Figure 3

Genome wide distribution of common hyper- and hypomethylated probes. y axis scale ranges between 1.9 and 5.1 (a) Distribution of all common hyper- and hypomethylated probes across the genome (from Fig. 2b,c and Table 1). There was no significant difference when all hyper- and hypomethylated probes are plotted together. (b) Common hyper- (above the chromosomes) and hypo- (below the chromosomes) methylated probes in promoters (Prom, blue), Enhancers (Enh, green), and gene bodies (Body, red) are distributed across the human genome. For hypermethylated probes, the values range from +1.9 to +7 and for hypomethylated probes the range is between −1.9 and −7. Promoters show high density of hypomethylated probes, while gene bodies and enhancers show high density of hypermethylated probes across the human genome. Notably, enhancers show low density of hypomethylated probes. (c) The ratio of common hypomethylated promoter probes was significantly higher than common gene body and enhancers probes. In contrary, the ratio of common hypermethylated gene body probes is significantly higher than both enhancer and promoter probes. The ratio of common hypermethylated enhancer probes was also significantly higher than promoters. (paired t-test). (d) Closer look at selected chromosomes shows that specific regions in the human genome corresponding to the dark bands are largely devoid of hyper- and hypomethylated probes corresponding to gene body, enhancer and promoter (arrows).