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Cecalev D, Viçoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development 2024; 151:dev202891. [PMID: 39140247 PMCID: PMC11361640 DOI: 10.1242/dev.202891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.
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Affiliation(s)
- Daniela Cecalev
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Beatriz Viçoso
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Rafael Galupa
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
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2
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Pallier PN, Ferrara M, Romagnolo F, Ferretti MT, Soreq H, Cerase A. Chromosomal and environmental contributions to sex differences in the vulnerability to neurological and neuropsychiatric disorders: Implications for therapeutic interventions. Prog Neurobiol 2022; 219:102353. [PMID: 36100191 DOI: 10.1016/j.pneurobio.2022.102353] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/22/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Neurological and neuropsychiatric disorders affect men and women differently. Multiple sclerosis, Alzheimer's disease, anxiety disorders, depression, meningiomas and late-onset schizophrenia affect women more frequently than men. By contrast, Parkinson's disease, autism spectrum condition, attention-deficit hyperactivity disorder, Tourette's syndrome, amyotrophic lateral sclerosis and early-onset schizophrenia are more prevalent in men. Women have been historically under-recruited or excluded from clinical trials, and most basic research uses male rodent cells or animals as disease models, rarely studying both sexes and factoring sex as a potential source of variation, resulting in a poor understanding of the underlying biological reasons for sex and gender differences in the development of such diseases. Putative pathophysiological contributors include hormones and epigenetics regulators but additional biological and non-biological influences may be at play. We review here the evidence for the underpinning role of the sex chromosome complement, X chromosome inactivation, and environmental and epigenetic regulators in sex differences in the vulnerability to brain disease. We conclude that there is a pressing need for a better understanding of the genetic, epigenetic and environmental mechanisms sustaining sex differences in such diseases, which is critical for developing a precision medicine approach based on sex-tailored prevention and treatment.
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Affiliation(s)
- Patrick N Pallier
- Blizard Institute, Centre for Neuroscience, Surgery and Trauma, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
| | - Maria Ferrara
- Institute of Psychiatry, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy; Department of Psychiatry, Yale University, School of Medicine, New Haven, CT, United States; Women's Brain Project (WBP), Switzerland
| | - Francesca Romagnolo
- Institute of Psychiatry, Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | | | - Hermona Soreq
- The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, 9190401, Israel
| | - Andrea Cerase
- EMBL-Rome, Via Ramarini 32, 00015 Monterotondo, RM, Italy; Blizard Institute, Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; Department of Biology, University of Pisa, SS12 Abetone e Brennero 4, 56127 Pisa, Italy.
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3
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Chen CY, Shi W, Balaton BP, Matthews AM, Li Y, Arenillas DJ, Mathelier A, Itoh M, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Brown CJ, Wasserman WW. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. Sci Rep 2016; 6:37324. [PMID: 27857184 PMCID: PMC5114649 DOI: 10.1038/srep37324] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/24/2016] [Indexed: 12/27/2022] Open
Abstract
Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.
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Affiliation(s)
- Chih-Yu Chen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenqiang Shi
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradley P Balaton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Allison M Matthews
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yifeng Li
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - David J Arenillas
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Masayoshi Itoh
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Hideya Kawaji
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Piero Carninci
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan
| | - Alistair R R Forrest
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Contribution of common and rare variants of the PTCHD1 gene to autism spectrum disorders and intellectual disability. Eur J Hum Genet 2015; 23:1694-701. [PMID: 25782667 DOI: 10.1038/ejhg.2015.37] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/20/2015] [Accepted: 02/03/2015] [Indexed: 11/09/2022] Open
Abstract
Recent findings revealed rare copy number variants and missense changes in the X-linked gene PTCHD1 in autism spectrum disorder (ASD) and intellectual disability (ID). Here, we aim to explore the contribution of common PTCHD1 variants in ASD and gain additional evidence for the role of rare variants of this gene in ASD and ID. A two-stage case-control association study investigated 28 tag single nucleotide polymorphisms (SNPs) in 994 ASD cases and 1035 controls from four European populations. Mutation screening was performed in 673 individuals who included 240 ASD cases, 183 ID patients and 250 controls. The case-control association study showed a significant association with rs7052177 (P=6.13E-4) in the ASD discovery sample that was replicated in an independent sample (P=0.03). A Mantel-Haenszel meta-analysis for rs7052177T considering the four European populations showed an odds ratio of 0.58 (P=7E-05). This SNP is predicted to be located in a transcription factor binding site. No rare missense PTCHD1 variants were found in our ASD cohort and only one was identified in the ID sample. A duplication (27 bp) in the promoter region, absent from 590 controls, was found in three ASD patients (Fisher exact test, P=0.024). A gene reporter assay showed a significant decrease in the transcriptional activity (26%) driven by this variant. Moreover, we found that the longest allele of a trinucleotide repeat located upstream from PTCHD1 was associated with ASD (P=0.003, permP=0.0186). Our results further support the involvement of PTCHD1 in ASD, suggesting that both common and rare variants contribute to the disorder.
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Chang D, Gao F, Slavney A, Ma L, Waldman YY, Sams AJ, Billing-Ross P, Madar A, Spritz R, Keinan A. Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases. PLoS One 2014; 9:e113684. [PMID: 25479423 PMCID: PMC4257614 DOI: 10.1371/journal.pone.0113684] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/30/2014] [Indexed: 12/12/2022] Open
Abstract
Many complex human diseases are highly sexually dimorphic, suggesting a potential contribution of the X chromosome to disease risk. However, the X chromosome has been neglected or incorrectly analyzed in most genome-wide association studies (GWAS). We present tailored analytical methods and software that facilitate X-wide association studies (XWAS), which we further applied to reanalyze data from 16 GWAS of different autoimmune and related diseases (AID). We associated several X-linked genes with disease risk, among which (1) ARHGEF6 is associated with Crohn's disease and replicated in a study of ulcerative colitis, another inflammatory bowel disease (IBD). Indeed, ARHGEF6 interacts with a gastric bacterium that has been implicated in IBD. (2) CENPI is associated with three different AID, which is compelling in light of known associations with AID of autosomal genes encoding centromere proteins, as well as established autosomal evidence of pleiotropy between autoimmune diseases. (3) We replicated a previous association of FOXP3, a transcription factor that regulates T-cell development and function, with vitiligo; and (4) we discovered that C1GALT1C1 exhibits sex-specific effect on disease risk in both IBDs. These and other X-linked genes that we associated with AID tend to be highly expressed in tissues related to immune response, participate in major immune pathways, and display differential gene expression between males and females. Combined, the results demonstrate the importance of the X chromosome in autoimmunity, reveal the potential of extensive XWAS, even based on existing data, and provide the tools and incentive to properly include the X chromosome in future studies.
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Affiliation(s)
- Diana Chang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, United States of America
| | - Feng Gao
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Andrea Slavney
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, United States of America
| | - Li Ma
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Yedael Y. Waldman
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Aaron J. Sams
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Paul Billing-Ross
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, United States of America
| | - Aviv Madar
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Richard Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, United States of America
- Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, United States of America
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Mácha J, Teichmanová R, Sater AK, Wells DE, Tlapáková T, Zimmerman LB, Krylov V. Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis. BMC Genomics 2012; 13:315. [PMID: 22800176 PMCID: PMC3472169 DOI: 10.1186/1471-2164-13-315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/25/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The X and Y sex chromosomes are conspicuous features of placental mammal genomes. Mammalian sex chromosomes arose from an ordinary pair of autosomes after the proto-Y acquired a male-determining gene and degenerated due to suppression of X-Y recombination. Analysis of earlier steps in X chromosome evolution has been hampered by the long interval between the origins of teleost and amniote lineages as well as scarcity of X chromosome orthologs in incomplete avian genome assemblies. RESULTS This study clarifies the genesis and remodelling of the Eutherian X chromosome by using a combination of sequence analysis, meiotic map information, and cytogenetic localization to compare amniote genome organization with that of the amphibian Xenopus tropicalis. Nearly all orthologs of human X genes localize to X. tropicalis chromosomes 2 and 8, consistent with an ancestral X-conserved region and a single X-added region precursor. This finding contradicts a previous hypothesis of three evolutionary strata in this region. Homologies between human, opossum, chicken and frog chromosomes suggest a single X-added region predecessor in therian mammals, corresponding to opossum chromosomes 4 and 7. A more ancient X-added ancestral region, currently extant as a major part of chicken chromosome 1, is likely to have been present in the progenitor of synapsids and sauropsids. Analysis of X chromosome gene content emphasizes conservation of single protein coding genes and the role of tandem arrays in formation of novel genes. CONCLUSIONS Chromosomal regions orthologous to Therian X chromosomes have been located in the genome of the frog X. tropicalis. These X chromosome ancestral components experienced a series of fusion and breakage events to give rise to avian autosomes and mammalian sex chromosomes. The early branching tetrapod X. tropicalis' simple diploid genome and robust synteny to amniotes greatly enhances studies of vertebrate chromosome evolution.
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Affiliation(s)
- Jaroslav Mácha
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Radka Teichmanová
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Amy K Sater
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Dan E Wells
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Tereza Tlapáková
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Lyle B Zimmerman
- Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK
| | - Vladimír Krylov
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
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Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H. The evolution of gene expression levels in mammalian organs. Nature 2011; 478:343-8. [PMID: 22012392 DOI: 10.1038/nature10532] [Citation(s) in RCA: 839] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 09/05/2011] [Indexed: 01/01/2023]
Abstract
Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals.
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Affiliation(s)
- David Brawand
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
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Zechner U, Hameister H. Sex Chromosomes in Vertebrates: XX/XY against ZZ/ZW. Sex Dev 2011; 5:266-71. [DOI: 10.1159/000331233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2011] [Indexed: 01/22/2023] Open
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