Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing
department or school: Medicine, Faculty of
department or school: Other UBC
department or school: Medical Genetics, Department of
data provider: DSpace
identifier citation: Epigenetics & Chromatin. 2021 Feb 17;14(1):12
contributor: Children's Hospital (Vancouver, B.C.). Research Institute
contributor: University of British Columbia. Centre for Molecular Medicine and Therapeutics
rights copyright: The Author(s)
creator: Balaton, Bradley P.
creator: Fornes, Oriol
creator: Wasserman, Wyeth W.
creator: Brown, Carolyn Janet
issued: 2021-02-17T19:20:39Z
issued: 2021-02-17
description: Background: X-chromosome inactivation (XCI) in eutherian mammals is the epigenetic inactivation of one of the two X chromosomes in XX females in order to compensate for dosage differences with XY males. Not all genes are inactivated, and the proportion escaping from inactivation varies between human and mouse (the two species that have been extensively studied). Results: We used DNA methylation to predict the XCI status of X-linked genes with CpG islands across 12 different species: human, chimp, bonobo, gorilla, orangutan, mouse, cow, sheep, goat, pig, horse and dog. We determined the XCI status of 342 CpG islands on average per species, with most species having 80–90% of genes subject to XCI. Mouse was an outlier, with a higher proportion of genes subject to XCI than found in other species. Sixteen genes were found to have discordant X-chromosome inactivation statuses across multiple species, with five of these showing primate-specific escape from XCI. These discordant genes tended to cluster together within the X chromosome, along with genes with similar patterns of escape from XCI. CTCF-binding, ATAC-seq signal and LTR repeats were enriched at genes escaping XCI when compared to genes subject to XCI; however, enrichment was only observed in three or four of the species tested. LINE and DNA repeats showed enrichment around subject genes, but again not in a consistent subset of species. Conclusions: In this study, we determined XCI status across 12 species, showing mouse to be an outlier with few genes that escape inactivation. Inactivation status is largely conserved across species. The clustering of genes that change XCI status across species implicates a domain-level control. In contrast, the relatively consistent, but not universal correlation of inactivation status with enrichment of repetitive elements or CTCF binding at promoters demonstrates gene-based influences on inactivation state. This study broadens enrichment analysis of regulatory elements to speci…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/77314
note: Balaton et al. Epigenetics & Chromatin (2021) 14:12 https://doi.org/10.1186/s13072-021-00386-8RESEARCHCross-species examination of X-chromosome inactivation highlights domains of escape from silencingBradley P. Balaton1, Oriol Fornes1,2,3, Wyeth W. Wasserman1,2,3 and Carolyn J. Brown1* Abstract Background: X-chromosome inactivation (XCI) in eutherian mammals is the epigenetic inactivation of one of the two X chromosomes in XX females in order to compensate for dosage differences with XY males. Not all genes are inactivated, and the proportion escaping from inactivation varies between human and mouse (the two species that have been extensively studied).Results: We used DNA methylation to predict the XCI status of X-linked genes with CpG islands across 12 different species: human, chimp, bonobo, gorilla, orangutan, mouse, cow, sheep, goat, pig, horse and dog. We determined the XCI status of 342 CpG islands on average per species, with most species having 80–90% of genes subject to XCI. Mouse was an outlier, with a higher proportion of genes subject to XCI than found in other species. Sixteen genes were found to have discordant X-chromosome inactivation statuses across multiple species, with five of these show-ing primate-specific escape from XCI. These discordant genes tended to cluster together within the X chromosome, along with genes with similar patterns of escape from XCI. CTCF-binding, ATAC-seq signal and LTR repeats were enriched at genes escaping XCI when compared to genes subject to XCI; however, enrichment was only observed in three or four of the species tested. LINE and DNA repeats showed enrichment around subject genes, but again not in a consistent subset of species.Conclusions: In this study, we determined XCI status across 12 species, showing mouse to be an outlier with few genes that escape inactivation. Inactivation status is largely conserved across species. The clustering of genes that change XCI status across species implicates a domain-level cont…
has type: Article
is shown at: 10.14288/1.0395897
language: eng
peer review status: Reviewed
provider: Vancouver : University of British Columbia Library
publisher: BioMed Central
publisher DOI: 10.1186/s13072-021-00386-8
rights: Attribution 4.0 International (CC BY 4.0)
rights URI: http://creativecommons.org/licenses/by/4.0/
scholar level: Faculty
subject: X-chromosome inactivation
subject: Cross-species
subject: DNA methylation
subject: Escape from X-chromosome inactivation
subject: CpG islands
subject: Dosage compensation
subject: Mammals
subject: ATAC-seq
subject: CTCF
subject: Repetitive elements
type: Text
identifier URI: http://hdl.handle.net/2429/77314