51
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Larson EL, Kopania EEK, Hunnicutt KE, Vanderpool D, Keeble S, Good JM. Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids. G3 (BETHESDA, MD.) 2022; 12:jkab407. [PMID: 34864964 PMCID: PMC9210296 DOI: 10.1093/g3journal/jkab407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/16/2021] [Indexed: 01/09/2023]
Abstract
Hybrid sterility is a complex phenotype that can result from the breakdown of spermatogenesis at multiple developmental stages. Here, we disentangle two proposed hybrid male sterility mechanisms in the house mice, Mus musculus domesticus and M. m. musculus, by comparing patterns of gene expression in sterile F1 hybrids from a reciprocal cross. We found that hybrid males from both cross directions showed disrupted X chromosome expression during prophase of meiosis I consistent with a loss of meiotic sex chromosome inactivation (MSCI) and Prdm9-associated sterility, but that the degree of disruption was greater in mice with an M. m. musculus X chromosome consistent with previous studies. During postmeiotic development, gene expression on the X chromosome was only disrupted in one cross direction, suggesting that misexpression at this later stage was genotype-specific and not a simple downstream consequence of MSCI disruption which was observed in both reciprocal crosses. Instead, disrupted postmeiotic expression may depend on the magnitude of earlier disrupted MSCI, or the disruption of particular X-linked genes or gene networks. Alternatively, only hybrids with a potential deficit of Sly copies, a Y-linked ampliconic gene family, showed overexpression in postmeiotic cells, consistent with a previously proposed model of antagonistic coevolution between the X- and Y-linked ampliconic genes contributing to disrupted expression late in spermatogenesis. The relative contributions of these two regulatory mechanisms and their impact on sterility phenotypes await further study. Our results further support the hypothesis that X-linked hybrid sterility in house mice has a variable genetic basis, and that genotype-specific disruption of gene regulation contributes to overexpression of the X chromosome at different stages of development. Overall, these findings underscore the critical role of epigenetic regulation of the X chromosome during spermatogenesis and suggest that these processes are prone to disruption in hybrids.
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Affiliation(s)
- Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Kelsie E Hunnicutt
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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52
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Ramos L, Antunes A. Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes. Genomics 2022; 114:110277. [PMID: 35104609 DOI: 10.1016/j.ygeno.2022.110277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/28/2022]
Abstract
Sexual reproduction is a diverse and widespread process. In gonochoristic species, the differentiation of sexes occurs through diverse mechanisms, influenced by environmental and genetic factors. In most vertebrates, a master-switch gene is responsible for triggering a sex determination network. However, only a few genes have acquired master-switch functions, and this process is associated with the evolution of sex-chromosomes, which have a significant influence in evolution. Additionally, their highly repetitive regions impose challenges for high-quality sequencing, even using high-throughput, state-of-the-art techniques. Here, we review the mechanisms involved in sex determination and their role in the evolution of species, particularly vertebrates, focusing on sex chromosomes and the challenges involved in sequencing these genomic elements. We also address the improvements provided by the growth of sequencing projects, by generating a massive number of near-gapless, telomere-to-telomere, chromosome-level, phased assemblies, increasing the number and quality of sex-chromosome sequences available for further studies.
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Affiliation(s)
- Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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53
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Zhang X, Wagner S, Holleley CE, Deakin JE, Matsubara K, Deveson IW, O'Meally D, Patel HR, Ezaz T, Li Z, Wang C, Edwards M, Graves JAM, Georges A. Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation. Proc Natl Acad Sci U S A 2022; 119:e2116475119. [PMID: 35074916 PMCID: PMC8795496 DOI: 10.1073/pnas.2116475119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Pogona vitticeps has female heterogamety (ZZ/ZW), but the master sex-determining gene is unknown, as it is for all reptiles. We show that nr5a1 (Nuclear Receptor Subfamily 5 Group A Member 1), a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-nr5a1 and W-nr5a1), which are both expressed and can recombine. Three transcript isoforms of Z-nr5a1 were detected in gonads of adult ZZ males, two of which encode a functional protein. However, ZW females produced 16 isoforms, most of which contained premature stop codons. The array of transcripts produced by the W-borne allele (W-nr5a1) is likely to produce truncated polypeptides that contain a structurally normal DNA-binding domain and could act as a competitive inhibitor to the full-length intact protein. We hypothesize that an altered configuration of the W chromosome affects the conformation of the primary transcript generating inhibitory W-borne isoforms that suppress testis determination. Under this hypothesis, the genetic sex determination (GSD) system of P. vitticeps is a W-borne dominant female-determining gene that may be controlled epigenetically.
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Affiliation(s)
- Xiuwen Zhang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Susan Wagner
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Clare E Holleley
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
- Australian National Wildlife Collection, Commonwealth Scientific and Industrial Research Organisation, Crace, ACT 2911, Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Kazumi Matsubara
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Hardip R Patel
- Genome Sciences Department, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Zhao Li
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Chexu Wang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Melanie Edwards
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
- School of Life Sciences, La Trobe University, Bundoora, VIC 3186, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
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54
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Chang CH, Gregory LE, Gordon KE, Meiklejohn CD, Larracuente AM. Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes. eLife 2022; 11:e75795. [PMID: 34989337 PMCID: PMC8794474 DOI: 10.7554/elife.75795] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/18/2021] [Indexed: 02/06/2023] Open
Abstract
Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long-read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.
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Affiliation(s)
- Ching-Ho Chang
- Department of Biology, University of RochesterRochesterUnited States
| | - Lauren E Gregory
- Department of Biology, University of RochesterRochesterUnited States
| | - Kathleen E Gordon
- School of Biological Sciences, University of Nebraska-LincolnLincolnUnited States
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-LincolnLincolnUnited States
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55
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Sakamoto T, Innan H. Muller's ratchet of the Y chromosome with gene conversion. Genetics 2022; 220:iyab204. [PMID: 34791206 PMCID: PMC8733426 DOI: 10.1093/genetics/iyab204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Muller's ratchet is a process in which deleterious mutations are fixed irreversibly in the absence of recombination. The degeneration of the Y chromosome, and the gradual loss of its genes, can be explained by Muller's ratchet. However, most theories consider single-copy genes, and may not be applicable to Y chromosomes, which have a number of duplicated genes in many species, which are probably undergoing concerted evolution by gene conversion. We developed a model of Muller's ratchet to explore the evolution of the Y chromosome. The model assumes a nonrecombining chromosome with both single-copy and duplicated genes. We used analytical and simulation approaches to obtain the rate of gene loss in this model, with special attention to the role of gene conversion. Homogenization by gene conversion makes both duplicated copies either mutated or intact. The former promotes the ratchet, and the latter retards, and we ask which of these counteracting forces dominates under which conditions. We found that the effect of gene conversion is complex, and depends upon the fitness effect of gene duplication. When duplication has no effect on fitness, gene conversion accelerates the ratchet of both single-copy and duplicated genes. If duplication has an additive fitness effect, the ratchet of single-copy genes is accelerated by gene duplication, regardless of the gene conversion rate, whereas gene conversion slows the degeneration of duplicated genes. Our results suggest that the evolution of the Y chromosome involves several parameters, including the fitness effect of gene duplication by increasing dosage and gene conversion rate.
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Affiliation(s)
- Takahiro Sakamoto
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Hideki Innan
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
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56
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Teves ME, Roldan ERS. Sperm bauplan and function and underlying processes of sperm formation and selection. Physiol Rev 2022; 102:7-60. [PMID: 33880962 PMCID: PMC8812575 DOI: 10.1152/physrev.00009.2020] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 01/03/2023] Open
Abstract
The spermatozoon is a highly differentiated and polarized cell, with two main structures: the head, containing a haploid nucleus and the acrosomal exocytotic granule, and the flagellum, which generates energy and propels the cell; both structures are connected by the neck. The sperm's main aim is to participate in fertilization, thus activating development. Despite this common bauplan and function, there is an enormous diversity in structure and performance of sperm cells. For example, mammalian spermatozoa may exhibit several head patterns and overall sperm lengths ranging from ∼30 to 350 µm. Mechanisms of transport in the female tract, preparation for fertilization, and recognition of and interaction with the oocyte also show considerable variation. There has been much interest in understanding the origin of this diversity, both in evolutionary terms and in relation to mechanisms underlying sperm differentiation in the testis. Here, relationships between sperm bauplan and function are examined at two levels: first, by analyzing the selective forces that drive changes in sperm structure and physiology to understand the adaptive values of this variation and impact on male reproductive success and second, by examining cellular and molecular mechanisms of sperm formation in the testis that may explain how differentiation can give rise to such a wide array of sperm forms and functions.
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Affiliation(s)
- Maria Eugenia Teves
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Eduardo R S Roldan
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
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57
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Lukaszewicz A, Lange J, Keeney S, Jasin M. De novo deletions and duplications at recombination hotspots in mouse germlines. Cell 2021; 184:5970-5984.e18. [PMID: 34793701 PMCID: PMC8616837 DOI: 10.1016/j.cell.2021.10.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/10/2021] [Accepted: 10/27/2021] [Indexed: 11/23/2022]
Abstract
Numerous DNA double-strand breaks (DSBs) arise during meiosis to initiate homologous recombination. These DSBs are usually repaired faithfully, but here, we uncover a distinct type of mutational event in which deletions form via joining of ends from two closely spaced DSBs (double cuts) within a single hotspot or at adjacent hotspots on the same or different chromatids. Deletions occur in normal meiosis but are much more frequent when DSB formation is dysregulated in the absence of the ATM kinase. Events between chromosome homologs point to multi-chromatid damage and aborted gap repair. Some deletions contain DNA from other hotspots, indicating that double cutting at distant sites creates substrates for insertional mutagenesis. End joining at double cuts can also yield tandem duplications or extrachromosomal circles. Our findings highlight the importance of DSB regulation and reveal a previously hidden potential for meiotic mutagenesis that is likely to affect human health and genome evolution.
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Affiliation(s)
- Agnieszka Lukaszewicz
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Memorial Sloan Kettering Cancer Center, Howard Hughes Medical Institute, New York, NY 10065, USA.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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58
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Bonito M, D’Atanasio E, Ravasini F, Cariati S, Finocchio A, Novelletto A, Trombetta B, Cruciani F. New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion. Hum Mol Genet 2021; 30:2272-2285. [PMID: 34244762 PMCID: PMC8600007 DOI: 10.1093/hmg/ddab189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
About one-quarter of the euchromatic portion of the male-specific region of the human Y chromosome consists of large duplicated sequences that are organized in eight palindromes (termed P1-P8), which undergo arm-to arm gene conversion, a proposed mechanism for maintaining their sequence integrity. Although the relevance of gene conversion in the evolution of palindromic sequences has been profoundly recognized, the dynamic of this mechanism is still nuanced. To shed light into the evolution of these genomic elements, we performed a high-depth (50×) targeted next-generation sequencing of the palindrome P6 in 157 subjects belonging to the most divergent evolutionary lineages of the Y chromosome. We found 118 new paralogous sequence variants, which were placed into the context of a robust Y chromosome phylogeny based on 7240 SNPs of the X-degenerate region. We mapped along the phylogeny 80 gene conversion events that shaped the diversity of P6 arms during recent human history. In contrast to previous studies, we demonstrated that arm-to-arm gene conversion, which occurs at a rate of 6.01 × 10 -6 conversions/base/year, is not biased toward the retention of the ancestral state of sequences. We also found a significantly lower mutation rate of the arms (6.18 × 10-10 mutations/base/year) compared with the spacer (9.16 × 10-10 mutations/base/year), a finding that may explain the observed higher inter-species conservation of arms, without invoking any bias of conversion. Finally, by formally testing the mutation/conversion balance in P6, we found that the arms of this palindrome reached a steady-state equilibrium between mutation and gene conversion.
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Affiliation(s)
- Maria Bonito
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Eugenia D’Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 0185, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Selene Cariati
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Andrea Finocchio
- Department of Biology, University of Rome Tor Vergata, Rome 0133, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome Tor Vergata, Rome 0133, Italy
| | - Beniamino Trombetta
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
- Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 0185, Italy
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59
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Haines BA, Barradale F, Dumont BL. Patterns and mechanisms of sex ratio distortion in the Collaborative Cross mouse mapping population. Genetics 2021; 219:6355587. [PMID: 34740238 DOI: 10.1093/genetics/iyab136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022] Open
Abstract
In species with single-locus, chromosome-based mechanisms of sex determination, the laws of segregation predict an equal ratio of females to males at birth. Here, we show that departures from this Mendelian expectation are commonplace in the 8-way recombinant inbred Collaborative Cross (CC) mouse population. More than one-third of CC strains exhibit significant sex ratio distortion (SRD) at wean, with twice as many male-biased than female-biased strains. We show that these pervasive sex biases persist across multiple breeding environments, are stable over time, and are not mediated by random maternal effects. SRD exhibits a heritable component, but QTL mapping analyses fail to nominate any large effect loci. These findings, combined with the reported absence of sex ratio biases in the CC founder strains, suggest that SRD manifests from multilocus combinations of alleles only uncovered in recombined CC genomes. We explore several potential complex genetic mechanisms for SRD, including allelic interactions leading to sex-biased lethality, genetic sex reversal, chromosome drive mediated by sex-linked selfish elements, and incompatibilities between specific maternal and paternal genotypes. We show that no one mechanism offers a singular explanation for this population-wide SRD. Instead, our data present preliminary evidence for the action of distinct mechanisms of SRD at play in different strains. Taken together, our work exposes the pervasiveness of SRD in the CC population and nominates the CC as a powerful resource for investigating diverse genetic causes of biased sex chromosome transmission.
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Affiliation(s)
| | | | - Beth L Dumont
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.,Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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60
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eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature 2021; 599:308-314. [PMID: 34671165 PMCID: PMC9295135 DOI: 10.1038/s41586-021-04009-w] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Extrachromosomal circular DNA elements (eccDNAs) have been described in the literature for several decades, and are known for their broad existence across different species1,2. However, their biogenesis and functions are largely unknown. By developing a new circular DNA enrichment method, here we purified and sequenced full-length eccDNAs with Nanopore sequencing. We found that eccDNAs map across the entire genome in a close to random manner, suggesting a biogenesis mechanism of random ligation of genomic DNA fragments. Consistent with this idea, we found that apoptosis inducers can increase eccDNA generation, which is dependent on apoptotic DNA fragmentation followed by ligation by DNA ligase 3. Importantly, we demonstrated that eccDNAs can function as potent innate immunostimulants in a manner that is independent of eccDNA sequence but dependent on eccDNA circularity and the cytosolic DNA sensor Sting. Collectively, our study not only revealed the origin, biogenesis and immunostimulant function of eccDNAs but also uncovered their sensing pathway and potential clinical implications in immune response.
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61
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Jackson EK, Bellott DW, Skaletsky H, Page DC. GC-biased gene conversion in X-chromosome palindromes conserved in human, chimpanzee, and rhesus macaque. G3 GENES|GENOMES|GENETICS 2021; 11:6317831. [PMID: 34849781 PMCID: PMC8981503 DOI: 10.1093/g3journal/jkab224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/03/2022]
Abstract
Gene conversion is GC-biased across a wide range of taxa. Large palindromes on mammalian
sex chromosomes undergo frequent gene conversion that maintains arm-to-arm sequence
identity greater than 99%, which may increase their susceptibility to the effects of
GC-biased gene conversion. Here, we demonstrate a striking history of GC-biased gene
conversion in 12 palindromes conserved on the X chromosomes of human, chimpanzee, and
rhesus macaque. Primate X-chromosome palindrome arms have significantly higher GC content
than flanking single-copy sequences. Nucleotide replacements that occurred in human and
chimpanzee palindrome arms over the past 7 million years are one-and-a-half times as
GC-rich as the ancestral bases they replaced. Using simulations, we show that our observed
pattern of nucleotide replacements is consistent with GC-biased gene conversion with a
magnitude of 70%, similar to previously reported values based on analyses of human
meioses. However, GC-biased gene conversion since the divergence of human and rhesus
macaque explains only a fraction of the observed difference in GC content between
palindrome arms and flanking sequence, suggesting that palindromes are older than 29
million years and/or had elevated GC content at the time of their formation. This work
supports a greater than 2:1 preference for GC bases over AT bases during gene conversion
and demonstrates that the evolution and composition of mammalian sex chromosome
palindromes is strongly influenced by GC-biased gene conversion.
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Affiliation(s)
- Emily K Jackson
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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62
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Subrini J, Turner J. Y chromosome functions in mammalian spermatogenesis. eLife 2021; 10:67345. [PMID: 34606444 PMCID: PMC8489898 DOI: 10.7554/elife.67345] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
The mammalian Y chromosome is critical for male sex determination and spermatogenesis. However, linking each Y gene to specific aspects of male reproduction has been challenging. As the Y chromosome is notoriously hard to sequence and target, functional studies have mostly relied on transgene-rescue approaches using mouse models with large multi-gene deletions. These experimental limitations have oriented the field toward the search for a minimum set of Y genes necessary for male reproduction. Here, considering Y-chromosome evolutionary history and decades of discoveries, we review the current state of research on its function in spermatogenesis and reassess the view that many Y genes are disposable for male reproduction.
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Affiliation(s)
- Jeremie Subrini
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - James Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
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63
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Janssenswillen S, Roelants K, Carpentier S, de Rooster H, Metzemaekers M, Vanschoenwinkel B, Proost P, Bossuyt F. Odorant-binding proteins in canine anal sac glands indicate an evolutionarily conserved role in mammalian chemical communication. BMC Ecol Evol 2021; 21:182. [PMID: 34565329 PMCID: PMC8474896 DOI: 10.1186/s12862-021-01910-w] [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: 11/16/2020] [Accepted: 09/10/2021] [Indexed: 11/29/2022] Open
Abstract
Background Chemical communication is an important aspect of the behavioural ecology of a wide range of mammals. In dogs and other carnivores, anal sac glands are thought to convey information to conspecifics by secreting a pallet of small volatile molecules produced by symbiotic bacteria. Because these glands are unique to carnivores, it is unclear how their secretions relate to those of other placental mammals that make use of different tissues and secretions for chemical communication. Here we analyse the anal sac glands of domestic dogs to verify the secretion of proteins and infer their evolutionary relationship to those involved in the chemical communication of non-carnivoran mammals. Results Proteomic analysis of anal sac gland secretions of 17 dogs revealed the consistently abundant presence of three related proteins. Homology searches against online databases indicate that these proteins are evolutionary related to ‘odorant binding proteins’ (OBPs) found in a wide range of mammalian secretions and known to contribute to chemical communication. Screening of the dog’s genome sequence show that the newly discovered OBPs are encoded by a single cluster of three genes in the pseudoautosomal region of the X-chromosome. Comparative genomic screening indicates that the same locus is shared by a wide range of placental mammals and that it originated at least before the radiation of extant placental orders. Phylogenetic analyses suggest a dynamic evolution of gene duplication and loss, resulting in large gene clusters in some placental taxa and recurrent loss of this locus in others. The homology of OBPs in canid anal sac glands and those found in other mammalian secretions implies that these proteins maintained a function in chemical communication throughout mammalian evolutionary history by multiple shifts in expression between secretory tissues involved in signal release and nasal mucosa involved in signal reception. Conclusions Our study elucidates a poorly understood part of the biology of a species that lives in close association with humans. In addition, it shows that the protein repertoire underlying chemical communication in mammals is more evolutionarily stable than the variation of involved glands and tissues would suggest. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01910-w.
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Affiliation(s)
- Sunita Janssenswillen
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Kim Roelants
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Sebastien Carpentier
- Proteomics Core - SyBioMa, Katholieke Universiteit Leuven, Herestraat 49 - 03.313, 3000, Leuven, Belgium
| | - Hilde de Rooster
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Mieke Metzemaekers
- Rega Institute, Molecular Immunology, Katholieke Universiteit Leuven, Herestraat 49 - Bus1042, 3000, Leuven, Belgium
| | - Bram Vanschoenwinkel
- Community Ecology Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Center for Environmental Management, University of the Free State, Bloemfontein, 9030, South Africa
| | - Paul Proost
- Rega Institute, Molecular Immunology, Katholieke Universiteit Leuven, Herestraat 49 - Bus1042, 3000, Leuven, Belgium
| | - Franky Bossuyt
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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64
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Kratochvíl L, Stöck M, Rovatsos M, Bullejos M, Herpin A, Jeffries DL, Peichel CL, Perrin N, Valenzuela N, Pokorná MJ. Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200097. [PMID: 34304593 PMCID: PMC8310716 DOI: 10.1098/rstb.2020.0097] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Las Lagunillas Campus S/N, 23071 Jaén, Spain
| | - Amaury Herpin
- INRAE, LPGP, 35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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65
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Reddy HM, Bhattacharya R, Tiwari S, Mishra K, Annapurna P, Jehan Z, Praveena NM, Alex JL, Dhople VM, Singh L, Sivaramakrishnan M, Chaturvedi A, Rangaraj N, Shiju TM, Sreedevi B, Kumar S, Dereddi RR, Rayabandla SM, Jesudasan RA. Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis. BMC Biol 2021; 19:198. [PMID: 34503492 PMCID: PMC8428117 DOI: 10.1186/s12915-021-01125-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 08/17/2021] [Indexed: 12/03/2022] Open
Abstract
Background Deciphering the functions of Y chromosome in mammals has been slow owing to the presence of repeats. Some of these repeats transcribe coding RNAs, the roles of which have been studied. Functions of the noncoding transcripts from Y chromosomal repeats however, remain unclear. While a majority of the genes expressed during spermatogenesis are autosomal, mice with different deletions of the long arm of the Y chromosome (Yq) were previously also shown to be characterized by subfertility, sterility and sperm abnormalities, suggesting the presence of effectors of spermatogenesis at this location. Here we report a set of novel noncoding RNAs from mouse Yq and explore their connection to some of the autosomal genes expressed in testis. Results We describe a set of novel mouse male-specific Y long arm (MSYq)-derived long noncoding (lnc) transcripts, named Pirmy and Pirmy-like RNAs. Pirmy shows a large number of splice variants in testis. We also identified Pirmy-like RNAs present in multiple copies at different loci on mouse Y chromosome. Further, we identified eight differentially expressed autosome-encoded sperm proteins in a mutant mouse strain, XYRIIIqdel (2/3 Yq-deleted). Pirmy and Pirmy-like RNAs have homology to 5′/3′UTRs of these deregulated autosomal genes. Several lines of experiments show that these short homologous stretches correspond to piRNAs. Thus, Pirmy and Pirmy-like RNAs act as templates for several piRNAs. In vitro functional assays reveal putative roles for these piRNAs in regulating autosomal genes. Conclusions Our study elucidates a set of autosomal genes that are potentially regulated by MSYq-derived piRNAs in mouse testis. Sperm phenotypes from the Yq-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of MSYq-derived ncRNAs in male sterility and speciation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01125-x.
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Affiliation(s)
- Hemakumar M Reddy
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Present address: Brown University BioMed Division, Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street room 257, Sidney Frank Life Sciences Building, Providence, RI, 02912, USA
| | - Rupa Bhattacharya
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,, Pennington, NJ, 08534, USA
| | - Shrish Tiwari
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Kankadeb Mishra
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Department of Cell Biology, Memorial Sloan Kettering Cancer Centre, Rockefeller Research Laboratory, 430 East 67th Street, RRL 445, New York, NY, 10065, USA
| | - Pranatharthi Annapurna
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Departments of Orthopaedic Surgery & Bioengineering, University of Pennsylvania, 376A Stemmler Hall, 36th Street & Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Zeenath Jehan
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Department of Genetics and Molecular Medicines, Vasavi Medical and Research Centre, 6-1-91 Khairatabad, Hyderabad, 500 004, India
| | | | - Jomini Liza Alex
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Vishnu M Dhople
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Department of Functional Genomics, Ernst-Moritz-Arndt-University of Greifswald Interfaculty Institute for Genetics and Functional Genomics, Friedrich-Ludwig-Jahn-Straße 15 a, 17487, Greifswald, Germany
| | - Lalji Singh
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Mahadevan Sivaramakrishnan
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Jubilant Biosystems Ltd., #96, Industrial Suburb, 2nd Stage, Yeshwantpur, Bangalore, Karnataka, 560022, India
| | - Anurag Chaturvedi
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Nandini Rangaraj
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Thomas Michael Shiju
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, 44120, USA
| | - Badanapuram Sreedevi
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Sachin Kumar
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India
| | - Ram Reddy Dereddi
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Institute for Anatomy and Cell Biology, building-307, Heidelberg, Germany
| | - Sunayana M Rayabandla
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India.,Telangana Social Welfare Residential Degree College for Women, Suryapet, Telangana, 508213, India
| | - Rachel A Jesudasan
- Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, Telangana, 500007, India. .,Department of Genetics, Osmania University, Hyderabad, Telangana, 500007, India. .,Inter University Centre for Genomics & Gene Technology, Karyavattom Campus, University of Kerala, Trivandrum, Kerala, India.
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66
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Zhou Q. Y chromosome evolution spurs behavioural diversity in male fish. Nat Ecol Evol 2021; 5:892-893. [PMID: 33958754 DOI: 10.1038/s41559-021-01463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China. .,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria. .,Department of Gastroenterology/Department of Cardiology of the Second Affiliated Hospital School of Medicine and Life Sciences Institute, Zhejiang University, Hangzhou, China.
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67
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van der Bijl W, Mank JE. Widespread cryptic variation in genetic architecture between the sexes. Evol Lett 2021; 5:359-369. [PMID: 34367661 PMCID: PMC8327960 DOI: 10.1002/evl3.245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/06/2021] [Accepted: 06/13/2021] [Indexed: 11/08/2022] Open
Abstract
The majority of the genome is shared between the sexes, and it is expected that the genetic architecture of most traits is shared as well. This common architecture has been viewed as a major source of constraint on the evolution of sexual dimorphism (SD). SD is nonetheless common in nature, leading to assumptions that it results from differential regulation of shared genetic architecture. Here, we study the effect of thousands of gene knockout mutations on 202 mouse phenotypes to explore how regulatory variation affects SD. We show that many traits are dimorphic to some extent, and that a surprising proportion of knockouts have sex-specific phenotypic effects. Many traits, regardless whether they are monomorphic or dimorphic, harbor cryptic differences in genetic architecture between the sexes, resulting in sexually discordant phenotypic effects from sexually concordant regulatory changes. This provides an alternative route to dimorphism through sex-specific genetic architecture, rather than differential regulation of shared architecture.
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Affiliation(s)
- Wouter van der Bijl
- Department of ZoologyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Judith E. Mank
- Department of ZoologyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- BiosciencesUniversity of ExeterPenryn CampusPenrynTR10 9FEUK
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68
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Jackson EK, Bellott DW, Cho TJ, Skaletsky H, Hughes JF, Pyntikova T, Page DC. Large palindromes on the primate X Chromosome are preserved by natural selection. Genome Res 2021; 31:1337-1352. [PMID: 34290043 PMCID: PMC8327919 DOI: 10.1101/gr.275188.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/17/2021] [Indexed: 12/27/2022]
Abstract
Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserved between species. We identified 26 palindromes on the human X Chromosome, constituting more than 2% of its sequence, and characterized orthologous palindromes in the chimpanzee and the rhesus macaque using a clone-based sequencing approach that incorporates full-length nanopore reads. Many of these palindromes are missing or misassembled in the current reference assemblies of these species' genomes. We find that 12 human X palindromes have been conserved for at least 25 million years, with orthologs in both chimpanzee and rhesus macaque. Insertions and deletions between species are significantly depleted within the X palindromes' protein-coding genes compared to their noncoding sequence, demonstrating that natural selection has preserved these gene families. The spacers that separate the left and right arms of palindromes are a site of localized structural instability, with seven of 12 conserved palindromes showing no spacer orthology between human and rhesus macaque. Analysis of the 1000 Genomes Project data set revealed that human X-palindrome spacers are enriched for deletions relative to arms and flanking sequence, including a common spacer deletion that affects 13% of human X Chromosomes. This work reveals an abundance of conserved palindromes on primate X Chromosomes and suggests that protein-coding gene families in palindromes (most of which remain poorly characterized) promote X-palindrome survival in the face of ongoing structural instability.
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Affiliation(s)
- Emily K Jackson
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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69
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Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish. Genome Res 2021; 31:1486-1497. [PMID: 34131005 PMCID: PMC8327910 DOI: 10.1101/gr.274282.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
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Affiliation(s)
- Alice S Naftaly
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Shana Pau
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Biology, University of Texas Arlington, Arlington, Texas 76019, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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70
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Son JH, Meisel RP. Gene-Level, but Not Chromosome-Wide, Divergence between a Very Young House Fly Proto-Y Chromosome and Its Homologous Proto-X Chromosome. Mol Biol Evol 2021; 38:606-618. [PMID: 32986844 PMCID: PMC7826193 DOI: 10.1093/molbev/msaa250] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The upregulation of the proto-Y allele may be favored in males because of this gene's function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.
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Affiliation(s)
- Jae Hak Son
- Department of Biology and Biochemistry, University of Houston, Houston, TX.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX
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71
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Hong SH, Han G, Lee SJ, Cocquet J, Cho C. Testicular germ cell-specific lncRNA, Teshl, is required for complete expression of Y chromosome genes and a normal offspring sex ratio. SCIENCE ADVANCES 2021; 7:7/24/eabg5177. [PMID: 34108217 PMCID: PMC8189594 DOI: 10.1126/sciadv.abg5177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/23/2021] [Indexed: 05/09/2023]
Abstract
Heat shock factor 2 (HSF2) regulates the transcription of the male-specific region of the mouse Y chromosome long arm (MSYq) multicopy genes only in testes, but the molecular mechanism underlying this tissue specificity remains largely unknown. Here, we report that the testicular germ cell-specific long noncoding RNA (lncRNA), NR_038002, displays a characteristic spatiotemporal expression pattern in the nuclei of round and elongating spermatids. NR_038002-knockout male mice produced sperm with abnormal head morphology and exhibited reduced fertility accompanied by a female-biased sex ratio in offspring. Molecular analyses revealed that NR_038002 interacts with HSF2 and thereby activates expression of the MSYq genes. We designate NR_038002 as testicular germ cell-specific HSF2-interacting lncRNA (Teshl). Together, our study is the first to demonstrate that the testis specificity of HSF2 activity is regulated by the lncRNA Teshl and establishes a Teshl-HSF2-MSYq molecular axis for normal Y-bearing sperm qualities and consequent balanced offspring sex ratio.
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Affiliation(s)
- Seong Hyeon Hong
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Gwidong Han
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Seung Jae Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Julie Cocquet
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, F-75014 Paris, France
| | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.
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72
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Xiao C, Li J, Xie T, Chen J, Zhang S, Elaksher SH, Jiang F, Jiang Y, Zhang L, Zhang W, Xiang Y, Wu Z, Zhao S, Du X. The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat. Ecol Evol 2021; 11:7779-7795. [PMID: 34188851 PMCID: PMC8216945 DOI: 10.1002/ece3.7611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 02/05/2023] Open
Abstract
The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.
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Affiliation(s)
- Changyi Xiao
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Tanghui Xie
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jianhai Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Institutes for Systems GeneticsFrontiers Science Center for Disease‐related Molecular NetworkWest China HospitalSichuan UniversityChengduChina
| | - Sijia Zhang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Salma Hassan Elaksher
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Genetics and Genetic Engineering DepartmentFaculty of AgricultureBenha UniversityMoshtohorEgypt
| | - Fan Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yaoxin Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Wei Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Zhenyang Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- College of Agroforestry Engineering and PlanningTongren UniversityTongrenChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Xiaoyong Du
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
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73
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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74
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Clifton BD, Jimenez J, Kimura A, Chahine Z, Librado P, Sánchez-Gracia A, Abbassi M, Carranza F, Chan C, Marchetti M, Zhang W, Shi M, Vu C, Yeh S, Fanti L, Xia XQ, Rozas J, Ranz JM. Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study. Mol Biol Evol 2021; 37:2584-2600. [PMID: 32359138 PMCID: PMC7475035 DOI: 10.1093/molbev/msaa109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3-7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3' ends, with 3-5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Jamie Jimenez
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Zeinab Chahine
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Pablo Librado
- Laboratoire AMIS CNRS UMR 5288, Faculté de Médicine de Purpan, Université Paul Sabatier, Toulouse, France
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Mashya Abbassi
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Francisco Carranza
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Carolus Chan
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Marcella Marchetti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Christine Vu
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Shudan Yeh
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA.,Department of Life Sciences, National Central University, Taoyuan City, Zhongli District, Taiwan
| | - Laura Fanti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
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75
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Song Z, Lin J, Li Z, Huang C. The nuclear functions of long noncoding RNAs come into focus. Noncoding RNA Res 2021; 6:70-79. [PMID: 33898883 PMCID: PMC8053782 DOI: 10.1016/j.ncrna.2021.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Corresponding author. School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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76
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Rogers TF, Pizzari T, Wright AE. Multi-Copy Gene Family Evolution on the Avian W Chromosome. J Hered 2021; 112:250-259. [PMID: 33758922 DOI: 10.1093/jhered/esab016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/20/2020] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift, and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies as few studies have systematically tested for copy number variation on W chromosomes. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the avian W. First, we quantified gene copy number and variability across the duck W chromosome. We find a limited number of gene families as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Next, we investigated the evolution of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. In particular, we investigated the factors driving the expansion of HINTW using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors. Although we find the potential for selection related to fecundity in explaining small-scale gene amplification of HINTW in the chicken, purifying selection seems to be the dominant mode of evolution in the duck. Together, this challenges the assumption that HINTW is key for female fecundity across the avian phylogeny.
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Affiliation(s)
- Thea F Rogers
- Department of Animal and Plant Sciences, University of Sheffield, UK
| | - Tommaso Pizzari
- Department of Animal and Plant Sciences, University of Sheffield, UK
| | - Alison E Wright
- Edward Grey Institute, Department of Zoology, University of Oxford, UK
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77
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Mechanisms of meiotic drive in symmetric and asymmetric meiosis. Cell Mol Life Sci 2021; 78:3205-3218. [PMID: 33449147 DOI: 10.1007/s00018-020-03735-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/13/2020] [Accepted: 12/08/2020] [Indexed: 12/22/2022]
Abstract
Meiotic drive, the non-Mendelian transmission of chromosomes to the next generation, functions in asymmetric or symmetric meiosis across unicellular and multicellular organisms. In asymmetric meiosis, meiotic drivers act to alter a chromosome's spatial position in a single egg. In symmetric meiosis, meiotic drivers cause phenotypic differences between gametes with and without the driver. Here we discuss existing models of meiotic drive, highlighting the underlying mechanisms and regulation governing systems for which the most is known. We focus on outstanding questions surrounding these examples and speculate on how new meiotic drive systems evolve and how to detect them.
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78
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An 8.22 Mb Assembly and Annotation of the Alpaca ( Vicugna pacos) Y Chromosome. Genes (Basel) 2021; 12:genes12010105. [PMID: 33467186 PMCID: PMC7830431 DOI: 10.3390/genes12010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.
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79
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Raznahan A, Disteche CM. X-chromosome regulation and sex differences in brain anatomy. Neurosci Biobehav Rev 2021; 120:28-47. [PMID: 33171144 PMCID: PMC7855816 DOI: 10.1016/j.neubiorev.2020.10.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 01/08/2023]
Abstract
Humans show reproducible sex-differences in cognition and psychopathology that may be contributed to by influences of gonadal sex-steroids and/or sex-chromosomes on regional brain development. Gonadal sex-steroids are well known to play a major role in sexual differentiation of the vertebrate brain, but far less is known regarding the role of sex-chromosomes. Our review focuses on this latter issue by bridging together two literatures that have to date been largely disconnected. We first consider "bottom-up" genetic and molecular studies focused on sex-chromosome gene content and regulation. This literature nominates specific sex-chromosome genes that could drive developmental sex-differences by virtue of their sex-biased expression and their functions within the brain. We then consider the complementary "top down" view, from magnetic resonance imaging studies that map sex- and sex chromosome effects on regional brain anatomy, and link these maps to regional gene-expression within the brain. By connecting these top-down and bottom-up approaches, we emphasize the potential role of X-linked genes in driving sex-biased brain development and outline key goals for future work in this field.
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Affiliation(s)
- Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, Bethesda, MD, 20892, USA.
| | - Christine M Disteche
- Department of Pathology and Medicine, University of Washington, Seattle, WA 98195, USA.
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80
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Murphy WJ, Foley NM, Bredemeyer KR, Gatesy J, Springer MS. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annu Rev Anim Biosci 2020; 9:29-53. [PMID: 33228377 DOI: 10.1146/annurev-animal-061220-023149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.
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Affiliation(s)
- William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA
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81
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Hughes JF, Skaletsky H, Pyntikova T, Koutseva N, Raudsepp T, Brown LG, Bellott DW, Cho TJ, Dugan-Rocha S, Khan Z, Kremitzki C, Fronick C, Graves-Lindsay TA, Fulton L, Warren WC, Wilson RK, Owens E, Womack JE, Murphy WJ, Muzny DM, Worley KC, Chowdhary BP, Gibbs RA, Page DC. Sequence analysis in Bos taurus reveals pervasiveness of X-Y arms races in mammalian lineages. Genome Res 2020; 30:1716-1726. [PMID: 33208454 PMCID: PMC7706723 DOI: 10.1101/gr.269902.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022]
Abstract
Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X-Y crossing-over unleashed a second dynamic: selfish X-Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X-Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X-Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - Terje Raudsepp
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Laura G Brown
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Shannon Dugan-Rocha
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Colin Kremitzki
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Catrina Fronick
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Tina A Graves-Lindsay
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Lucinda Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Wesley C Warren
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K Wilson
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Elaine Owens
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - James E Womack
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - William J Murphy
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bhanu P Chowdhary
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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82
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Martínez-Pacheco M, Tenorio M, Almonte L, Fajardo V, Godínez A, Fernández D, Cornejo-Páramo P, Díaz-Barba K, Halbert J, Liechti A, Székely T, Urrutia AO, Cortez D. Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals. Genome Biol Evol 2020; 12:2015-2028. [PMID: 32790864 PMCID: PMC7674692 DOI: 10.1093/gbe/evaa173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.
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Affiliation(s)
| | | | - Laura Almonte
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | - Alan Godínez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | | | | | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.,Ecology Institute, UNAM, Mexico
| | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
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83
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Singchat W, Ahmad SF, Laopichienpong N, Suntronpong A, Panthum T, Griffin DK, Srikulnath K. Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome. Cells 2020; 9:cells9112386. [PMID: 33142713 PMCID: PMC7692289 DOI: 10.3390/cells9112386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | | | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
- Correspondence: ; Tel.: +66-2562-5644
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84
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Xu L, Irestedt M, Zhou Q. Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds. Genes (Basel) 2020; 11:E1267. [PMID: 33126459 PMCID: PMC7692361 DOI: 10.3390/genes11111267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
The female-specific W chromosomes of most Neognathae birds are highly degenerated and gene-poor. Previous studies have demonstrated that the gene repertoires of the Neognathae bird W chromosomes, despite being in small numbers, are conserved across bird species, likely due to purifying selection maintaining the regulatory and dosage-sensitive genes. Here we report the discovery of DNA-based sequence duplications from the Z to the W chromosome in birds-of-paradise (Paradisaeidae, Passeriformes), through sequence transposition. The original transposition involved nine genes, but only two of them (ANXA1 and ALDH1A1) survived on the W chromosomes. Both ANXA1 and ALDH1A1 are predicted to be dosage-sensitive, and the expression of ANXA1 is restricted to ovaries in all the investigated birds. These analyses suggest the newly transposed gene onto the W chromosomes can be favored for their role in restoring dosage imbalance or through female-specific selection. After examining seven additional songbird genomes, we further identified five other transposed genes on the W chromosomes of Darwin's finches and one in the great tit, expanding the observation of the Z-to-W transpositions to a larger range of bird species, but not all transposed genes exhibit dosage-sensitivity or ovary-biased expression We demonstrate a new mechanism by which the highly degenerated W chromosomes of songbirds can acquire genes from the homologous Z chromosomes, but further functional investigations are needed to validate the evolutionary forces underlying the transpositions.
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Affiliation(s)
- Luohao Xu
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden;
| | - Qi Zhou
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310012, China
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310012, China
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85
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Abstract
The male-specific Y chromosome harbors genes important for sperm production. Because Y is repetitive, its DNA sequence was deciphered for only a few species, and its evolution remains elusive. Here we compared the Y chromosomes of great apes (human, chimpanzee, bonobo, gorilla, and orangutan) and found that many of their repetitive sequences and multicopy genes were likely already present in their common ancestor. Y repeats had increased intrachromosomal contacts, which might facilitate preservation of genes and gene regulatory elements. Chimpanzee and bonobo, experiencing high sperm competition, underwent many DNA changes and gene losses on the Y. Our research is significant for understanding the role of the Y chromosome in reproduction of nonhuman great apes, all of which are endangered. The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly available human, chimpanzee, and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan, which includes chimpanzee and bonobo, experienced accelerated substitution rates. Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan. Furthermore, we inferred that the great ape common ancestor already possessed multicopy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Our results highlight the dynamic mode of Y chromosome evolution and open avenues for studies of male-specific dispersal in endangered great ape species.
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86
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Price TAR, Windbichler N, Unckless RL, Sutter A, Runge JN, Ross PA, Pomiankowski A, Nuckolls NL, Montchamp-Moreau C, Mideo N, Martin OY, Manser A, Legros M, Larracuente AM, Holman L, Godwin J, Gemmell N, Courret C, Buchman A, Barrett LG, Lindholm AK. Resistance to natural and synthetic gene drive systems. J Evol Biol 2020; 33:1345-1360. [PMID: 32969551 PMCID: PMC7796552 DOI: 10.1111/jeb.13693] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Scientists are rapidly developing synthetic gene drive elements intended for release into natural populations. These are intended to control or eradicate disease vectors and pests, or to spread useful traits through wild populations for disease control or conservation purposes. However, a crucial problem for gene drives is the evolution of resistance against them, preventing their spread. Understanding the mechanisms by which populations might evolve resistance is essential for engineering effective gene drive systems. This review summarizes our current knowledge of drive resistance in both natural and synthetic gene drives. We explore how insights from naturally occurring and synthetic drive systems can be integrated to improve the design of gene drives, better predict the outcome of releases and understand genomic conflict in general.
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Affiliation(s)
- Tom A. R. Price
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | - Andreas Sutter
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jan-Niklas Runge
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Perran A. Ross
- Bio21 and the School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Pomiankowski
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Catherine Montchamp-Moreau
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Saclay, Gif sur Yvette 91190, France
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2 Canada
| | - Oliver Y. Martin
- Department of Biology (D-BIOL) & Institute of Integrative Biology (IBZ), ETH Zurich, Universitätsstrasse 16, CH 8092 Zurich, Switzerland
| | - Andri Manser
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Matthieu Legros
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Luke Holman
- School of Biosciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Neil Gemmell
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Cécile Courret
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Saclay, Gif sur Yvette 91190, France
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Anna Buchman
- University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Verily Life Sciences, 269 E Grand Ave, South San Francisco, CA 94080
| | - Luke G. Barrett
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
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87
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The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized. Genes (Basel) 2020; 11:genes11101126. [PMID: 32992746 PMCID: PMC7599627 DOI: 10.3390/genes11101126] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/19/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Sex chromosomes are unique genomic regions with sex-specific or sex-biased inherent patterns and are expected to be more frequently subject to sex-specific selection. Substantial knowledge on the evolutionary patterns of sex-linked genes have been gained from the studies on the male heterogametic systems (XY male, XX female), but the understanding of the role of sex-specific selection in the evolution of female-heterogametic sex chromosomes (ZW female, ZZ male) is limited. Here we collect the W-linked genes of 27 birds, covering the three major avian clades: Neoaves (songbirds), Galloanserae (chicken), and Palaeognathae (ratites and tinamous). We find that the avian W chromosomes exhibit very conserved gene content despite their independent evolution of recombination suppression. The retained W-linked genes have higher dosage-sensitive and higher expression level than the lost genes, suggesting the role of purifying selection in their retention. Moreover, they are not enriched in ancestrally female-biased genes, and have not acquired new ovary-biased expression patterns after becoming W-linked. They are broadly expressed across female tissues, and the expression profile of the W-linked genes in females is not deviated from that of the homologous Z-linked genes. Together, our new analyses suggest that female-specific positive selection on the avian W chromosomes is limited, and the gene content of the W chromosomes is mainly shaped by purifying selection.
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88
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Li R, Yang P, Li M, Fang W, Yue X, Nanaei HA, Gan S, Du D, Cai Y, Dai X, Yang Q, Cao C, Deng W, He S, Li W, Ma R, Liu M, Jiang Y. A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1116-1130. [PMID: 32997330 DOI: 10.1007/s11427-020-1807-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 01/21/2023]
Abstract
The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages. Here, we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome (oMSY), using nanopore sequencing and Hi-C technologies. The oMSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons. Three major paternal lineages (HY1a, HY1b and HY2) were defined across domestic sheep, of which HY2 was newly detected. Surprisingly, HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b. Demographic analysis of Y chromosomes, mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep, the wild mouflons in Southeastern Anatolia. Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.
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Affiliation(s)
- Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Wenwen Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Duo Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Qimeng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chunna Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunan Agricultural University, Kunming, 650201, China
| | - Sangang He
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, 830026, China
| | - Wenrong Li
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, 830026, China
| | - Runlin Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingjun Liu
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, 830026, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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89
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Liu J, Ali M, Zhou Q. Establishment and evolution of heterochromatin. Ann N Y Acad Sci 2020; 1476:59-77. [PMID: 32017156 PMCID: PMC7586837 DOI: 10.1111/nyas.14303] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome is packaged into transcriptionally active euchromatin and silent heterochromatin, with most studies focused on the former encompassing the majority of protein-coding genes. The recent development of various sequencing techniques has refined this classic dichromatic partition and has better illuminated the composition, establishment, and evolution of this genomic and epigenomic "dark matter" in the context of topologically associated domains and phase-separated droplets. Heterochromatin includes genomic regions that can be densely stained by chemical dyes, which have been shown to be enriched for repetitive elements and epigenetic marks, including H3K9me2/3 and H3K27me3. Heterochromatin is usually replicated late, concentrated at the nuclear periphery or around nucleoli, and usually lacks highly expressed genes; and now it is considered to be as neither genetically inert nor developmentally static. Heterochromatin guards genome integrity against transposon activities and exerts important regulatory functions by targeting beyond its contained genes. Both its nucleotide sequences and regulatory proteins exhibit rapid coevolution between species. In addition, there are dynamic transitions between euchromatin and heterochromatin during developmental and evolutionary processes. We summarize here the ever-changing characteristics of heterochromatin and propose models and principles for the evolutionary transitions of heterochromatin that have been mainly learned from studies of Drosophila and yeast. Finally, we highlight the role of sex chromosomes in studying heterochromatin evolution.
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Affiliation(s)
- Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Mujahid Ali
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
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90
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Abstract
Sex differences are prevalent in normal development, physiology and disease pathogeneses. Recent studies have demonstrated that mosaic loss of Y chromosome and aberrant activation of its genes could modify the disease processes in male biased manners. This mini review discusses the nature of the genes on the human Y chromosome and identifies two general categories of genes: those sharing dosage-sensitivity functions with their X homologues and those with testis-specific expression and functions. Mosaic loss of the former disrupts the homeostasis important for the maintenance of health while aberrant activation of the latter promotes pathogenesis in non-gonadal tissues, thereby contributing to genetic predispositions to diseases in men.
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Affiliation(s)
- Yun-Fai Chris Lau
- Division of Cell and Developmental Genetics, Department of Medicine, San Francisco VA Health Care System, University of California, San Francisco, 4150 Clement Street, San Francisco, CA 94121 USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, USA
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91
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Cai J, Deng J, Gu W, Ni Z, Liu Y, Kamra Y, Saxena A, Hu Y, Yuan H, Xiao Q, Lu Y, Xu Q. Impact of Local Alloimmunity and Recipient Cells in Transplant Arteriosclerosis. Circ Res 2020; 127:974-993. [PMID: 32689904 DOI: 10.1161/circresaha.119.316470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RATIONALE Transplant arteriosclerosis is the major limitation to long-term survival of solid organ transplantation. Although both immune and nonimmune cells have been suggested to contribute to this process, the complex cellular heterogeneity within the grafts, and the underlying mechanisms regulating the disease progression remain largely uncharacterized. OBJECTIVE We aimed to delineate the cellular heterogeneity within the allografts, and to explore possible mechanisms underlying this process. METHODS AND RESULTS Here, we reported the transcriptional profiling of 11 868 cells in a mouse model of transplant arteriosclerosis by single-cell RNA sequencing. Unbiased clustering analyses identified 21 cell clusters at different stages of diseases, and focused analysis revealed several previously unknown subpopulations enriched in the allografts. Interestingly, we found evidence of the local formation of tertiary lymphoid tissues and suggested a possible local modulation of alloimmune responses within the grafts. Intercellular communication analyses uncovered a potential role of several ligands and receptors, including Ccl21a and Cxcr3, in regulating lymphatic endothelial cell-induced early chemotaxis and infiltration of immune cells. In vivo mouse experiments confirmed the therapeutic potential of CCL21 and CXCR3 neutralizing antibodies in transplant arteriosclerosis. Combinational use of genetic lineage tracing and single-cell techniques further indicate the infiltration of host-derived c-Kit+ stem cells as heterogeneous populations in the allografts. Finally, we compared the immune response between mouse allograft and atherosclerosis models in single-cell RNA-seq analysis. By analyzing susceptibility genes of disease traits, we also identified several cell clusters expressing genes associated with disease risk. CONCLUSIONS Our study provides a transcriptional and cellular landscape of transplant arteriosclerosis, which could be fundamental to understanding the initiation and progression of this disease. CCL21/CXCR3 was also identified as important regulators of immune response and may serve as potential therapeutic targets in disease treatment.
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Affiliation(s)
- Jingjing Cai
- From the Center of Pharmacology (J.C., Y.L., H.Y., Y.L.), The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jiacheng Deng
- Department of Cardiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, China (J.D., W.G., Y.H., Q.X.).,School of Cardiovascular Medicine and Sciences, King's College BHF Centre, London, United Kingdom (J.D., W.G., Z.N.)
| | - Wenduo Gu
- Department of Cardiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, China (J.D., W.G., Y.H., Q.X.).,School of Cardiovascular Medicine and Sciences, King's College BHF Centre, London, United Kingdom (J.D., W.G., Z.N.)
| | - Zhichao Ni
- School of Cardiovascular Medicine and Sciences, King's College BHF Centre, London, United Kingdom (J.D., W.G., Z.N.)
| | - Yuanyuan Liu
- From the Center of Pharmacology (J.C., Y.L., H.Y., Y.L.), The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yogesh Kamra
- Genomics Research Platform, Biomedical Research Centre at Guy's Hospital, London, United Kingdom (Y.K., A.S.)
| | - Alka Saxena
- Genomics Research Platform, Biomedical Research Centre at Guy's Hospital, London, United Kingdom (Y.K., A.S.)
| | - Yanhua Hu
- Department of Cardiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, China (J.D., W.G., Y.H., Q.X.)
| | - Hong Yuan
- From the Center of Pharmacology (J.C., Y.L., H.Y., Y.L.), The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Cardiology (H.Y.), The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingzhong Xiao
- Department of Cardiology, the First Affiliated Hospital, School of Medicine, Zhejiang University, China (J.D., W.G., Y.H., Q.X.).,Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (Q. Xiao, Q. Xu)
| | - Yao Lu
- From the Center of Pharmacology (J.C., Y.L., H.Y., Y.L.), The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingbo Xu
- Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (Q. Xiao, Q. Xu)
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92
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Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA. Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome Biol 2020; 21:177. [PMID: 32684159 PMCID: PMC7368989 DOI: 10.1186/s13059-020-02097-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. RESULTS We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). CONCLUSIONS Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.
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Affiliation(s)
- Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Shaugnessy R. McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Joseph A. Ross
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | | | - James R. Urton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jennifer N. Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael A. White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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93
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020; 18:78. [PMID: 32605573 PMCID: PMC7329446 DOI: 10.1186/s12915-020-00808-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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94
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020. [PMID: 32605573 DOI: 10.1101/589804v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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95
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Highly efficient synchronization of sheep skin fibroblasts at G2/M phase and isolation of sheep Y chromosomes by flow cytometric sorting. Sci Rep 2020; 10:9933. [PMID: 32555328 PMCID: PMC7303189 DOI: 10.1038/s41598-020-66905-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/29/2020] [Indexed: 01/08/2023] Open
Abstract
At present, based on whole genome sequencing, sequences and genes annotation of the sheep (Ovis aries) Y chromosome are still absent. The isolation of Y chromosomes followed by sequencing has been approved as an effective approach to analyze this complex chromosome in other species. In this study, we established a highly efficient synchronization method for G2/M phase of sheep fibroblasts, which was successfully applied to flow-sorting chromosomes of sheep, with a focus on isolation and sequencing of the ovine Y chromosome. The isolated (~80,000) Y chromosomes were verified by fluorescence quantitative real-time polymerase chain reaction, further confirmed by fluorescence in situ hybridization, and amplified by the MALBAC method before next-generation sequencing. The sequence results indicated that 68.90% of reads were Y chromosome-related sequences as they are homologous to the bovine Y chromosome. The remaining 31.1% of reads were aligned to the sheep reference genome, including 13.57% reads to chromosome X and 6.68% to chromosome 17. Importantly, the paired-end reads that are properly aligned to the bovine Y sequence assembly accounted for 46.49%, indicating the success in the ovine Y chromosome isolation and the high quality of the Y chromosome sequences. This study not only set up a foundation for future sequencing, assembly and annotation of the ovine Y chromosome, but also provide a validated approach to overcoming difficulties in sequencing Y chromosome in other mammalian species.
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96
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Bímová BV, Macholán M, Ďureje Ľ, Bímová KB, Martincová I, Piálek J. Sperm quality, aggressiveness and generation turnover may facilitate unidirectional Y chromosome introgression across the European house mouse hybrid zone. Heredity (Edinb) 2020; 125:200-211. [PMID: 32528080 DOI: 10.1038/s41437-020-0330-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
The widespread and locally massive introgression of Y chromosomes of the eastern house mouse (Mus musculus musculus) into the range of the western subspecies (M. m. domesticus) in Central Europe calls for an explanation of its underlying mechanisms. Given the paternal inheritance pattern, obvious candidates for traits mediating the introgression are characters associated with sperm quantity and quality. We can also expect traits such as size, aggression or the length of generation cycles to facilitate the spread. We have created two consomic strains carrying the non-recombining region of the Y chromosome of the opposite subspecies, allowing us to study introgression in both directions, something impossible in nature due to the unidirectionality of introgression. We analyzed several traits potentially related to male fitness. Transmission of the domesticus Y onto the musculus background had negative effects on all studied traits. Likewise, domesticus males possessing the musculus Y had, on average, smaller body and testes and lower sperm count than the parental strain. However, the same consomic males tended to produce less- dissociated sperm heads, to win more dyadic encounters, and to have shorter generation cycles than pure domesticus males. These data suggest that the domesticus Y is disadvantageous on the musculus background, while introgression in the opposite direction can confer a recognizable, though not always significant, selective advantage. Our results are thus congruent with the unidirectional musculus → domesticus Y chromosome introgression in Central Europe. In addition to some previous studies, they show this to be a multifaceted phenomenon demanding a multidisciplinary approach.
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Affiliation(s)
- Barbora Vošlajerová Bímová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic.,Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Veveří 97, 602 00, Brno, Czech Republic
| | - Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Veveří 97, 602 00, Brno, Czech Republic. .,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Ľudovít Ďureje
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
| | - Kateřina Berchová Bímová
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences in Prague, Kamýcká 1176, 165 00, Prague, Czech Republic
| | - Iva Martincová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
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97
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Pirogov A, Pfaffelhuber P, Börsch-Haubold A, Haubold B. High-complexity regions in mammalian genomes are enriched for developmental genes. Bioinformatics 2020; 35:1813-1819. [PMID: 30395202 PMCID: PMC6546125 DOI: 10.1093/bioinformatics/bty922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/17/2018] [Accepted: 11/02/2018] [Indexed: 12/01/2022] Open
Abstract
Motivation Unique sequence regions are associated with genetic function in vertebrate genomes. However, measuring uniqueness, or absence of long repeats, along a genome is conceptually and computationally difficult. Here we use a variant of the Lempel-Ziv complexity, the match complexity, Cm, and augment it by deriving its null distribution for random sequences. We then apply Cm to the human and mouse genomes to investigate the relationship between sequence complexity and function. Results We implemented Cm in the program macle and show through simulation that the newly derived null distribution of Cm is accurate. This allows us to delineate high-complexity regions in the human and mouse genomes. Using our program macle2go, we find that these regions are twofold enriched for genes. Moreover, the genes contained in these regions are more than 10-fold enriched for developmental functions. Availability and implementation Source code for macle and macle2go is available from www.github.com/evolbioinf/macle and www.github.com/evolbioinf/macle2go, respectively; Cm browser tracks from guanine.evolbio.mgp.de/complexity. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anton Pirogov
- Lehrstuhl für Informatik, RWTH Aachen University, Max-Planck-Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | | | | | - Bernhard Haubold
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
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98
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Li Q, Li T, Xiao X, Ahmad DW, Zhang N, Li H, Chen Z, Hou J, Liao M. Specific expression and alternative splicing of mouse genes during spermatogenesis. Mol Omics 2020; 16:258-267. [PMID: 32211685 DOI: 10.1039/c9mo00163h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Considering the high abundance of spliced RNAs in testis compared to other tissues, it is needed to construct the landscape of alternative splicing during spermatogenesis. However, there is still a lack of the systematic analysis of alternative RNA splicing in spermatogenesis. Here, we constructed a landscape of alternative RNA splicing during mouse spermatogenesis based on integrated RNA-seq data sets. Our results presented several novel alternatively spliced genes (Eif2s3y, Erdr1 Uty and Zfy1) in the Y chromosome with a specific expression pattern. Remarkably, the alternative splicing genes were grouped into co-expression networks involved in the microtubule cytoskeleton organization and post-transcriptional regulation of the gene expression, indicating the potential pathway to germ cell generation. Furthermore, based on the co-expression networks, we identified Atxn2l as a potential key gene in spermatogenesis, which presented dynamic expression patterns in different alternative splicing types. Ultimately, we proposed splicing regulatory networks for understanding novel and innovative alternative splicing regulation mechanisms during spermatogenesis. In summary, our research provides a systematic analysis of alternative RNA splicing and some novel spliced genes related to spermatogenesis.
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Affiliation(s)
- Qun Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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99
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Genomic Structure, Evolutionary Origins, and Reproductive Function of a Large Amplified Intrinsically Disordered Protein-Coding Gene on the X Chromosome ( Laidx) in Mice. G3-GENES GENOMES GENETICS 2020; 10:1997-2005. [PMID: 32253194 PMCID: PMC7263670 DOI: 10.1534/g3.120.401221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mouse sex chromosomes are enriched for co-amplified gene families, present in tens to hundreds of copies. Co-amplification of Slx/Slxl1 on the X chromosome and Sly on the Y chromosome are involved in dose-dependent meiotic drive, however the role of other co-amplified genes remains poorly understood. Here we demonstrate that the co-amplified gene family on the X chromosome, Srsx, along with two additional partial gene annotations, is actually part of a larger transcription unit, which we name Laidx. Laidx is harbored in a 229 kb amplicon that represents the ancestral state as compared to a 525 kb Y-amplicon containing the rearranged Laidy. Laidx contains a 25,011 nucleotide open reading frame, predominantly expressed in round spermatids, predicted to encode an 871 kD protein. Laidx has orthologous copies with the rat and also the 825-MY diverged parasitic Chinese liver fluke, Clonorchis sinensis, the likely result of a horizontal gene transfer of rodent Laidx to an ancestor of the liver fluke. To assess the male reproductive functions of Laidx, we generated mice carrying a multi-megabase deletion of the Laidx-ampliconic region. Laidx-deficient male mice do not show detectable reproductive defects in fertility, fecundity, testis histology, and offspring sex ratio. We speculate that Laidx and Laidy represent a now inactive X vs. Y chromosome conflict that occurred in an ancestor of present day mice.
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100
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Oertelt-Prigione S, Mariman E. The impact of sex differences on genomic research. Int J Biochem Cell Biol 2020; 124:105774. [PMID: 32470538 DOI: 10.1016/j.biocel.2020.105774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 01/23/2023]
Abstract
Sex and gender differences affect all dimensions of human health ranging from the biological basis of disease to therapeutic access, choice and response. Genomics research has long ignored the role of sex differences as potential modulators and the concept is gaining more attention only recently. In the present review we summarize the current knowledge of the impact of sex differences on genomic and epigenomic research, the potential interaction of genomics and gender and the role of these differences in disease etiopathogenesis. Sex differences can emerge from differences in the sex chromosomes themselves, from their interaction with the genome and from the influence of hormones on genomic processes. The impact of these processes on the incidence of autoimmune and oncologic disease is well documented. The growing field of systems biology, which aims at integrating information from different networks of the human body, could also greatly benefit from this approach. In the present review we summarize the current knowledge and provide recommendations for the future performance of sex-sensitive genomics research.
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Affiliation(s)
- Sabine Oertelt-Prigione
- Department of Primary and Community Care, Radboud Institute of Health Sciences, Radboudumc, Nijmegen, The Netherlands; Institute of Legal and Forensic Medicine, Charité - Universitätsmedizin, Berlin, Germany.
| | - Edwin Mariman
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
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