Given the intermediate methylation levels of tissue-specific enhancer regions, we directly annotated intermediate methylation (IM) regions, based on the complementary DNA methylation assays of MeDIP31,45 and MRE-Seq22,39 in 19 reference epigenomes and 6 additional samples which had both assays available46. This resulted in more than 18,000 IM regions, showing 57% CpG methylation on average, that are strongly enriched in genes, enhancer chromatin states (EnhBiv, EnhG, Enh), and evolutionarily-conserved regions. IM was associated with intermediate levels of active histone modification and DNaseI hypersensitivity. Near TSSs, IM correlated with intermediate gene expression, and in exons it was associated with an intermediate level of exon inclusion46. IM signatures were equally strong within tissue samples, peripheral blood, and purified cell types, suggesting that IM is not simply reflecting differential methylation between cell types, but likely reflects a stable state of cell-to-cell variability within a population of cells of the same type.
