Fig. 1

Genome-wide DNA methylation segmentation across different cell types. IGV snapshot showing DNA methylation profiles of different cell types (from top to bottom: monocytes, macrophages, naive/central/effector/terminal memory T cells, naive/germinal center/class switched memory B cells, plasma, GM12878, HepG2, HepaRG, and primary human hepatocytes) with the corresponding MethylSeekR segments: highly methylated domains (red); HMDs, partially methylated domains (light pink); PMDs, low methylated regions (light blue); LMRs and unmethylated regions (blue); UMRs (only one track per cell type shown for simplicity). Below the block of methylation data, three broad histone marks and RNA-seq profiles of hepatocytes are displayed. PMDs can be seen as long regions with highly disordered methylation levels and tend to be largely overlapping between the different cell types. However, there are cell type-specific PMDs (the highlighted region shows a hepatocyte-specific PMD). PMDs are gene-poor and transcriptionally inactive regions and have heterochromatic signature (H3K27me3 and H3K9me3). In contrast, HMDs are transcriptionally active and rich-gene regions with enrichment of active histone mark H3K36me3