th day of gestation) or after puberty (7.5 months after birth). The structure of the gonads was analyzed by histological and immunohistological methods. Serum concentrations of testosterone and anti-Müllerian hormone were determined using ELISA. The morphology and the endocrine function of the gonads collected just at the arrest of the exposure were similar in polluted and control animals in both sexes. No differences were observed as well in gonads collected after puberty. Sperm was collected at the head of the epididymis in adults. Sperm motility and DNA fragmentation were measured. Among all parameters analyzed, only the sperm DNA fragmentation rate was increased three-fold in exposed males. Mechanisms responsible for these modifications and their physiological consequences are to be further clarified.
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42
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Causes and evolutionary consequences of primordial germ-cell specification mode in metazoans. Proc Natl Acad Sci U S A 2018; 114:5784-5791. [PMID: 28584112 DOI: 10.1073/pnas.1610600114] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In animals, primordial germ cells (PGCs) give rise to the germ lines, the cell lineages that produce sperm and eggs. PGCs form in embryogenesis, typically by one of two modes: a likely ancestral mode wherein germ cells are induced during embryogenesis by cell-cell signaling (induction) or a derived mechanism whereby germ cells are specified by using germ plasm-that is, maternally specified germ-line determinants (inheritance). The causes of the shift to germ plasm for PGC specification in some animal clades remain largely unknown, but its repeated convergent evolution raises the question of whether it may result from or confer an innate selective advantage. It has been hypothesized that the acquisition of germ plasm confers enhanced evolvability, resulting from the release of selective constraint on somatic gene networks in embryogenesis, thus leading to acceleration of an organism's protein-sequence evolution, particularly for genes expressed at early developmental stages, and resulting in high speciation rates in germ plasm-containing lineages (denoted herein as the "PGC-specification hypothesis"). Although that hypothesis, if supported, could have major implications for animal evolution, our recent large-scale coding-sequence analyses from vertebrates and invertebrates provided important examples of genera that do not support the hypothesis of liberated constraint under germ plasm. Here, we consider reasons why germ plasm might be neither a direct target of selection nor causally linked to accelerated animal evolution. We explore alternate scenarios that could explain the repeated evolution of germ plasm and propose potential consequences of the inheritance and induction modes to animal evolutionary biology.
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43
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Pronounced maternal parent-of-origin bias for type-1 NF1 microdeletions. Hum Genet 2018; 137:365-373. [PMID: 29730711 DOI: 10.1007/s00439-018-1888-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/24/2018] [Indexed: 01/02/2023]
Abstract
Neurofibromatosis type 1 (NF1) is caused, in 4.7-11% of cases, by large deletions encompassing the NF1 gene and its flanking regions within 17q11.2. Different types of large NF1 deletion occur which are distinguishable by their breakpoint location and underlying mutational mechanism. Most common are the type-1 NF1 deletions of 1.4 Mb which exhibit recurrent breakpoints caused by nonallelic homologous recombination (NAHR), also termed unequal crossover. Here, we analyzed 37 unrelated families of patients with de novo type-1 NF1 deletions by means of short tandem repeat (STR) profiling to determine the parental origin of the deletions. We observed that 33 of the 37 type-1 deletions were of maternal origin (89.2% of cases; p < 0.0001). Analysis of the patients' siblings indicated that, in 14 informative cases, ten (71.4%) deletions resulted from interchromosomal unequal crossover during meiosis I. Our findings indicate a strong maternal parent-of-origin bias for type-1 NF1 deletions. A similarly pronounced maternal transmission bias has been reported for recurrent copy number variants (CNVs) within 16p11.2 associated with autism, but not so far for any other NAHR-mediated pathogenic CNVs. Region-specific genomic features are likely to be responsible for the maternal bias in the origin of both the 16p11.2 CNVs and type-1 NF1 deletions.
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44
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Charlesworth B, Campos JL, Jackson BC. Faster-X evolution: Theory and evidence from Drosophila. Mol Ecol 2018; 27:3753-3771. [PMID: 29431881 DOI: 10.1111/mec.14534] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 12/13/2022]
Abstract
A faster rate of adaptive evolution of X-linked genes compared with autosomal genes can be caused by the fixation of recessive or partially recessive advantageous mutations, due to the full expression of X-linked mutations in hemizygous males. Other processes, including recombination rate and mutation rate differences between X chromosomes and autosomes, may also cause faster evolution of X-linked genes. We review population genetics theory concerning the expected relative values of variability and rates of evolution of X-linked and autosomal DNA sequences. The theoretical predictions are compared with data from population genomic studies of several species of Drosophila. We conclude that there is evidence for adaptive faster-X evolution of several classes of functionally significant nucleotides. We also find evidence for potential differences in mutation rates between X-linked and autosomal genes, due to differences in mutational bias towards GC to AT mutations. Many aspects of the data are consistent with the male hemizygosity model, although not all possible confounding factors can be excluded.
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Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - José L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Benjamin C Jackson
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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45
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Link V, Aguilar-Gómez D, Ramírez-Suástegui C, Hurst LD, Cortez D. Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals. Genome Biol Evol 2018; 9:2198-2210. [PMID: 28922870 PMCID: PMC5604096 DOI: 10.1093/gbe/evx155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/12/2022] Open
Abstract
In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12–3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain >68% of these variations in monotremes, and in control species, rodents, and primates.
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Affiliation(s)
- Vivian Link
- Department of Biology, University of Fribourg, Switzerland
| | | | | | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Somerset, United Kingdom
| | - Diego Cortez
- Center for Genomic Sciences, UNAM, Cuernavaca, México
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46
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Lynch M, Blanchard J, Houle D, Kibota T, Schultz S, Vassilieva L, Willis J. PERSPECTIVE: SPONTANEOUS DELETERIOUS MUTATION. Evolution 2017; 53:645-663. [PMID: 28565627 DOI: 10.1111/j.1558-5646.1999.tb05361.x] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/1998] [Accepted: 01/25/1999] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Lynch
- Department of Biology; University of Oregon; Eugene Oregon 97403
| | - Jeff Blanchard
- Department of Biology; University of Oregon; Eugene Oregon 97403
| | - David Houle
- Department of Zoology; University of Toronto; Toronto Ontario M5S 1A1 Canada
| | - Travis Kibota
- Biology Department; Clark College; Vancouver Washington 98663
| | - Stewart Schultz
- Department of Biology; University of Miami; Coral Gables Florida 33124
| | | | - John Willis
- Department of Biology; University of Oregon; Eugene Oregon 97403
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47
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Differences between germline and somatic mutation rates in humans and mice. Nat Commun 2017; 8:15183. [PMID: 28485371 PMCID: PMC5436103 DOI: 10.1038/ncomms15183] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
The germline mutation rate has been extensively studied and has been found to vary greatly between species, but much less is known about the somatic mutation rate in multicellular organisms, which remains very difficult to determine. Here, we present data on somatic mutation rates in mice and humans, obtained by sequencing single cells and clones derived from primary fibroblasts, which allows us to make the first direct comparison with germline mutation rates in these two species. The results indicate that the somatic mutation rate is almost two orders of magnitude higher than the germline mutation rate and that both mutation rates are significantly higher in mice than in humans. Our findings demonstrate both the privileged status of germline genome integrity and species-specific differences in genome maintenance. Germline mutation rates are known to vary between species but somatic mutation rates are less well understood. Here the authors compare mice and humans, observing that somatic mutation rates were nearly two orders of magnitude higher in both species, with both mutation rates significantly higher in mice.
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48
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Ma R, Deng L, Xia Y, Wei X, Cao Y, Guo R, Zhang R, Guo J, Liang D, Wu L. A clear bias in parental origin of de novo pathogenic CNVs related to intellectual disability, developmental delay and multiple congenital anomalies. Sci Rep 2017; 7:44446. [PMID: 28322228 PMCID: PMC5359547 DOI: 10.1038/srep44446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/08/2017] [Indexed: 12/28/2022] Open
Abstract
Copy number variation (CNV) is of great significance in human evolution and disorders. Through tracing the parent-of-origin of de novo pathogenic CNVs, we are expected to investigate the relative contributions of germline genomic stability on reproductive health. In our study, short tandem repeat (STR) and single nucleotide polymorphism (SNP) were used to determine the parent-of-origin of 87 de novo pathogenic CNVs found in unrelated patients with intellectual disability (ID), developmental delay (DD) and multiple congenital anomalies (MCA). The results shown that there was a significant difference on the distribution of the parent-of-origin for different CNVs types (Chi-square test, p = 4.914 × 10−3). An apparently paternal bias existed in deletion CNVs and a maternal bias in duplication CNVs, indicating that the relative contribution of paternal germline variations is greater than that of maternal to the origin of deletions, and vice versa to the origin of duplications. By analyzing the sequences flanking the breakpoints, we also confirmed that non-allelic homologous recombination (NAHR) served as the major mechanism for the formation of recurrent CNVs whereas non-SDs-based mechanisms played a part in generating rare non-recurrent CNVs and might relate to the paternal germline bias in deletion CNVs.
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Affiliation(s)
- Ruiyu Ma
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Linbei Deng
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yan Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Xianda Wei
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Yingxi Cao
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Ruolan Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Rui Zhang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Jing Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Desheng Liang
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
| | - Lingqian Wu
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, P.R. China
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Abstract
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
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50
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Multiplex shRNA Screening of Germ Cell Development by in Vivo Transfection of Mouse Testis. G3-GENES GENOMES GENETICS 2017; 7:247-255. [PMID: 27856695 PMCID: PMC5217113 DOI: 10.1534/g3.116.036087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Spermatozoa are one of the few mammalian cell types that cannot be fully derived in vitro, severely limiting the application of modern genomic techniques to study germ cell biology. The current gold standard approach of characterizing single-gene knockout mice is slow as generation of each mutant line can take 6–9 months. Here, we describe an in vivo approach to rapid functional screening of germline genes based on a new nonsurgical, nonviral in vivo transfection method to deliver nucleic acids into testicular germ cells. By coupling multiplex transfection of short hairpin RNA (shRNA) constructs with pooled amplicon sequencing as a readout, we were able to screen many genes for spermatogenesis function in a quick and inexpensive experiment. We transfected nine mouse testes with a pilot pool of RNA interference (RNAi) against well-characterized genes to show that this system is highly reproducible and accurate. With a false negative rate of 18% and a false positive rate of 12%, this method has similar performance as other RNAi screens in the well-described Drosophila model system. In a separate experiment, we screened 26 uncharacterized genes computationally predicted to be essential for spermatogenesis and found numerous candidates for follow-up studies. Finally, as a control experiment, we performed a long-term selection screen in neuronal N2a cells, sampling shRNA frequencies at five sequential time points. By characterizing the effect of both libraries on N2a cells, we show that our screening results from testis are tissue-specific. Our calculations indicate that the current implementation of this approach could be used to screen thousands of protein-coding genes simultaneously in a single mouse testis. The experimental protocols and analysis scripts provided will enable other groups to use this procedure to study diverse aspects of germ cell biology ranging from epigenetics to cell physiology. This approach also has great promise as an applied tool for validating diagnoses made from medical genome sequencing, or designing synthetic biological sequences that can act as potent and highly specific male contraceptives.
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