Fig. 1

Correlation of chromatin marks and gene transcription regulators with DNA methylation in promoters and putative enhancers. The promoters are labeled as Promoter, TSS. The putative enhancers are distributed across different classes including repeat-associated regions {Short Interspersed Nuclear Element (SINE), Long Interspersed Nuclear Element (LINE), Simple repeat, Long Terminal Repeat (LTR), DNA Transposon, Low complexity, DNA Transposon}, Intergenic, Intron, coding regions {Exon, 3’UTR, Transcription Termination Site (TTS)}, Non-coding regions, CpG island, and Others. The promoters and different classes of enhancers are split into (a) DNA hypermethylated (DNA methylation >0.5) and (b) DNA hypomethylated (DNA methylation ≤0.5) groups. In each DNA methylation group, regulatory sites are classified based on their genomic location (rows). For each class, Spearman’s rank correlations, ρ, between DNA methylation of ESCs and 9 different chromatin marks, the repressive histone 3 (H3), the gene transcription marker RNA polymerase 2 (Pol2), the enhancer marker histone acetyltransferase P300, and insulator marker CCCTC-binding factor are presented in columns. Red, white and blue colors show positive, null and negative correlations, respectively