Figure 4.

Transcription level has significant correlation with promoter DNAm as well as heterochromatin DNAm. Box and whisker plots comparing the average male (Xa) DNAm (PB) of the genes from the highest expression quartile and the lowest expression quartile by CpG density class (HIC, IC, LC; Ref. 22). (A) Promoters, (B) enhancers and insulators, (C) transcribed regions of genes and (D) repressed and heterochromatic regions were defined based on the chromatin states in Ref. 20. Significance based on a Wilcox test comparison of means is as follow: *P-values 0.05–0.001, **P-values 0.001–2.2E − 16 and ***P-values < 2.2E − 16). (E) Summary of X-linked DNAm patterns. The Xa and Xi DNAm patterns of females are summarized for genes that are subject to XCI and genes that escape from XCI. The average Xa and Xi DNAm values given are an average of all CpGs used in this analysis within the denoted category. The presence of individual CpGs (ovals) is meant only as a graphical representation and does not accurately denote CpG density. Chromatin states were combined with intergenic and intragenic data to separate CpGs within the gene body from CpGs between genes.