We used chromatin states to study the relationship between histone modification patterns, RNA expression levels, DNA methylation, and DNA accessibility. Consistent with previous studies19,23,43-44, we found low DNA methylation and high accessibility in promoter states, high DNA methylation and low accessibility in transcribed states, and intermediate DNA methylation and accessibility in enhancer states (Fig. 4d-e, Extended Data 3a,b). These differences in methylation level were stronger for higher-expression genes than for lower-expression genes, leading to a more pronounced DNA methylation profile (Extended Data 3c, Fig. S5, Table S4f). Genes proximal to H3K27ac-marked enhancers show significantly higher expression levels (Extended Data 3d), and conversely, higher-expression genes were significantly more likely to neighbor H3K27ac-containing enhancers (Extended Data 3e).
