Extended Data Fig. 5: Local density of the methylome and specific histone marks alter 5mCpG maintenance activity.
(a) Box plot of 5mCpG maintenance levels in 1 kb genomic bins categorized based on the number of CpG sites in the bin and the absolute methylation levels. ‘Low 5mC’ indicates methylation levels lower than 20%, ‘Medium 5mC’ indicates methylation levels between 20% and 80%, and ‘High 5mC’ indicates methylation levels greater than 80%. N.D. stands for “Not detected”. 1 kb regions in which at least 5 unique CpG dyads are detected were included in this panel. The number of bins in each category is denoted above each boxplot. Data in this panel corresponds to mESCs grown in SL condition and profiled using M-M-Dyad-seq. (b) 5mCpG maintenance levels at fully methylated regions (FMR), lowly methylated regions (LMR), and unmethylated regions (UMR) as stratified by Stadler et al.53. Data in this panel corresponds to mESCs grown in SL condition and profiled using M-M-Dyad-seq. Dots indicate independent biological replicates (n = 3). (c-k) Box plots of 5mCpG maintenance levels as a function of absolute 5mCpG levels at individual loci enriched for a histone mark (‘I’) or a meta-region (‘M’) containing all enriched loci corresponding to a histone mark for all 1kb bins in the genome (c), H3K9me2 (d), H3K9ac (e), H3K36me3 (f), H3K27me3 (g), H3K27ac (h), H3K9me3 (i), H3K4me3 (j), H3K4me1 (k). Distributions for the meta-regions were obtained using bootstrapping, where resampling was performed 1,000 times per histone mark. Blue dots indicate average values found in genome-wide 1kb bins (same as data presented in panel (c)). (l) Standard error for the meta-regions in panels (c-k) and Fig. 3e.
