We next studied the relationship between DNA methylation dynamics and histone modifications across 95 epigenomes with methylation data, extending previous studies that focused on individual lineages19,47-49. We found that the distribution of methylation levels for CpGs in some chromatin states varied significantly across tissue and cell types (Fig. 4g, Extended Data 4f, Table S4a). For example: TssAFlnk states are largely unmethylated in terminally-differentiated cells and tissues, but frequently methylated for several pluripotent and ESC-derived cells (Bonferroni-corrected F-test p<.01); Enh and EnhG states are highly methylated in pluripotent cells, but show a broader distribution of intermediate methylation in differentiated cells and tissues (p<.01); EnhBiv states are unmethylated in most primary cells and tissues, but show a broader distribution of methylation levels in pluripotent cells, possibly reflecting cell-to-cell heterogeneity (p<.01); the repressed state ReprPC shows varying methylation levels among epigenomes; the Het state showed high levels of methylation in almost all epigenomes.
