Distribution of H3K27me3 on the X chromosome in XEN cells. (A) Boxplots of the distribution of H3K27me3 along X-linked intergenic regions and X-linked gene bodies of expressed X-linked genes (Exp.) or along genes that are not significantly expressed (Not exp.) in male and female extraendoderm stem (XEN) cells (GHP7/7 and GHP7/9 cell lines). Expression data were extracted from the Gene Expression Omnibus database [GSE:15519] . n = 1,054 intergenic regions and n = 642 X-linked genes. *P < 0.05 by Kolmogorov–Smirnov test. (B) Representative examples of H3K27me3 distribution along expressed genes enriched in H3K27me3 in female compared to male XEN cells ([K27-high]) and along expressed genes showing low levels of H3K27me3 in female and in male XEN cells ([K27-low]) (GHP7/7 and GHP7/9 cell lines). mm9 University of California Santa Clara (UCSC) Genome Browser screenshots are shown. IP, immunoprecipitated DNA; IN, input DNA. (C) Scatterplot of H3K27me3 percentages along the body of expressed X-linked genes in female (y-axis) relative to male (x-axis) XEN cells (GHP7/7 and GHP7/9 cell lines (see Additional file 4A for results in the GHP7/3 cell line and Additional file 2C for the complete data set). Each dot represents a single gene and its respective percentage of H3K27me3 in male and female XEN cells. k-means clustering was applied, which led to the identification of three classes of genes. K27-high genes (red dots) are concentrated in the upper left quadrant consistently, with them being depleted in H3K27me3 in male cells and enriched in H3K27me3 in female cells. K27-low genes (blue dots) are significantly depleted in H3K27me3 in both male and female cells. In agreement with H3K27me3 marking preferentially the silent state, very few expressed genes are enriched in H3K27me3 in both male and female cells ( genes; indicated by maroon dots). These  genes may have resulted from the fact that gene expression data  and our chromatin immunoprecipitation followed by chip hybridisation experiment data were obtained from different XEN cell lines. The pie chart underneath the scatterplot represents the percentage of expressed genes in each H3K27me3 class.