Figure 2: IM is associated with intermediate levels of epigenomic modifications and gene expression.
From: Intermediate DNA methylation is a conserved signature of genome regulation
(a) Distribution of IM CpGs over Refseq genome feature annotations. (b) Distance from each IM region to the nearest DHS (P<0.001, χ2; odds ratio=2.53). DHSs were compiled from 41 different cell types, covering approximately 8% of the genome. (c) Comparison of H3K4me3 and H3K4me1 signals between methylated (Meth), unmethylated (Unmeth) and IM regions in five different cell types using a generalized additive model (GAM; grey outlines indicate 95% confidence interval (CI); *donor for histone ChIP-seq does not match donor used in IM analysis). (d) Comparison of DHS signals between Meth, Unmeth and IM regions (grey outlines indicate 95% CI; *donor for DNase-seq does not match donor used in IM analysis). (e) Top panel, average whole-transcript expression of genes associated with Meth, Unmeth and IM regions. Bottom panel, average exon expression relative to its gene expression for exons within 1 kb of Meth, Unmeth and IM regions (error bars represent s.e.m.; **P<0.005, Wilcoxon; ***P<0.0001, Wilcoxon). Expression analysis was based on mRNA-seq data from breast myoepithelial cells. Total transcript-associated regions: IM=6,776; Meth=3,270; Unmeth=5,605. Total exon-associated regions: IM=14,336; Meth=6,642; Unmeth=9,331.
