Abstract
BackgroundX chromosome inactivation is the epigenetic silencing of the majority of the genes on one of the X chromosomes in XX therian mammals. In humans, approximately 15 % of genes consistently escape from this inactivation and another 15 % of genes vary between individuals or tissues in whether they are subject to, or escape from, inactivation. Multiple studies have provided inactivation status calls for a large subset of the genes on the X chromosome; however, these studies vary in which genes they were able to make calls for and in some cases which call they give a specific gene.MethodsThis analysis aggregated three published studies that have examined X chromosome inactivation status of genes across the X chromosome, generating consensus calls and identifying discordancies. The impact of expression level and chromosomal location on X chromosome inactivation status was also assessed.ResultsOverall, we assigned a consensus XCI status 639 genes, including 78 % of protein-coding genes expressed outside of the testes, with a lower frequency for non-coding RNA and testis-specific genes. Study-specific discordancies suggest that there may be instability of XCI during cell culture and also highlight study-specific variations in call type. We observe an enrichment of discordant genes at boundaries between genes subject to and escaping from inactivation.ConclusionsThis study has compiled a comprehensive list of X-chromosome inactivation statuses for genes and also discovered some biases which will help guide future studies examining X-chromosome inactivation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13293-015-0053-7) contains supplementary material, which is available to authorized users.
Highlights
X chromosome inactivation is the epigenetic silencing of the majority of the genes on one of the X chromosomes in XX therian mammals
There is a roughly equal distribution of genes that have been examined in one, two, or three of these studies; very few genes have an X-chromosome inactivation (XCI) status call in all four studies because the Carrel SNP study has a small sample size of 84 (Fig. 1a)
Comparing the distribution of transcript types between genes with XCI status calls and those without, protein-coding genes are much more likely to have a call whereas genes for non-coding RNA such as miRNA and tRNA are more likely to not have an XCI status call (Fig. 1b)
Summary
X chromosome inactivation is the epigenetic silencing of the majority of the genes on one of the X chromosomes in XX therian mammals. Sex is chromosomally determined with the presence or absence of the Y chromosome generally resulting in XY males and XX females. There is clear sexual dimorphism, with major contributing factors including expression of sex-linked genes and differential hormone regulation of some gene pathways [1,2,3]. XCI allows XX females and XY males to have similar levels of expression for the majority of X-linked genes [2, 7].
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