1
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Pal I, Bhattacharyya A, V-Ghaffari B, Williams ED, Xiao M, Rutherford MA, Rubio ME. Female GluA3-KO mice show early onset hearing loss and afferent swellings in ambient sound levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581467. [PMID: 38659964 PMCID: PMC11042237 DOI: 10.1101/2024.02.21.581467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
AMPA-type glutamate receptors (AMPAR) mediate excitatory cochlear transmission. However, the unique roles of AMPAR subunits are unresolved. Lack of subunit GluA3 (Gria3KO) in male mice reduced cochlear output by 8-weeks of age. Since Gria3 is X-linked and considering sex differences in hearing vulnerability, we hypothesized accelerated presbycusis in Gria3KO females. Here, auditory brainstem responses (ABR) were similar in 3-week-old female Gria3WT and Gria3KO mice. However, when raised in ambient sound, ABR thresholds were elevated and wave-1 amplitudes were diminished at 5-weeks and older in Gria3KO. In contrast, these metrics were similar between genotypes when raised in quiet. Paired synapses were similar in number, but lone ribbons and ribbonless synapses were increased in female Gria3KO mice in ambient sound compared to Gria3WT or to either genotype raised in quiet. Synaptic GluA4:GluA2 ratios increased relative to Gria3WT, particularly in ambient sound, suggesting an activity-dependent increase in calcium-permeable AMPARs in Gria3KO. Swollen afferent terminals were observed by 5-weeks only in Gria3KO females reared in ambient sound. We propose that lack of GluA3 induces sex-dependent vulnerability to AMPAR-mediated excitotoxicity.
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Affiliation(s)
- Indra Pal
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Atri Bhattacharyya
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO 63110
| | - Babak V-Ghaffari
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO 63110
| | - Essence D. Williams
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Maolei Xiao
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO 63110
| | - Mark A. Rutherford
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO 63110
| | - María Eulalia Rubio
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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2
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Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. The molecular evolution of spermatogenesis across mammals. Nature 2023; 613:308-316. [PMID: 36544022 PMCID: PMC9834047 DOI: 10.1038/s41586-022-05547-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.
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Affiliation(s)
- Florent Murat
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany. .,INRAE, LPGP, Rennes, France.
| | - Noe Mbengue
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
| | - Sofia Boeg Winge
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Timo Trefzer
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Julia Schmidt
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Thoomke Brüning
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Francesco Lamanna
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Christian Conrad
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Rüdiger Behr
- German Primate Center (DPZ), Platform Degenerative Diseases, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Miquel Crusafont Catalan Institute of Paleontology, Autonomous University of Barcelona, Barcelona, Spain
| | - Frank Grützner
- The Robinson Research Institute, School of Biological Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Kaessmann
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
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3
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Lozier NR, Muscio S, Pal I, Cai HM, Rubio ME. Sex differences in glutamate AMPA receptor subunits mRNA with fast gating kinetics in the mouse cochlea. Front Syst Neurosci 2023; 17:1100505. [PMID: 36936507 PMCID: PMC10017478 DOI: 10.3389/fnsys.2023.1100505] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Evidence shows that females have increased supra-threshold peripheral auditory processing compared to males. This is indicated by larger auditory brainstem responses (ABR) wave I amplitude, which measures afferent spiral ganglion neuron (SGN)-auditory nerve synchrony. However, the underlying molecular mechanisms of this sex difference are mostly unknown. We sought to elucidate sex differences in ABR wave I amplitude by examining molecular markers known to affect synaptic transmission kinetics. Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) mediate fast excitatory transmission in mature SGN afferent synapses. Each AMPAR channel is a tetramer composed of GluA2, 3, and 4 subunits (Gria2, 3, and 4 genes), and those lacking GluA2 subunits have larger currents, are calcium-permeable, and have faster gating kinetics. Moreover, alternatively spliced flip and flop isoforms of each AMPAR subunit affect channel kinetics, having faster kinetics those AMPARs containing Gria3 and Gria4 flop isoforms. We hypothesized that SGNs of females have more fast-gating AMPAR subunit mRNA than males, which could contribute to more temporally precise synaptic transmission and increased SGN synchrony. Our data show that the index of Gria3 relative to Gria2 transcripts on SGN was higher in females than males (females: 48%; males: 43%), suggesting that females have more SGNs with higher Gria3 mRNA relative to Gria2. Analysis of the relative abundance of the flip and flop alternatively spliced isoforms showed that females have a 2-fold increase in fast-gating Gria3 flop mRNA, while males have more slow-gating (2.5-fold) of the flip. We propose that Gria3 may in part mediate greater SGN synchrony in females. Significance Statement: Females of multiple vertebrate species, including fish and mammals, have been reported to have enhanced sound-evoked synchrony of afferents in the auditory nerve. However, the underlying molecular mediators of this physiologic sex difference are unknown. Elucidating potential molecular mechanisms related to sex differences in auditory processing is important for maintaining healthy ears and developing potential treatments for hearing loss in both sexes. This study found that females have a 2-fold increase in Gria3 flop mRNA, a fast-gating AMPA-type glutamate receptor subunit. This difference may contribute to greater neural synchrony in the auditory nerve of female mice compared to males, and this sex difference may be conserved in all vertebrates.
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Affiliation(s)
- Nicholas R. Lozier
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Steven Muscio
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Indra Pal
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Hou-Ming Cai
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, United States
| | - María E. Rubio
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, United States
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: María E. Rubio
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4
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Kumar S, De Leon EM, Granados J, Whitworth DJ, VandeBerg JL. Monodelphis domestica Induced Pluripotent Stem Cells Reveal Metatherian Pluripotency Architecture. Int J Mol Sci 2022; 23:12623. [PMID: 36293487 PMCID: PMC9604385 DOI: 10.3390/ijms232012623] [Citation(s) in RCA: 2] [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: 09/07/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Marsupials have been a powerful comparative model to understand mammalian biology. However, because of the unique characteristics of their embryology, marsupial pluripotency architecture remains to be fully understood, and nobody has succeeded in developing embryonic stem cells (ESCs) from any marsupial species. We have developed an integration-free iPSC reprogramming method and established validated iPSCs from two inbred strains of a marsupial, Monodelphis domestica. The monoiPSCs showed a significant (6181 DE-genes) and highly uniform (r2 [95% CI] = 0.973 ± 0.007) resetting of the cellular transcriptome and were similar to eutherian ESCs and iPSCs in their overall transcriptomic profiles. However, monoiPSCs showed unique regulatory architecture of the core pluripotency transcription factors and were more like marsupial epiblasts. Our results suggest that POU5F1 and the splice-variant-specific expression of POU5F3 synergistically regulate the opossum pluripotency gene network. It is plausible that POU5F1, POU5F3 splice variant XM_016427856.1, and SOX2 form a self-regulatory network. NANOG expression, however, was specific to monoiPSCs and epiblasts. Furthermore, POU5F1 was highly expressed in trophectoderm cells, whereas all other pluripotency transcription factors were significantly downregulated, suggesting that the regulatory architecture of core pluripotency genes of marsupials may be distinct from that of eutherians.
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Affiliation(s)
- Satish Kumar
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA
| | - Erica M. De Leon
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA
| | - Jose Granados
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA
| | - Deanne J. Whitworth
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
- School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia
| | - John L. VandeBerg
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
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5
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Mechanisms of Choice in X-Chromosome Inactivation. Cells 2022; 11:cells11030535. [PMID: 35159344 PMCID: PMC8833938 DOI: 10.3390/cells11030535] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/04/2022] Open
Abstract
Early in development, placental and marsupial mammals harbouring at least two X chromosomes per nucleus are faced with a choice that affects the rest of their lives: which of those X chromosomes to transcriptionally inactivate. This choice underlies phenotypical diversity in the composition of tissues and organs and in their response to the environment, and can determine whether an individual will be healthy or affected by an X-linked disease. Here, we review our current understanding of the process of choice during X-chromosome inactivation and its implications, focusing on the strategies evolved by different mammalian lineages and on the known and unknown molecular mechanisms and players involved.
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6
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Talon I, Janiszewski A, Theeuwes B, Lefevre T, Song J, Bervoets G, Vanheer L, De Geest N, Poovathingal S, Allsop R, Marine JC, Rambow F, Voet T, Pasque V. Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals. Genome Biol 2021; 22:302. [PMID: 34724962 PMCID: PMC8558763 DOI: 10.1186/s13059-021-02518-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chromosome, while the other X chromosome is inactive. Moreover, the inactive X chromosome is reactivated during development in the inner cell mass and in germ cells through X chromosome reactivation, which can be studied in vitro by reprogramming of somatic cells to pluripotency. How chromatin processes and gene regulatory networks evolved to regulate X chromosome dosage in the somatic state and during X chromosome reactivation remains unclear. RESULTS Using genome-wide approaches, allele-specific ATAC-seq and single-cell RNA-seq, in female embryonic fibroblasts and during reprogramming to pluripotency, we show that chromatin accessibility on the upregulated mammalian active X chromosome is increased compared to autosomes. We further show that increased accessibility on the active X chromosome is erased by reprogramming, accompanied by erasure of transcriptional X chromosome upregulation and the loss of increased transcriptional burst frequency. In addition, we characterize gene regulatory networks during reprogramming and X chromosome reactivation, revealing changes in regulatory states. Our data show that ZFP42/REX1, a pluripotency-associated gene that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency. CONCLUSIONS Our data reveal the existence of intrinsic compensatory mechanisms that involve modulation of chromatin accessibility to counteract X-to-Autosome gene dosage imbalances caused by evolutionary or in vitro X chromosome loss and X chromosome inactivation in mammalian cells.
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Affiliation(s)
- Irene Talon
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Bart Theeuwes
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Thomas Lefevre
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Juan Song
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Vanheer
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Natalie De Geest
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Suresh Poovathingal
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Ryan Allsop
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
| | - Jean-Christophe Marine
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Laboratory of Reproductive Genomics, Centre for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven – University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), 3000 Leuven, Belgium
- Leuven Stem Cell Institute (SCIL), 3000 Leuven, Belgium
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7
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Mahadevaiah SK, Sangrithi MN, Hirota T, Turner JMA. A single-cell transcriptome atlas of marsupial embryogenesis and X inactivation. Nature 2020; 586:612-617. [PMID: 32814901 DOI: 10.1038/s41586-020-2629-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/20/2020] [Indexed: 11/09/2022]
Abstract
Single-cell RNA sequencing of embryos can resolve the transcriptional landscape of development at unprecedented resolution. To date, single-cell RNA-sequencing studies of mammalian embryos have focused exclusively on eutherian species. Analysis of mammalian outgroups has the potential to identify deeply conserved lineage specification and pluripotency factors, and can extend our understanding of X dosage compensation. Metatherian (marsupial) mammals diverged from eutherians around 160 million years ago. They exhibit distinctive developmental features, including late implantation1 and imprinted X chromosome inactivation2, which is associated with expression of the XIST-like noncoding RNA RSX3. Here we perform a single-cell RNA-sequencing analysis of embryogenesis and X chromosome inactivation in a marsupial, the grey short-tailed opossum (Monodelphis domestica). We resolve the developmental trajectory and transcriptional signatures of the epiblast, primitive endoderm and trophectoderm, and identify deeply conserved lineage-specific markers that pre-date the eutherian-marsupial divergence. RSX coating and inactivation of the X chromosome occurs early and rapidly. This observation supports the hypothesis that-in organisms with early X chromosome inactivation-imprinted X chromosome inactivation prevents biallelic X silencing. We identify XSR, an RSX antisense transcript expressed from the active X chromosome, as a candidate for the regulator of imprinted X chromosome inactivation. Our datasets provide insights into the evolution of mammalian embryogenesis and X dosage compensation.
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Affiliation(s)
| | - Mahesh N Sangrithi
- Division of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Takayuki Hirota
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK.
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8
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Meiotic Executioner Genes Protect the Y from Extinction. Trends Genet 2020; 36:728-738. [PMID: 32773168 DOI: 10.1016/j.tig.2020.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/24/2023]
Abstract
The Y has been described as a wimpy degraded relic of the X, with imminent demise should it lose sex-determining function. Why then has it persisted in almost all mammals? Here we present a novel mechanistic explanation for its evolutionary perseverance: the persistent Y hypothesis. The Y chromosome bears genes that act as their own judge, jury, and executioner in the tightly regulated meiotic surveillance pathways. These executioners are crucial for successful meiosis, yet need to be silenced during the meiotic sex chromosome inactivation window, otherwise germ cells die. Only rare transposition events to the X, where they remain subject to obligate meiotic silencing, are heritable, posing strong evolutionary constraint for the Y chromosome to persist.
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9
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Matsuno Y, Yamashita T, Wagatsuma M, Yamakage H. Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation. Mob DNA 2019; 10:33. [PMID: 31384315 PMCID: PMC6664574 DOI: 10.1186/s13100-019-0173-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/08/2019] [Indexed: 01/01/2023] Open
Abstract
Background Associations between X-inactive transcript (Xist)–long noncoding RNA (lncRNA) and chromatin are critical intermolecular interactions in the X-chromosome inactivation (XCI) process. Despite high-resolution analyses of the Xist RNA-binding sites, specific interaction sequences are yet to be identified. Based on elusive features of the association between Xist RNA and chromatin and the possible existence of multiple low-affinity binding sites in Xist RNA, we defined short motifs (≥5 nucleotides), termed as redundant UC/TC (r-UC/TC) or AG (r-AG) motifs, which may help in the mediation of triplex formation between the lncRNAs and duplex DNA. Results The study showed that r-UC motifs are densely dispersed throughout mouse and human Xist/XIST RNAs, whereas r-AG motifs are even more densely dispersed along opossum RNA-on-the-silent X (Rsx) RNA, and also along both full-length and truncated long interspersed nuclear elements (LINE-1s, L1s) of the three species. Predicted secondary structures of the lncRNAs showed that the length range of these sequence motifs available for forming triplexes was even shorter, mainly 5- to 9-nucleotides long. Quartz crystal microbalance (QCM) measurements and Monte Carlo (MC) simulations indicated that minimum-length motifs can reinforce the binding state by increasing the copy number of the motifs in the same RNA or DNA molecule. Further, r-AG motifs in L1s had a similar length-distribution pattern, regardless of the similarities in the length or sequence of L1s across the three species; this also applies to high-frequency mutations in r-AG motifs, which suggests convergence in L1 sequence variations. Conclusions Multiple short motifs in both RNA and duplex DNA molecules could be brought together to form triplexes with either Hoogsteen or reverse Hoogsteen hydrogen bonding, by which their associations are cooperatively enhanced. This novel triplex interaction could be involved in associations between lncRNA and chromatin in XCI, particularly at the sites of L1s. Potential binding of Xist/XIST/Rsx RNAs specifically at L1s is most likely preserved through the r-AG motifs conserved in mammalian L1s through convergence in L1 nucleotide variations and by maintaining a particular r-UC/r-AG motif ratio in each of these lncRNAs, irrespective of their poorly conserved sequences. Electronic supplementary material The online version of this article (10.1186/s13100-019-0173-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoko Matsuno
- 1Division of Clinical Preventive Medicine, Niigata University, Niigata, Japan
| | - Takefumi Yamashita
- 2Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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10
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Inoue A, Chen Z, Yin Q, Zhang Y. Maternal Eed knockout causes loss of H3K27me3 imprinting and random X inactivation in the extraembryonic cells. Genes Dev 2018; 32:1525-1536. [PMID: 30463900 PMCID: PMC6295166 DOI: 10.1101/gad.318675.118] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/22/2018] [Indexed: 11/28/2022]
Abstract
In this study, Inoue et al. investigated the regulatory mechanisms and functions of the maternal H3K27me3 mechanism. They found that maternal Eed, an essential component of the Polycomb group complex 2 (PRC2), is required for establishing H3K27me3 imprinting, and their results also reveal unique XCI dynamics in the absence of Xist imprinting. Genomic imprinting is essential for mammalian development. Recent studies have revealed that maternal histone H3 Lys27 trimethylation (H3K27me3) can mediate DNA methylation-independent genomic imprinting. However, the regulatory mechanisms and functions of this new imprinting mechanism are largely unknown. Here we demonstrate that maternal Eed, an essential component of the Polycomb group complex 2 (PRC2), is required for establishing H3K27me3 imprinting. We found that all H3K27me3-imprinted genes, including Xist, lose their imprinted expression in Eed maternal knockout (matKO) embryos, resulting in male-biased lethality. Surprisingly, although maternal X-chromosome inactivation (XmCI) occurs in Eed matKO embryos at preimplantation due to loss of Xist imprinting, it is resolved at peri-implantation. Ultimately, both X chromosomes are reactivated in the embryonic cell lineage prior to random XCI, and only a single X chromosome undergoes random XCI in the extraembryonic cell lineage. Thus, our study not only demonstrates an essential role of Eed in H3K27me3 imprinting establishment but also reveals a unique XCI dynamic in the absence of Xist imprinting.
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Affiliation(s)
- Azusa Inoue
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Qiangzong Yin
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
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The Methylome of Vertebrate Sex Chromosomes. Genes (Basel) 2018; 9:genes9050230. [PMID: 29723955 PMCID: PMC5977170 DOI: 10.3390/genes9050230] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/17/2018] [Accepted: 04/26/2018] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is a key epigenetic modification in vertebrate genomes known to be involved in the regulation of gene expression, X chromosome inactivation, genomic imprinting, chromatin structure, and control of transposable elements. DNA methylation is common to all eukaryote genomes, but we still lack a complete understanding of the variation in DNA methylation patterns on sex chromosomes and between the sexes in diverse species. To better understand sex chromosome DNA methylation patterns between different amniote vertebrates, we review literature that has analyzed the genome-wide distribution of DNA methylation in mammals and birds. In each system, we focus on DNA methylation patterns on the autosomes versus the sex chromosomes.
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Pintacuda G, Wei G, Roustan C, Kirmizitas BA, Solcan N, Cerase A, Castello A, Mohammed S, Moindrot B, Nesterova TB, Brockdorff N. hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing. Mol Cell 2017; 68:955-969.e10. [PMID: 29220657 PMCID: PMC5735038 DOI: 10.1016/j.molcel.2017.11.013] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/15/2017] [Accepted: 11/10/2017] [Indexed: 01/01/2023]
Abstract
The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome silencing induced by the non-coding RNA Xist. Polycomb recruitment is initiated by the PCGF3/5-PRC1 complex, which catalyzes chromosome-wide H2A lysine 119 ubiquitylation, signaling recruitment of other PRC1 complexes, and PRC2. However, the molecular mechanism for PCGF3/5-PRC1 recruitment by Xist RNA is not understood. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt sequence encompassing the Xist B-repeat element. Deletion of XR-PID abolishes Xist-dependent Polycomb recruitment, in turn abrogating Xist-mediated gene silencing and reversing Xist-induced chromatin inaccessibility. We identify the RNA-binding protein hnRNPK as the principal XR-PID binding factor required to recruit PCGF3/5-PRC1. Accordingly, synthetically tethering hnRNPK to Xist RNA lacking XR-PID is sufficient for Xist-dependent Polycomb recruitment. Our findings define a key pathway for Polycomb recruitment by Xist RNA, providing important insights into mechanisms of chromatin modification by non-coding RNA. A 600 nt element in Xist RNA, XR-PID, is required for Polycomb recruitment Deletion of XR-PID abrogates Xist-mediated chromosome silencing hnRNPK binds XR-PID to recruit the Polycomb-initiating complex PCGF3/5-PRC1 Tethering hnRNPK to Xist RNA bypasses the requirement for XR-PID
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Affiliation(s)
- Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Chloë Roustan
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Burcu Anil Kirmizitas
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Nicolae Solcan
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrea Cerase
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alfredo Castello
- Posttranscriptional Networks in Infection and Cell Cycle Progression, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Shabaz Mohammed
- Proteomics Technology Development and Application, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Benoît Moindrot
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Tatyana B Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Waters SA, Livernois AM, Patel H, O’Meally D, Craig JM, Marshall Graves JA, Suter CM, Waters PD. Landscape of DNA Methylation on the Marsupial X. Mol Biol Evol 2017; 35:431-439. [DOI: 10.1093/molbev/msx297] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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The X factor: X chromosome dosage compensation in the evolutionarily divergent monotremes and marsupials. Semin Cell Dev Biol 2016; 56:117-121. [PMID: 26806635 DOI: 10.1016/j.semcdb.2016.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/21/2015] [Accepted: 01/06/2016] [Indexed: 11/22/2022]
Abstract
Marsupials and monotremes represent evolutionarily divergent lineages from the majority of extant mammals which are eutherian, or placental, mammals. Monotremes possess multiple X and Y chromosomes that appear to have arisen independently of eutherian and marsupial sex chromosomes. Dosage compensation of X-linked genes occurs in monotremes on a gene-by-gene basis, rather than through chromosome-wide silencing, as is the case in eutherians and marsupials. Specifically, studies in the platypus have shown that for any given X-linked gene, a specific proportion of nuclei within a cell population will silence one locus, with the percentage of cells undergoing inactivation at that locus being highly gene-specific. Hence, it is perhaps not surprising that the expression level of X-linked genes in female platypus is almost double that in males. This is in contrast to the situation in marsupials where one of the two X chromosomes is inactivated in females by the long non-coding RNA RSX, a functional analogue of the eutherian XIST. However, marsupial X chromosome inactivation differs from that seen in eutherians in that it is exclusively the paternal X chromosome that is silenced. In addition, marsupials appear to have globally upregulated X-linked gene expression in both sexes, thus balancing their expression levels with those of the autosomes, a process initially proposed by Ohno in 1967 as being a fundamental component of the X chromosome dosage compensation mechanism but which may not have evolved in eutherians.
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How Many Non-coding RNAs Does It Take to Compensate Male/Female Genetic Imbalance? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 886:33-49. [PMID: 26659486 DOI: 10.1007/978-94-017-7417-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genetic sex determination in mammals relies on dimorphic sex chromosomes that confer phenotypic/physiologic differences between males and females. In this heterogametic system, X and Y chromosomes diverged from an ancestral pair of autosomes, creating a genetic disequilibrium between XX females and XY males. Dosage compensation mechanisms alleviate intrinsic gene dosage imbalance, leading to equal expression levels of most X-linked genes in the two sexes. In therian mammals, this is achieved through inactivation of one of the two X chromosomes in females. Failure to undergo X-chromosome inactivation (XCI) results in developmental arrest and death. Although fundamental for survival, a surprising loose conservation in the mechanisms to achieve XCI during development in therian lineage has been, and continues, to be uncovered. XCI involves the concerted action of non-coding RNAs (ncRNAs), including the well-known Xist RNA, and has thus become a classical paradigm to study the mode of action of this particular class of transcripts. In this chapter, we will describe the processes coping with sex chromosome genetic imbalance and how ncRNAs underlie dosage compensation mechanisms and influence male-female differences in mammals. Moreover, we will discuss how ncRNAs have been tinkered with during therian evolution to adapt XCI mechanistic to species-specific constraints.
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Abstract
Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol 2015; 16:52. [PMID: 25887447 PMCID: PMC4391730 DOI: 10.1186/s13059-015-0618-0] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammals, X chromosome genes are present in one copy in males and two in females. To balance the dosage of X-linked gene expression between the sexes, one of the X chromosomes in females is silenced. X inactivation is initiated by upregulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. RESULTS Here, we show a novel role for the lncRNA Firre in anchoring the inactive mouse X chromosome and preserving one of its main epigenetic features, H3K27me3. Similar to Dxz4, Firre is X-linked and expressed from a macrosatellite repeat locus associated with a cluster of CTCF and cohesin binding sites, and is preferentially located adjacent to the nucleolus. CTCF binding present initially in both male and female mouse embryonic stem cells is lost from the active X during development. Knockdown of Firre disrupts perinucleolar targeting and H3K27me3 levels in mouse fibroblasts, demonstrating a role in maintenance of an important epigenetic feature of the inactive X chromosome. No X-linked gene reactivation is seen after Firre knockdown; however, a compensatory increase in the expression of chromatin modifier genes implicated in X silencing is observed. Further experiments in female embryonic stem cells suggest that Firre does not play a role in X inactivation onset. CONCLUSIONS The X-linked lncRNA Firre helps to position the inactive X chromosome near the nucleolus and to preserve one of its main epigenetic features.
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Abstract
In many animals, males have one X and females have two X chromosomes. The difference in X chromosome dosage between the two sexes is compensated by mechanisms that regulate X chromosome transcription. Recent advances in genomic techniques have provided new insights into the molecular mechanisms of X chromosome dosage compensation. In this review, I summarize our current understanding of dosage imbalance in general, and then review the molecular mechanisms of X chromosome dosage compensation with an emphasis on the parallels and differences between the three well-studied model systems, M. musculus, D. melanogaster and C. elegans.
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Affiliation(s)
- Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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Paternal X inactivation does not correlate with X chromosome evolutionary strata in marsupials. BMC Evol Biol 2014; 14:267. [PMID: 25539578 PMCID: PMC4302592 DOI: 10.1186/s12862-014-0267-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
Background X chromosome inactivation is the transcriptional silencing of one X chromosome in the somatic cells of female mammals. In eutherian mammals (e.g. humans) one of the two X chromosomes is randomly chosen for silencing, with about 15% (usually in younger evolutionary strata of the X chromosome) of genes escaping this silencing. In contrast, in the distantly related marsupial mammals the paternally derived X is silenced, although not as completely as the eutherian X. A chromosome wide examination of X inactivation, using RNA-seq, was recently undertaken in grey short-tailed opossum (Monodelphis domestica) brain and extraembryonic tissues. However, no such study has been conduced in Australian marsupials, which diverged from their American cousins ~80 million years ago, leaving a large gap in our understanding of marsupial X inactivation. Results We used RNA-seq data from blood or liver of a family (mother, father and daughter) of tammar wallabies (Macropus eugenii), which in conjunction with available genome sequence from the mother and father, permitted genotyping of 42 expressed heterozygous SNPs on the daughter’s X. These 42 SNPs represented 34 X loci, of which 68% (23 of the 34) were confirmed as inactivated on the paternally derived X in the daughter’s liver; the remaining 11 X loci escaped inactivation. Seven of the wallaby loci sampled were part of the old X evolutionary stratum, of which three escaped inactivation. Three loci were classified as part of the newer X stratum, of which two escaped inactivation. A meta-analysis of previously published opossum X inactivation data revealed that 5 of 52 genes in the old X stratum escaped inactivation. Conclusions We demonstrate that chromosome wide inactivation of the paternal X is common to an Australian marsupial representative, but that there is more escape from inactivation than reported for opossum (32% v 14%). We also provide evidence that, unlike the human X chromosome, the location of loci within the oldest evolutionary stratum on the marsupial X does not correlate with their probability of escape from inactivation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0267-z) contains supplementary material, which is available to authorized users.
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Abstract
In mammals, the process of X-chromosome inactivation ensures equivalent levels of X-linked gene expression between males and females through the silencing of one of the two X chromosomes in female cells. The process is established early in development and is initiated by a unique locus, which produces a long noncoding RNA, Xist. The Xist transcript triggers gene silencing in cis by coating the future inactive X chromosome. It also induces a cascade of chromatin changes, including posttranslational histone modifications and DNA methylation, and leads to the stable repression of all X-linked genes throughout development and adult life. We review here recent progress in our understanding of the molecular mechanisms involved in the initiation of Xist expression, the propagation of the Xist RNA along the chromosome, and the cis-elements and trans-acting factors involved in the maintenance of the repressed state. We also describe the diverse strategies used by nonplacental mammals for X-chromosome dosage compensation and highlight the common features and differences between eutherians and metatherians, in particular regarding the involvement of long noncoding RNAs.
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Affiliation(s)
- Anne-Valerie Gendrel
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, 75248 Paris, France;
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Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics 2014; 15:89. [PMID: 24484454 PMCID: PMC3912494 DOI: 10.1186/1471-2164-15-89] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 01/23/2014] [Indexed: 01/05/2023] Open
Abstract
Background Imprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a small number of genes previously known to be imprinted in eutherians. We describe the first ab initio search for imprinted marsupial genes, in fibroblasts from the opossum, Monodelphis domestica, based on a genome-wide ChIP-seq strategy to identify promoters that are simultaneously marked by mutually exclusive, transcriptionally opposing histone modifications. Results We identified a novel imprinted gene (Meis1) and two additional monoallelically expressed genes, one of which (Cstb) showed allele-specific, but non-imprinted expression. Imprinted vs. allele-specific expression could not be resolved for the third monoallelically expressed gene (Rpl17). Transcriptionally opposing histone modifications H3K4me3, H3K9Ac, and H3K9me3 were found at the promoters of all three genes, but differential DNA methylation was not detected at CpG islands at any of these promoters. Conclusions In generating the first genome-wide histone modification profiles for a marsupial, we identified the first gene that is imprinted in a marsupial but not in eutherian mammals. This outcome demonstrates the practicality of an ab initio discovery strategy and implicates histone modification, but not differential DNA methylation, as a conserved mechanism for marking imprinted genes in all therian mammals. Our findings suggest that marsupials use multiple epigenetic mechanisms for imprinting and support the concept that lineage-specific selective forces can produce sets of imprinted genes that differ between metatherian and eutherian lines.
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Wang X, Douglas KC, Vandeberg JL, Clark AG, Samollow PB. Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica. Genome Res 2013; 24:70-83. [PMID: 24065774 PMCID: PMC3875863 DOI: 10.1101/gr.161919.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Evidence from a few genes in diverse species suggests that X-chromosome inactivation (XCI) in marsupials is characterized by exclusive, but leaky inactivation of the paternally derived X chromosome. To study the phenomenon of marsupial XCI more comprehensively, we profiled parent-of-origin allele-specific expression, DNA methylation, and histone modifications in fetal brain and extra-embryonic membranes in the gray, short-tailed opossum (Monodelphis domestica). The majority of X-linked genes (152 of 176 genes with trackable SNP variants) exhibited paternally imprinted expression, with nearly 100% of transcripts derived from the maternal allele; whereas 24 loci (14%) escaped inactivation, showing varying levels of biallelic expression. In addition to recently reported evidence of marsupial XCI regulation by the noncoding Rsx transcript, strong depletion of H3K27me3 at escaper gene loci in the present study suggests that histone state modifications also correlate strongly with opossum XCI. In contrast to mouse, the opossum did not show an association between X-linked gene expression and promoter DNA methylation, with one notable exception. Unlike all other X-linked genes examined, Rsx was differentially methylated on the maternal and paternal X chromosomes, and expression was exclusively from the inactive (paternal) X chromosome. Our study provides the first comprehensive catalog of parent-of-origin expression status for X-linked genes in a marsupial and sheds light on the regulation and evolution of imprinted XCI in mammals.
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Affiliation(s)
- Xu Wang
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, New York 14853, USA
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Affiliation(s)
- Jennifer A. Marshall Graves
- La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne 3186, Australia
- Research School of Biology, Australian National University, Canberra 2060, Australia;
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
| | - Marilyn B. Renfree
- Department of Zoology, University of Melbourne, Melbourne 3010, Australia
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Sado T, Sakaguchi T. Species-specific differences in X chromosome inactivation in mammals. Reproduction 2013; 146:R131-9. [PMID: 23847260 DOI: 10.1530/rep-13-0173] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In female mammals, the dosage difference in X-linked genes between XX females and XY males is compensated for by inactivating one of the two X chromosomes during early development. Since the discovery of the X inactive-specific transcript (XIST) gene in humans and its subsequent isolation of the mouse homolog, Xist, in the early 1990s, the molecular basis of X chromosome inactivation (X-inactivation) has been more fully elucidated using genetically manipulated mouse embryos and embryonic stem cells. Studies on X-inactivation in other mammals, although limited when compared with those in the mice, have revealed that, while their inactive X chromosome shares many features with those in the mice, there are marked differences in not only some epigenetic modifications of the inactive X chromosome but also when and how X-inactivation is initiated during early embryonic development. Such differences raise the issue about what extent of the molecular basis of X-inactivation in the mice is commonly shared among others. Recognizing similarities and differences in X-inactivation among mammals may provide further insight into our understanding of not only the evolutionary but also the molecular aspects for the mechanism of X-inactivation. Here, we reviewed species-specific differences in X-inactivation and discussed what these differences may reveal.
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Affiliation(s)
- Takashi Sado
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Livernois AM, Waters SA, Deakin JE, Marshall Graves JA, Waters PD. Independent evolution of transcriptional inactivation on sex chromosomes in birds and mammals. PLoS Genet 2013; 9:e1003635. [PMID: 23874231 PMCID: PMC3715422 DOI: 10.1371/journal.pgen.1003635] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/30/2013] [Indexed: 01/09/2023] Open
Abstract
X chromosome inactivation in eutherian mammals has been thought to be tightly controlled, as expected from a mechanism that compensates for the different dosage of X-borne genes in XX females and XY males. However, many X genes escape inactivation in humans, inactivation of the X in marsupials is partial, and the unrelated sex chromosomes of monotreme mammals have incomplete and gene-specific inactivation of X-linked genes. The bird ZW sex chromosome system represents a third independently evolved amniote sex chromosome system with dosage compensation, albeit partial and gene-specific, via an unknown mechanism (i.e. upregulation of the single Z in females, down regulation of one or both Zs in males, or a combination). We used RNA-fluorescent in situ hybridization (RNA-FISH) to demonstrate, on individual fibroblast cells, inactivation of 11 genes on the chicken Z and 28 genes on the X chromosomes of platypus. Each gene displayed a reproducible frequency of 1Z/1X-active and 2Z/2X-active cells in the homogametic sex. Our results indicate that the probability of inactivation is controlled on a gene-by-gene basis (or small domains) on the chicken Z and platypus X chromosomes. This regulatory mechanism must have been exapted independently to the non-homologous sex chromosomes in birds and mammals in response to an over-expressed Z or X in the homogametic sex, highlighting the universal importance that (at least partial) silencing plays in the evolution on amniote dosage compensation and, therefore, the differentiation of sex chromosomes. Dosage compensation is a mechanism that restores the expression of X chromosome genes back to their original level when Y homologues lose function. In placental and marsupial mammals this is achieved by upregulating the single X in males. The carry-through of overexpression to females would result in functional tetraploidy, so there is subsequent inactivation of one X chromosome in the somatic cells of females, leaving males (XY) and females (XX) with a single upregulated X. In contrast, genes on the five platypus (a monotreme mammal) X chromosomes and the chicken Z chromosome (which are orthologous but independently evolved) are expressed globally at a higher level in female platypus and male chicken respectively, indicating partial dosage compensation. Here, for the first time, we provide evidence for inactivation of genes on the chicken Z chromosome in ZZ males, and on all five Xs in female platypus. Our results suggest that the silencing of genes on sex chromosomes has evolved independently in birds and mammals, and is, therefore, a critical step in the pathway to dosage compensate independently evolved amniote sex chromosomes systems.
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Affiliation(s)
- Alexandra M. Livernois
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail: (AML); (PDW)
| | - Shafagh A. Waters
- School of Biotechnology & Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Janine E. Deakin
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jennifer A. Marshall Graves
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Paul D. Waters
- School of Biotechnology & Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: (AML); (PDW)
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Sado T, Brockdorff N. Advances in understanding chromosome silencing by the long non-coding RNA Xist. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110325. [PMID: 23166390 DOI: 10.1098/rstb.2011.0325] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In female mammals, one of the two X chromosomes becomes genetically silenced to compensate for dosage imbalance of X-linked genes between XX females and XY males. X chromosome inactivation (X-inactivation) is a classical model for epigenetic gene regulation in mammals and has been studied for half a century. In the last two decades, efforts have been focused on the X inactive-specific transcript (Xist) locus, discovered to be the master regulator of X-inactivation. The Xist gene produces a non-coding RNA that functions as the primary switch for X-inactivation, coating the X chromosome from which it is transcribed in cis. Significant progress has been made towards understanding how Xist is regulated at the onset of X-inactivation, but our understanding of the molecular basis of silencing mediated by Xist RNA has progressed more slowly. A picture has, however, begun to emerge, and new tools and resources hold out the promise of further advances to come. Here, we provide an overview of the current state of our knowledge, what is known about Xist RNA and how it may trigger chromosome silencing.
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Affiliation(s)
- Takashi Sado
- Division of Epigenomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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27
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Abstract
A plethora of noncoding (nc) RNAs has been revealed through the application of high-throughput analysis of the transcriptome, and this has led to an intensive search for possible biological functions attributable to these transcripts. A major category of functional ncRNAs that has emerged is for those that are implicated in coordinate gene silencing, either in cis or in trans. The archetype for this class is the well-studied long ncRNA Xist which functions in cis to bring about transcriptional silencing of an entire X chromosome in female mammals. An important step in X chromosome inactivation is the recruitment of the Polycomb repressive complex PRC2 that mediates histone H3 lysine 27 methylation, a hallmark of the inactive X chromosome, and recent studies have suggested that this occurs as a consequence of PRC2 interacting directly with Xist RNA. Accordingly, other ncRNAs have been linked to PRC2 targeting either in cis or in trans, and here also the mechanism has been proposed to involve direct interaction between PRC2 proteins and the different ncRNAs. In this review, I discuss the evidence for and against this hypothesis, in the process highlighting alternative models and discussing experiments that, in the future, will help to resolve existing discrepancies.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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28
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Abstract
Marsupial and eutherian mammals inactivate one X chromosome in female somatic cells in what is thought to be a means of compensating for the unbalanced X chromosome dosage between XX females and XY males. The hypothesis of X chromosome inactivation (XCI) was first published by Mary Lyon just over 50 years ago, with the discovery of XCI in marsupials occurring a decade later. However, we are still piecing together the evolutionary origins of this fascinating epigenetic mechanism. From the very first studies on marsupial X inactivation, it was apparent that, although there were some similarities between marsupial and eutherian XCI, there were also some striking differences. For instance, the paternally derived X was found to be preferentially silenced in marsupials, although the silencing was often incomplete, which was in contrast to the random and more tightly controlled inactivation of the X chromosome in eutherians. Many of these earlier studies used isozymes to study the activity of just a few genes in marsupials. The sequencing of several marsupial genomes and the advent of molecular cytogenetic techniques have facilitated more in-depth studies into marsupial X chromosome inactivation and allowed more detailed comparisons of the features of XCI to be made. Several important findings have come from such comparisons, among which is the absence of the XIST gene in marsupials, a non-coding RNA gene with a critical role in eutherian XCI, and the discovery of the marsupial RSX gene, which appears to perform a similar role to XIST. Here I review the history of marsupial XCI studies, the latest advances that have been made and the impact they have had towards unravelling the evolution of XCI in mammals.
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29
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Abstract
Differentiated sex chromosomes evolved because of suppressed recombination once sex became genetically controlled. In XX/XY and ZZ/ZW systems, the heterogametic sex became partially aneuploid after degeneration of the Y or W. Often, aneuploidy causes abnormal levels of gene expression throughout the entire genome. Dosage compensation mechanisms evolved to restore balanced expression of the genome. These mechanisms include upregulation of the heterogametic chromosome as well as repression in the homogametic sex. Remarkably, strategies for dosage compensation differ between species. In organisms where more is known about molecular mechanisms of dosage compensation, specific protein complexes containing noncoding RNAs are targeted to the X chromosome. In addition, the dosage-regulated chromosome often occupies a specific nuclear compartment. Some genes escape dosage compensation, potentially resulting in sex-specific differences in gene expression. This review focuses on dosage compensation in mammals, with comparisons to fruit flies, nematodes, and birds.
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Affiliation(s)
- Christine M Disteche
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA.
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30
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Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. Nature 2012; 487:254-8. [PMID: 22722828 PMCID: PMC3484893 DOI: 10.1038/nature11171] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 04/30/2012] [Indexed: 01/21/2023]
Abstract
In female (XX) mammals one of the two X chromosomes is inactivated to ensure an equal dose of X-linked genes with males (XY)1. X-inactivation in eutherian mammals is mediated by the non-coding RNA Xist2. Xist is not found in metatherians3 and how X-inactivation is initiated in these mammals has been the subject of speculation for decades4. Using the marsupial Monodelphis domestica we identify Rsx (RNA-on-the-silent X), an RNA that exhibits properties consistent with a role in X-inactivation. Rsx is a large, repeat-rich RNA that is expressed only in females and is transcribed from, and coats, the inactive X chromosome. In female germ cells, where both X chromosomes are active, Rsx is silenced, linking Rsx expression to X-inactivation and reactivation. Integration of an Rsx transgene on an autosome in mouse embryonic stem cells leads to gene silencing in cis. Our findings permit comparative studies of X-inactivation in mammals and pose questions about the mechanisms by which X-inactivation is achieved in eutherians.
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31
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Gschwend AR, Weingartner LA, Moore RC, Ming R. The sex-specific region of sex chromosomes in animals and plants. Chromosome Res 2012; 20:57-69. [PMID: 22105696 DOI: 10.1007/s10577-011-9255-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Our understanding of the evolution of sex chromosomes has increased greatly in recent years due to a number of molecular evolutionary investigations in divergent sex chromosome systems, and these findings are reshaping theories of sex chromosome evolution. In particular, the dynamics of the sex-determining region (SDR) have been demonstrated by recent findings in ancient and incipient sex chromosomes. Radical changes in genomic structure and gene content in the male specific region of the Y chromosome between human and chimpanzee indicated rapid evolution in the past 6 million years, defying the notion that the pace of evolution in the SDR was fast at early stages but slowed down overtime. The chicken Z and the human X chromosomes appeared to have acquired testis-expressed genes and expanded in intergenic regions. Transposable elements greatly contributed to SDR expansion and aided the trafficking of genes in the SDR and its X or Z counterpart through retrotransposition. Dosage compensation is not a destined consequence of sex chromosomes as once thought. Most X-linked microRNA genes escape silencing and are expressed in testis. Collectively, these findings are challenging many of our preconceived ideas of the evolutionary trajectory and fates of sex chromosomes.
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Affiliation(s)
- Andrea R Gschwend
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol 2012; 10:e1001328. [PMID: 22615540 PMCID: PMC3352821 DOI: 10.1371/journal.pbio.1001328] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 03/30/2012] [Indexed: 11/19/2022] Open
Abstract
As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore the original transcriptional output, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI). However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. Here we trace the evolution of dosage compensation using extensive transcriptome data from males and females representing all major mammalian lineages and birds. Our analyses suggest that the X has become globally upregulated in marsupials, whereas we do not detect a global upregulation of this chromosome in placental mammals. However, we find that a subset of autosomal genes interacting with X-linked genes have become downregulated in placentals upon the emergence of sex chromosomes. Thus, different driving forces may underlie the evolution of XCI and the highly efficient equilibration of X expression levels between the sexes observed for both of these lineages. In the egg-laying monotremes and birds, which have partially homologous sex chromosome systems, partial upregulation of the X (Z in birds) evolved but is largely restricted to the heterogametic sex, which provides an explanation for the partially sex-biased X (Z) expression and lack of global inactivation mechanisms in these lineages. Our findings suggest that dosage reductions imposed by sex chromosome differentiation events in amniotes were resolved in strikingly different ways.
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33
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Guioli S, Lovell-Badge R, Turner JMA. Error-prone ZW pairing and no evidence for meiotic sex chromosome inactivation in the chicken germ line. PLoS Genet 2012; 8:e1002560. [PMID: 22412389 PMCID: PMC3297585 DOI: 10.1371/journal.pgen.1002560] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 01/12/2012] [Indexed: 12/21/2022] Open
Abstract
In the male mouse the X and Y chromosomes pair and recombine within the small pseudoautosomal region. Genes located on the unsynapsed segments of the X and Y are transcriptionally silenced at pachytene by Meiotic Sex Chromosome Inactivation (MSCI). The degree to which MSCI is conserved in other vertebrates is currently unclear. In the female chicken the ZW bivalent is thought to undergo a transient phase of full synapsis at pachytene, starting from the homologous ends and spreading through the heterologous regions. It has been proposed that the repair of the ZW DNA double-strand breaks (DSBs) is postponed until diplotene and that the ZW bivalent is subject to MSCI, which is independent of its synaptic status. Here we present a distinct model of meiotic pairing and silencing of the ZW pair during chicken oogenesis. We show that, in most oocytes, DNA DSB foci on the ZW are resolved by the end of pachytene and that the ZW desynapses in broad synchrony with the autosomes. We unexpectedly find that ZW pairing is highly error prone, with many oocytes failing to engage in ZW synapsis and crossover formation. Oocytes with unsynapsed Z and W chromosomes nevertheless progress to the diplotene stage, suggesting that a checkpoint does not operate during pachytene in the chicken germ line. Using a combination of epigenetic profiling and RNA-FISH analysis, we find no evidence for MSCI, associated with neither the asynaptic ZW, as described in mammals, nor the synaptic ZW. The lack of conservation of MSCI in the chicken reopens the debate about the evolution of MSCI and its driving forces.
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Affiliation(s)
- Silvana Guioli
- Division of Stem Cell Biology and Developmental Genetics, Medical Research Council, National Institute for Medical Research, London, United Kingdom.
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34
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Sex chromosome inactivation in germ cells: emerging roles of DNA damage response pathways. Cell Mol Life Sci 2012; 69:2559-72. [PMID: 22382926 DOI: 10.1007/s00018-012-0941-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022]
Abstract
Sex chromosome inactivation in male germ cells is a paradigm of epigenetic programming during sexual reproduction. Recent progress has revealed the underlying mechanisms of sex chromosome inactivation in male meiosis. The trigger of chromosome-wide silencing is activation of the DNA damage response (DDR) pathway, which is centered on the mediator of DNA damage checkpoint 1 (MDC1), a binding partner of phosphorylated histone H2AX (γH2AX). This DDR pathway shares features with the somatic DDR pathway recognizing DNA replication stress in the S phase. Additionally, it is likely to be distinct from the DDR pathway that recognizes meiosis-specific double-strand breaks. This review article extensively discusses the underlying mechanism of sex chromosome inactivation.
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35
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Deakin JE. Marsupial genome sequences: providing insight into evolution and disease. SCIENTIFICA 2012; 2012:543176. [PMID: 24278712 PMCID: PMC3820666 DOI: 10.6064/2012/543176] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 09/26/2012] [Indexed: 05/08/2023]
Abstract
Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences.
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Affiliation(s)
- Janine E. Deakin
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
- *Janine E. Deakin:
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36
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Livernois AM, Graves JAM, Waters PD. The origin and evolution of vertebrate sex chromosomes and dosage compensation. Heredity (Edinb) 2011; 108:50-8. [PMID: 22086077 DOI: 10.1038/hdy.2011.106] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In mammals, birds, snakes and many lizards and fish, sex is determined genetically (either male XY heterogamy or female ZW heterogamy), whereas in alligators, and in many reptiles and turtles, the temperature at which eggs are incubated determines sex. Evidently, different sex-determining systems (and sex chromosome pairs) have evolved independently in different vertebrate lineages. Homology shared by Xs and Ys (and Zs and Ws) within species demonstrates that differentiated sex chromosomes were once homologous, and that the sex-specific non-recombining Y (or W) was progressively degraded. Consequently, genes are left in single copy in the heterogametic sex, which results in an imbalance of the dosage of genes on the sex chromosomes between the sexes, and also relative to the autosomes. Dosage compensation has evolved in diverse species to compensate for these dose differences, with the stringency of compensation apparently differing greatly between lineages, perhaps reflecting the concentration of genes on the original autosome pair that required dosage compensation. We discuss the organization and evolution of amniote sex chromosomes, and hypothesize that dosage insensitivity might predispose an autosome to evolving function as a sex chromosome.
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Affiliation(s)
- A M Livernois
- Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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37
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011; 12:R81. [PMID: 21854559 PMCID: PMC3277949 DOI: 10.1186/gb-2011-12-8-r81] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/22/2011] [Accepted: 08/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
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Affiliation(s)
- Marilyn B Renfree
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anthony T Papenfuss
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Janine E Deakin
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - James Lindsay
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Thomas Heider
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Katherine Belov
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Paul D Waters
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Elizabeth A Pharo
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Geoff Shaw
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Emily SW Wong
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Christophe M Lefèvre
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Kevin R Nicholas
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Yoko Kuroki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Matthew J Wakefield
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Kyall R Zenger
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Chenwei Wang
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Malcolm Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Danielle Hickford
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hongshi Yu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kirsty R Short
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hannah V Siddle
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephen R Frankenberg
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Keng Yih Chew
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Brandon R Menzies
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jessica M Stringer
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Shunsuke Suzuki
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Timothy A Hore
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Margaret L Delbridge
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Amir Mohammadi
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Nanette Y Schneider
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Yanqiu Hu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - William O'Hara
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Shafagh Al Nadaf
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Chen Wu
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Zhi-Ping Feng
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Benjamin G Cocks
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Jianghui Wang
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephen MJ Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Susan Fairley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Kathryn Beal
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Javier Herrero
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dawn M Carone
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Sumio Sugano
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Sakaki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shinji Kondo
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yuichiro Nishida
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shoji Tatsumoto
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ion Mandiou
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Arthur Hsu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kaighin A McColl
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Benjamin Lansdell
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - George Weinstock
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Elizabeth Kuczek
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
- Westmead Institute for Cancer Research, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Annette McGrath
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter Wilson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Artem Men
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mehlika Hazar-Rethinam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Allison Hall
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - John Davis
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - David Wood
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sarah Williams
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yogi Sundaravadanam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lora R Lewis
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret B Morgan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Geoffrey O Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - San Juana Ruiz
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lynne Nazareth
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew Cree
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Gerald Fowler
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandita Joshi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Chyn Jing
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Fremiet Lara
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jixin Deng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua Y Shen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Xing-Zhi Song
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Janette Edson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Carmen Troon
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Daniel Thomas
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amber Stephens
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lankesha Yapa
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Tanya Levchenko
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Desmond W Cooper
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Terence P Speed
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Jennifer A M Graves
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrew J Pask
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Susan M Forrest
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
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De La Fuente R, Baumann C, Viveiros MM. Role of ATRX in chromatin structure and function: implications for chromosome instability and human disease. Reproduction 2011; 142:221-34. [PMID: 21653732 PMCID: PMC3253860 DOI: 10.1530/rep-10-0380] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Functional differentiation of chromatin structure is essential for the control of gene expression, nuclear architecture, and chromosome stability. Compelling evidence indicates that alterations in chromatin remodeling proteins play an important role in the pathogenesis of human disease. Among these, α-thalassemia mental retardation X-linked protein (ATRX) has recently emerged as a critical factor involved in heterochromatin formation at mammalian centromeres and telomeres as well as facultative heterochromatin on the murine inactive X chromosome. Mutations in human ATRX result in an X-linked neurodevelopmental condition with various degrees of gonadal dysgenesis (ATRX syndrome). Patients with ATRX syndrome may exhibit skewed X chromosome inactivation (XCI) patterns, and ATRX-deficient mice exhibit abnormal imprinted XCI in the trophoblast cell line. Non-random or skewed XCI can potentially affect both the onset and severity of X-linked disease. Notably, failure to establish epigenetic modifications associated with the inactive X chromosome (Xi) results in several conditions that exhibit genomic and chromosome instability such as fragile X syndrome as well as cancer development. Insight into the molecular mechanisms of ATRX function and its interacting partners in different tissues will no doubt contribute to our understanding of the pathogenesis of ATRX syndrome as well as the epigenetic origins of aneuploidy. In turn, this knowledge will be essential for the identification of novel drug targets and diagnostic tools for cancer progression as well as the therapeutic management of global epigenetic changes commonly associated with malignant neoplastic transformation.
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Affiliation(s)
- Rabindranath De La Fuente
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA.
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39
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Payer B, Lee JT, Namekawa SH. X-inactivation and X-reactivation: epigenetic hallmarks of mammalian reproduction and pluripotent stem cells. Hum Genet 2011; 130:265-80. [PMID: 21667284 PMCID: PMC3744832 DOI: 10.1007/s00439-011-1024-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/27/2011] [Indexed: 01/07/2023]
Abstract
X-chromosome inactivation is an epigenetic hallmark of mammalian development. Chromosome-wide regulation of the X-chromosome is essential in embryonic and germ cell development. In the male germline, the X-chromosome goes through meiotic sex chromosome inactivation, and the chromosome-wide silencing is maintained from meiosis into spermatids before the transmission to female embryos. In early female mouse embryos, X-inactivation is imprinted to occur on the paternal X-chromosome, representing the epigenetic programs acquired in both parental germlines. Recent advances revealed that the inactive X-chromosome in both females and males can be dissected into two elements: repeat elements versus unique coding genes. The inactive paternal X in female preimplantation embryos is reactivated in the inner cell mass of blastocysts in order to subsequently allow the random form of X-inactivation in the female embryo, by which both Xs have an equal chance of being inactivated. X-chromosome reactivation is regulated by pluripotency factors and also occurs in early female germ cells and in pluripotent stem cells, where X-reactivation is a stringent marker of naive ground state pluripotency. Here we summarize recent progress in the study of X-inactivation and X-reactivation during mammalian reproduction and development as well as in pluripotent stem cells.
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Affiliation(s)
- Bernhard Payer
- Department of Genetics, Harvard Medical School, Boston, MA, USA. Howard Hughes Medical Institute, Boston, MA, USA. Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Jeannie T. Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA. Howard Hughes Medical Institute, Boston, MA, USA. Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Satoshi H. Namekawa
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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40
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Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat Rev Genet 2011; 12:542-53. [PMID: 21765457 DOI: 10.1038/nrg3035] [Citation(s) in RCA: 269] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In female mammals, one of the two X chromosomes is silenced for dosage compensation between the sexes. X-chromosome inactivation is initiated in early embryogenesis by the Xist RNA that localizes to the inactive X chromosome. During development, the inactive X chromosome is further modified, a specialized form of facultative heterochromatin is formed and gene repression becomes stable and independent of Xist in somatic cells. The recent identification of several factors involved in this process has provided insights into the mechanism of Xist localization and gene silencing. The emerging picture is complex and suggests that chromosome-wide silencing can be partitioned into several steps, the molecular components of which are starting to be defined.
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41
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Evolutionary diversity and developmental regulation of X-chromosome inactivation. Hum Genet 2011; 130:307-27. [PMID: 21687993 PMCID: PMC3132430 DOI: 10.1007/s00439-011-1029-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Accepted: 05/31/2011] [Indexed: 12/26/2022]
Abstract
X-chromosome inactivation (XCI) results in the transcriptional silencing of one X-chromosome in females to attain gene dosage parity between XX female and XY male mammals. Mammals appear to have developed rather diverse strategies to initiate XCI in early development. In placental mammals XCI depends on the regulatory noncoding RNA X-inactive specific transcript (Xist), which is absent in marsupials and monotremes. Surprisingly, even placental mammals show differences in the initiation of XCI in terms of Xist regulation and the timing to acquire dosage compensation. Despite this, all placental mammals achieve chromosome-wide gene silencing at some point in development, and this is maintained by epigenetic marks such as chromatin modifications and DNA methylation. In this review, we will summarise recent findings concerning the events that occur downstream of Xist RNA coating of the inactive X-chromosome (Xi) to ensure its heterochromatinization and the maintenance of the inactive state in the mouse and highlight similarities and differences between mammals.
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42
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Arico JK, Katz DJ, van der Vlag J, Kelly WG. Epigenetic patterns maintained in early Caenorhabditis elegans embryos can be established by gene activity in the parental germ cells. PLoS Genet 2011; 7:e1001391. [PMID: 21695223 PMCID: PMC3111476 DOI: 10.1371/journal.pgen.1001391] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Accepted: 05/06/2011] [Indexed: 12/21/2022] Open
Abstract
Epigenetic information, such as parental imprints, can be transmitted with genetic information from parent to offspring through the germ line. Recent reports show that histone modifications can be transmitted through sperm as a component of this information transfer. How the information that is transferred is established in the parent and maintained in the offspring is poorly understood. We previously described a form of imprinted X inactivation in Caenorhabditis elegans where dimethylation on histone 3 at lysine 4 (H3K4me2), a mark of active chromatin, is excluded from the paternal X chromosome (Xp) during spermatogenesis and persists through early cell divisions in the embryo. Based on the observation that the Xp (unlike the maternal X or any autosome) is largely transcriptionally inactive in the paternal germ line, we hypothesized that transcriptional activity in the parent germ line may influence epigenetic information inherited by and maintained in the embryo. We report that chromatin modifications and histone variant patterns assembled in the germ line can be retained in mature gametes. Furthermore, despite extensive chromatin remodeling events at fertilization, the modification patterns arriving with the gametes are largely retained in the early embryo. Using transgenes, we observe that expression in the parental germline correlates with differential chromatin assembly that is replicated and maintained in the early embryo. Expression in the adult germ cells also correlates with more robust expression in the somatic lineages of the offspring. These results suggest that differential expression in the parental germ lines may provide a potential mechanism for the establishment of parent-of-origin epigenomic content. This content can be maintained and may heritably affect gene expression in the offspring.
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Affiliation(s)
- Jackelyn K. Arico
- Biology Department, Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
- Graduate Program in Biochemistry and Cell and Developmental Biology, Emory University, Atlanta, Georgia, United States of America
| | - David J. Katz
- Biology Department, Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Johan van der Vlag
- Nephrology Research Laboratory, Nijmegen Centre for Molecular Life Sciences, Department of Nephrology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - William G. Kelly
- Biology Department, Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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43
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The single active X in human cells: evolutionary tinkering personified. Hum Genet 2011; 130:281-93. [PMID: 21655936 DOI: 10.1007/s00439-011-1016-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 05/23/2011] [Indexed: 10/18/2022]
Abstract
All mammals compensate for sex differences in numbers of X chromosomes by transcribing only a single X chromosome in cells of both sexes; however, they differ from one another in the details of the compensatory mechanisms. These species variations result from chance mutations, species differences in the staging of developmental events, and interactions between events that occur concurrently. Such variations, which have only recently been appreciated, do not interfere with the strategy of establishing a single active X, but they influence how it is carried out. In an overview of X dosage compensation in human cells, I point out the evolutionary variations. I also argue that it is the single active X that is chosen, rather than inactive ones. Further, I suggest that the initial events in the process-those that precede silencing of future inactive X chromosomes-include randomly choosing the future active X, most likely by repressing its XIST locus.
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Chaumeil J, Waters PD, Koina E, Gilbert C, Robinson TJ, Marshall Graves JA. Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals. PLoS One 2011; 6:e19040. [PMID: 21541345 PMCID: PMC3081832 DOI: 10.1371/journal.pone.0019040] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 03/25/2011] [Indexed: 11/18/2022] Open
Abstract
X chromosome inactivation (XCI) is the transcriptional silencing of one X in female mammals, balancing expression of X genes between females (XX) and males (XY). In placental mammals non-coding XIST RNA triggers silencing of one X (Xi) and recruits a characteristic suite of epigenetic modifications, including the histone mark H3K27me3. In marsupials, where XIST is missing, H3K27me3 association seems to have different degrees of stability, depending on cell-types and species. However, the complete suite of histone marks associated with the Xi and their stability throughout cell cycle remain a mystery, as does the evolution of an ancient mammal XCI system. Our extensive immunofluorescence analysis (using antibodies against specific histone modifications) in nuclei of mammals distantly related to human and mouse, revealed a general absence from the mammalian Xi territory of transcription machinery and histone modifications associated with active chromatin. Specific repressive modifications associated with XCI in human and mouse were also observed in elephant (a distantly related placental mammal), as was accumulation of XIST RNA. However, in two marsupial species the Xi either lacked these modifications (H4K20me1), or they were restricted to specific windows of the cell cycle (H3K27me3, H3K9me2). Surprisingly, the marsupial Xi was stably enriched for modifications associated with constitutive heterochromatin in all eukaryotes (H4K20me3, H3K9me3). We propose that marsupial XCI is comparable to a system that evolved in the common therian (marsupial and placental) ancestor. Silent chromatin of the early inactive X was exapted from neighbouring constitutive heterochromatin and, in early placental evolution, was augmented by the rise of XIST and the stable recruitment of specific histone modifications now classically associated with XCI.
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Affiliation(s)
- Julie Chaumeil
- Comparative Genomics Group, Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail: (PW); (JC)
| | - Paul D. Waters
- Comparative Genomics Group, Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail: (PW); (JC)
| | - Edda Koina
- Comparative Genomics Group, Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Clément Gilbert
- Evolutionary Genomics Group, Department of Zoology, University of Stellenbosch, Matieland, South Africa
| | - Terence J. Robinson
- Evolutionary Genomics Group, Department of Zoology, University of Stellenbosch, Matieland, South Africa
| | - Jennifer A. Marshall Graves
- Comparative Genomics Group, Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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He S, Liu S, Zhu H. The sequence, structure and evolutionary features of HOTAIR in mammals. BMC Evol Biol 2011; 11:102. [PMID: 21496275 PMCID: PMC3103462 DOI: 10.1186/1471-2148-11-102] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 04/16/2011] [Indexed: 12/20/2022] Open
Abstract
Background An increasing number of long noncoding RNAs (lncRNAs) have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. Results To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals. Conclusions HOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR.
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Affiliation(s)
- Sha He
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
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46
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Nguyen DK, Yang F, Kaul R, Alkan C, Antonellis A, Friery KF, Zhu B, de Jong PJ, Disteche CM. Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X. Genome Res 2011; 21:402-9. [PMID: 21282478 DOI: 10.1101/gr.108563.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In Mus spretus, the chloride channel 4 gene Clcn4-2 is X-linked and dosage compensated by X up-regulation and X inactivation, while in the closely related mouse species Mus musculus, Clcn4-2 has been translocated to chromosome 7. We sequenced Clcn4-2 in M. spretus and identified the breakpoints of the evolutionary translocation in the Mus lineage. Genetic and epigenetic differences were observed between the 5'ends of the autosomal and X-linked loci. Remarkably, Clcn4-2 introns have been truncated on chromosome 7 in M. musculus as compared with the X-linked loci from seven other eutherian mammals. Intron sequences specifically preserved in the X-linked loci were significantly enriched in AT-rich oligomers. Genome-wide analyses showed an overall enrichment in AT motifs unique to the eutherian X (except for genes that escape X inactivation), suggesting a role for these motifs in regulation of the X chromosome.
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Affiliation(s)
- Di Kim Nguyen
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
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47
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Abstract
Germ cell development is controlled by unique gene expression programs and involves epigenetic reprogramming of histone modifications and DNA methylation. The central event is meiosis, during which homologous chromosomes pair and recombine, processes that involve histone alterations. At unpaired regions, chromatin is repressed by meiotic silencing. After meiosis, male germ cells undergo chromatin remodeling, including histone-to-protamine replacement. Male and female germ cells are also differentially marked by parental imprints, which contribute to sex determination in insects and mediate genomic imprinting in mammals. Here, we review epigenetic transitions during gametogenesis and discuss novel insights from animal and human studies.
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Affiliation(s)
- Satya K Kota
- Institute of Molecular Genetics, CNRS UMR5535 and University of Montpellier I & II, 1919 route de Mende, 34293 Montpellier, France
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48
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Histone H3 trimethylation at lysine 9 marks the inactive metaphase X chromosome in the marsupial Monodelphis domestica. Chromosoma 2010; 120:177-83. [PMID: 21110203 DOI: 10.1007/s00412-010-0300-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 11/01/2010] [Accepted: 11/11/2010] [Indexed: 10/18/2022]
Abstract
In somatic cells of female marsupial and eutherian mammals, X chromosome inactivation (XCI) occurs. XCI results in the transcriptional silencing of one of the two X chromosomes and is accompanied by specific covalent histone modifications attributable to the inactive chromatin state. Because data about repressed chromatin of the inactive X chromosome (Xi) in marsupials are sparse, we examined in more detail the distribution of active and inactive chromatin markers on metaphase X chromosomes of an American marsupial, Monodelphis domestica. Consistent with data reported previously both for eutherian and marsupial mammals, we found that the Xi of M. domestica lacks active histone markers-H3K4 dimethylation and H3K9 acetylation. We did not observe on metaphase spreads enrichment of the Xi with H3K27 trimethylation which is involved in XCI in eutherians and was detected on the Xi in the interphase nuclei of mature female M. domestica in an earlier study. Moreover, we found that the Xi of M. domestica was specifically marked with H3K9 trimethylation, which is known to be a component of the Xi chromatin in eutherians and is involved in both marsupials and eutherians in meiotic sex chromosome inactivation which has been proposed as an ancestral mechanism of XCI.
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49
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Abstract
Dosage compensation is a strategy to deal with the imbalance of sex chromosomal gene products relative to autosomes and also between the sexes. The mechanisms that ensure dosage compensation for X-chromosome activity have been extensively studied in mammals, worms, and flies. Although each entails very different mechanisms to equalize the dose of X-linked genes between the sexes, they all involve the co-ordinate regulation of hundreds of genes specifically on the sex chromosomes and not the autosomes. In addition to chromatin modifications and changes in higher order chromatin structure, nuclear organization is emerging as an important component of these chromosome-wide processes and in the specific targeting of dosage compensation complexes to the sex chromosomes. Preferential localization within the nucleus and 3D organization are thought to contribute to the differential treatment of two identical homologs within the same nucleus, as well as to the chromosome-wide spread and stable maintenance of heterochromatin.
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Affiliation(s)
- Jennifer C Chow
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR3215, INSERM U934, Paris, F-75248 France
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50
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Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation. Proc Natl Acad Sci U S A 2010; 107:17657-62. [PMID: 20861449 DOI: 10.1073/pnas.0910322107] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
X chromosome dosage compensation in female eutherian mammals is regulated by the noncoding Xist RNA and is associated with the differential acquisition of active and repressive histone modifications, resulting in repression of most genes on one of the two X chromosome homologs. Marsupial mammals exhibit dosage compensation; however, they lack Xist, and the mechanisms conferring epigenetic control of X chromosome dosage compensation remain elusive. Oviparous mammals, the monotremes, have multiple X chromosomes, and it is not clear whether they undergo dosage compensation and whether there is epigenetic dimorphism between homologous pairs in female monotremes. Here, using antibodies against DNA methylation, eight different histone modifications, and HP1, we conduct immunofluorescence on somatic cells of the female Australian marsupial possum Trichosurus vulpecula, the female platypus Ornithorhynchus anatinus, and control mouse cells. The two marsupial X's were different for all epigenetic features tested. In particular, unlike in the mouse, both repressive modifications, H3K9me3 and H4K20Me3, are enriched on one of the X chromosomes, and this is associated with the presence of HP1 and hypomethylation of DNA. Using sequential labeling, we determine that this DNA hypomethylated X correlates with histone marks of inactivity. These results suggest that female marsupials use a repressive histone-mediated inactivation mechanism and that this may represent an ancestral dosage compensation process that differs from eutherians that require Xist transcription and DNA methylation. In comparison to the marsupial, the monotreme exhibited no epigenetic differences between homologous X chromosomes, suggesting the absence of a dosage compensation process comparable to that in therians.
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