Fig. 5

Derepressed genes are transcribed and enriched for active chromatin marks in WT TSCs. a Inactive-X profiles of H3K27me3 in WT TSCs of derepressed and non-derepressed genes in Eed ^–/– TSCs and of X-inactivation escapees in WT TSCs. b Inactive-X profiles for DNAseI hypersensitivity (DNAseI HS), RNA PolII occupancy, H3K27ac, H3K4me2, and H3K36me3. c Correlation between percent paternal-X expression in WT and Eed ^–/– TSCs. d Paternal-X contribution for all expressed X-linked genes in WT TSCs. The x-axis indicates the rank order of each gene from least to most paternal-X expression in WT TSCs. Gray dots indicate non-derepressed genes and red dots mark genes that are derepressed in Eed ^–/– TSCs. The y-axis depicts percent paternal-X expression for each gene. The expressed paternal X-linked genes can be divided into five quintiles. The derepressed genes are over-represented in quintile 4. e Table of number of genes and their percent paternal-X expression within the quintiles described in (d). f Left, boxplots of absolute paternal-X expression (as RNA-seq reads per kilobase of gene per million reads [RPKM]) for non-derepressed and derepressed genes in quintile 4 (3–6% paternal-X:total X-chromosomal expression). Derepressed genes exhibit a significantly higher median expression level than non-derepressed genes (p < 0.001, Mann–Whitney U test). Right, boxplots of absolute paternal-X expression (Log₂ scaled, as RPKM) for all non-derepressed and derepressed genes. As with quintile 4, derepressed genes exhibit a significantly higher median expression level than non-derepressed genes (p < 0.05, Mann–Whitney U test)