Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation

Abstract

Background X-chromosome inactivation (XCI) is the epigenetic inactivation of one of two X chromosomes in XX eutherian mammals. The inactive X chromosome is the result of multiple silencing pathways that act in concert to deposit chromatin changes, including DNA methylation and histone modifications. Yet over 15% of genes escape or variably escape from inactivation and continue to be expressed from the otherwise inactive X chromosome. To the extent that they have been studied, epigenetic marks correlate with this expression. Results Using publicly available data, we compared XCI status calls with DNA methylation, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3. At genes subject to XCI we found heterochromatic marks enriched, and euchromatic marks depleted on the inactive X when compared to the active X. Genes escaping XCI were more similar between the active and inactive X. Using sample-specific XCI status calls, we found some marks differed significantly with variable XCI status, but which marks were significant was not consistent between genes. A model trained to predict XCI status from these epigenetic marks obtained over 75% accuracy for genes escaping and over 90% for genes subject to XCI. This model made novel XCI status calls for genes without allelic differences or CpG islands required for other methods. Examining these calls across a domain of variably escaping genes, we saw XCI status vary across individual genes rather than at the domain level. Lastly, we compared XCI status calls to genetic polymorphisms, finding multiple loci associated with XCI status changes at variably escaping genes, but none individually sufficient to induce an XCI status change. Conclusion The control of expression from the inactive X chromosome is multifaceted, but ultimately regulated at the individual gene level with detectable but limited impact of distant polymorphisms. On the inactive X, at silenced genes euchromatic marks are depleted while heterochromatic marks are enriched. Genes escaping inactivation show a less significant enrichment of heterochromatic marks and depletion of H3K27ac. Combining all examined marks improved XCI status prediction, particularly for genes without CpG islands or polymorphisms, as no single feature is a consistent feature of silenced or expressed genes.

X chromosome dosage and the genetic impact across human tissues

“…2 D). The observed changes in gene expression agreed with previous studies showing that escape genes tend to be expressed from the inactive X chromosome (Xi) at a level that is between 10 and 95% the expression level seen from the active X chromosome (Xa) [ 31 – 33 ]. The same pattern was observed in fat and muscle tissue (Fig.…”

MC profiling: a novel approach to analyze DNA methylation heterogeneity from bulk bisulfite sequencing data

“…First, we compared MC profiles of epiloci flanking genes with reported differential inactivation status. Consistent with previous findings (62)(63)(64), escapee epiloci showed homogeneous DNA methylation on both X copies, being unimodally fully methylated or unmethylated. Subject epiloci, on the contrary, were enriched for more heterogeneous MC profiles (D3 and D5), compatible with different DNA methylation status of the two alleles (62)(63)(64).…”

The inactive X chromosome accumulates widespread epigenetic variability with age

“…We first focused on CpGs whose mean methylation differed with age (aDMCs) using DGLM. To confirm the robustness of this approach, we compared results with those obtained using a conventional model fitted using limma [40] and the effect sizes were virtually identical (Additional file 1: Figure S1). In the discovery data set, we identified 1837 aDMCs in males but only 80 in females (P bonf < 0.05; Table 1 and for a full list: Additional file 2: TableS2 and Table S3).…”

“…Consensus XCI status calls per gene were previously defined [38] on the basis of three published studies [13, 14, 39] and resulted in genes classified into three categories: subject to XCI, escape XCI and variably escape XCI. These XCI status calls are referred to as meta-status calls [40]. For the annotation, we mapped CpGs to the nearest transcription start site (TSS) and when within 2kb from a TSS, the XCI status of the CpGs was set equal to the XCI status of the gene associated with the TSS.…”

“…Consensus XCI status calls per gene were previously defined [38] on the basis of three published studies [13,14,39] and resulted in genes classified into three categories: subject to XCI, escape XCI and variably escape XCI. These XCI status calls are referred to as meta-status calls [40].…”