Methylation patterns and substitution rates in different tissue types. (A) Comparison of the methylation patterns in Hd-rR: blastulae vs. liver, and testes vs. liver. The vertical and horizontal axes show methylation level. The methylation patterns in HNI are presented in Supplemental Fig. S5 and are similar to those in these figures. (B) SNP rates in CpG site blocks with three methylation states: hypomethylated in both of the two tissue types, hypermethylated in both, and differentially methylated between the two tissue types. Significant differences in SNP rates were seen between tissue-differentially and hypomethylated regions (P < 10−82 by a two-proportion z-test) (Supplemental Table S6), and between hypo- and hypermethylated CpG site blocks (P < 10−2170) (Supplemental Table S6). (C) Dinucleotide substitution rates in CpG site blocks with the three methylation states. The substitution rates of all dinucleotides, except for CC/GG/CG, in tissue-differentially methylated regions were significantly lower than those in hypomethylated regions (P < 10−3 by a two-proportion z-test) (Supplemental Table S7A). (D) Representative mutation patterns in hypomethylated, hypermethylated, and somatic cell-specific hypomethylated (germline-like-specific hypermethylated) regions. Somatic cell-specific hypomethylated regions exhibited the lowest mutation rates.
