Derivation of consensus inactivation status for X-linked genes from genome-wide studies

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.

Keywords: Allelic imbalance; DNA methylation; Dosage compensation; Escape from X-chromosome inactivation; Somatic cell hybrids; X-chromosome inactivation.

Fig. 1

The majority of X-linked protein-coding genes have an XCI status call. a The number of datasets contributing an XCI status call per gene. The number of calls is the number of studies which gave an XCI status call of subject, escape, or variable escape from XCI. Genes with no call were not mentioned in any of the studies but were included in Gencode for HG19 [38, 39]. b The distribution of RNA transcript types for genes with and without an XCI status call. Transcript type was taken from Gencode or an NCBI search [30]. CTAG are cancer-testes antigen genes which are protein-coding genes expressed exclusively in cancer and in testes and hypermethylated in other tissues making XCI status calls very difficult. Other mRNAs are mRNA genes that are not members of the CTAG family

Fig. 2

Consensus XCI status calls. a Distribution of our consensus XCI status calls. E is escape from XCI, S is subject to XCI, and VE is variably escaping from XCI in some individuals or tissues. The mostly E, S, or VE categories are genes which have two out of three or three out of four XCI status calls agree on a call of E, S, or VE and the last study disagree. The all E, S, or VE categories had at least one XCI status call for E, S, or VE and had no XCI status calls disagree. Discordant calls had either an even split of different XCI status calls or had one of each call. Genes with no call were left out of this graph. b The distribution of XCI status calls given by each individual study. See above for a description of E, S, and VE. E/VE and S/VE are calls from the Cotton DNAm study where most tissues were given a call of escape or subject, but some tissues were given a call of variable escape. For the sample sizes of each study see Table 1

Fig. 3

Comparison of discordancies. a The level of discordancies in each study. A gene is counted as discordant in a study if that study gives a call and at least two other studies agree on a different call. For the sample sizes of each study, see Table 1. b Comparison of the Carrel hybrid calls to calls from other studies. The number of escaping hybrids is, for each gene, in how many mouse-human hybrid cell lines (out of 9) did that gene escape XCI. The Y axis is how many genes one or more other studies agreed were subject to, escaping from, or variably escaping from XCI. c A magnified version of B to better show escape and variable escape from XCI

Fig. 4

Domains of XCI and the enrichment of discordant and mostly variable escape genes at boundaries. a Our consensus gene calls and the domains of XCI along the X chromosome. The top row is the XCI status calls for all genes with a call on the X while the second row is the domains of XCI called from the consensus calls (see Section 2). For the XCI status calls, the colors are defined in c. For the domains of XCI: red is subject, green is escape, orange is boundaries, and white space is between domains. A magnification of two regions is shown below, demonstrating how genes line up with domains. Domains are defined by the first and last gene in the domain, even if they start or end inside of other genes which do not share the same domain call. See Additional files 6 and 7 for the BED files used to generate the UCSC browser track upon which this graph is based. b Distribution of genes into XCI status domains. The graph shows what percent of genes with each call are in each domain type. Percent is determined by dividing the number of genes with that XCI status call in that domain type by the total number of genes with that XCI status call. The all calls category includes all genes on the X chromosome, including genes with no calls. c Distribution of genes at boundaries. This figure includes the subject and escape genes which define the edges of the boundaries