Fig. 3

Comparison of single-base resolution DNA methylomes at the KBTBD6 locus among mammalian species. A DNA methylation in oocytes (pink histogram lines) and sperm (blue histogram lines) of the human (Homo sapiens), rhesus monkey (Macaca mulatta), mouse (Mus musculus), pig (Sus scrofa), and cow (Bos taurus) are displayed encompassing the KBTBD6 promoter CpG islands. B DNA methylation in fetal, neonatal and/or adult tissues. Species other than in A include crab-eating macaque (Macaca fascicularis), chimpanzee (Pan troglodytes), gibbon (Nomascus leucogenys), horse (Equus caballus), dog (Canis lupus familiaris), goat (Capra hircus), and sheep (Ovis aries). Analyzed tissues include: f-Br, fetal brain; Br, brain; f-Mu, fetal muscle; Mu, muscle; He, heart; Li, liver; Lu, lung; Ki, kidney; Bl, blood; Pl, placenta; n-Br, neonatal brain; y-Mu, young skeletal muscle (d 40); a-Mu, adult skeletal muscle (d 180); a-Sn, angen stage of skin; and t-Sn, telogen stage of skin; e-Mu, embryonic muscle (embryonic d 110); a-Mu (sheep), adult skeletal muscle (2-year-old). C Read-based analysis on partially methylated domains (PMDs) [pig chr11:25,705,500–25706700, cow chr12:11,335,500–11,336,700, goat chr12:75,202,000–75,203,500, sheep chr10:11,665,250–11,666,500, horse chr17:28,812,781–28,813,430, and dog chr22:9,466,000–9,467,173; These regions are grey-shaded in B]. The number of qualified reads (at least 3 CpGs) with methylation levels ranging either from 0.0 to 0.2 (hypomethylated reads) or 0.8 to 1.0 (hypermethylated reads) was divided by the total number of qualified reads to plot percentages of hypo- and hyper-methylated reads in PMDs in each tissue. A threshold for allelically methylated regions was the percentage of 30%. Consecutive CpG sites (x-axis) within the allelically methylated regions are plotted for each read (y-axis) with open and closed circles indicating unmethylated and methylated CpG sites, respectively. D Phylogenetic tree of the twelve mammalian species and divergence time estimation. MYA, million years ago. A color code was used to highlight species showing partial DNA methylation (brown) as opposed to hypomethylation patterns (cyan)