Fig. 3. Sequence and epigenetic features of differentially methylated regions.

A Correlation of normalized read density at NMIs. r1 = BioCAP replicate 1, r2 = BioCAP replicate 2. B k-means clustering of mCG signal at merged NMIs (k = 5, 2 clusters shown). Y axis boxes refer to individual clusters. r1 = WGBS replicate 1, r2 = WGBS replicate 2. C BioCAP, mCG and ATAC-seq signal⁵⁶ at core NMIs (single replicate depicted for all heatmaps). D BioCAP signal at core and differential NMIs (highlighted in gray) overlapping transcription start sites (single replicate depicted). E Sequence motif enrichment at core NMIs. F Percentage of transcription start sites at protein-coding genes (n = 20,895) overlapped by NMI. G Percentage of differentially enriched NMIs at genomic features. H mCG profiles from merged WGBS replicates at DMRs (highlighted in gray). I Correlation of genomic DMR overlap. J k-means clustering (k = 5) of mCG signal at all DMRs. Y axis boxes refer to individual clusters. r1 = WGBS replicate 1, r2 = WGBS replicate 2.