Figure 3.

Hypermethylated genes have conserved promoter regions. (a) Hypermethylation prone promoters are depleted of repetitive elements. Shown are graphs of the frequency of LINEs, SINEs and LTRs at 1 kb intervals around hypermethylation prone and resistant TSSs. The significance of the differences in densities observed at prone and resistant genes were determined using Fisher's exact tests for the repeat counts ± 2 kb from the TSSs (*** P < 0.001, ** P < 0.01 and * P < 0.05). (b) Hypermethylation prone promoter regions are evolutionarily conserved. Shown are graphs of the level of conservation found in 500bp intervals around hypermethylation prone and resistant TSSs. Conservation was assessed through two different methods: one measuring the rate of basepair substitutions between species, 'bp Changes' [46], and the other measuring the rate of insertions and deletions between species, 'Indel. Pur.' [47]. The significance of observed differences between hypermethylation-prone and -resistant genes was assessed using a Wilcoxon rank sum test for the scores ± 2 kb from the TSSs. (c) Hypermethylation prone genes are found adjacent to lincRNAs. Shown is a chart of the percent of hypermethylation-prone and -resistant genes found neighboring a lincRNA [49]. The significance of differences between the gene sets was assessed using Fisher's exact tests. lincRNA, long intergenic non-coding RNAs; LTR, long terminal repeat; TSSs, transcriptional start sites.