Derivation of consensus inactivation status for X-linked genes from genome-wide studies. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Balaton, Bradley; Cotton, Allison; Brown, Carolyn
• Is Part Of: Biology of sex differences. Volume 6:Issue 1(2015)
• Page Start: 1
• Page End: 11
• Publication Date: 2015-12
• Subjects: X-chromosome inactivation -- Dosage compensation -- Escape from X-chromosome inactivation -- Somatic cell hybrids -- Allelic imbalance -- DNA methylation; Biology -- Sex differences -- Periodicals; Sex factors in disease -- Research; Sex differences -- Research -- Periodicals; 612.6
• DOI: 10.1186/s13293-015-0053-7
• Languages: English
• ISSNs: 2042-6410

Abstract

Abstract Background X 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. Methods This 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. Results Overall, 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. Conclusions This 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.