Fig. 2

RRMP analysis of methylation in CpG island and promoters. a, b Plots show the number of CpG islands (a) or promoters (b) with at least 100-fold combined coverage as a function of sequencing depth (x axis) for 1-cut RRMP (K562), XRBS (K562), WGBS (K562), and RRBS (SW1353). Enrichment for functional elements at a uniform sequencing depth of 10 billion base pairs is indicated. Vertical gray line indicates break in x-axis scale. c, Plot shows coverage depth of CpGs in WGBS, XRBS, 1-cut RRMP, and 4-cut RRMP at a uniform sequencing depth of 10 billion base pairs. d–f Heat maps compare individual CpG methylation values between 1-cut RRMP and WGBS (d, r = 0.88), 1 cut-RRMP and XRBS (e, r = 0.85), 1 cut-RRMP and 4-cut RRMP (f, r = 0.98) for K562 cells. Analysis limited to CpGs with at least 20-fold coverage (n = 128,501, 160,804 and 1,659,714 CpGs). Percentages indicate the fraction of CpGs that differed between conditions (difference in beta values > 0.5). g, h Heatmaps compare average DNA methylation values from 1-cut RRMP datasets with signal for H3K4me3 (g) and H3K27ac (h) for K562 cells. Percentages indicate the fraction of hypermethylated (beta value >  = 10%) and hypomethylated(beta value < 10%) regions with Chip-seq signal > 1