Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s

Methylated non-CpGs (mCpH; H means A, C, and T) have emerged as key epigenetic marks in mammalian embryonic stem cells (ESCs) and neurons, regulating cell type-specific functions. In these two cell types, mCpHs show distinct motifs and correlations to transcription that could be a key in understanding the cell type-specific regulations. Thus, we attempted to uncover the underlying mechanism of the differences in ESCs and neurons by conducting a comprehensive analysis of public whole genome bisulfite sequencing data. Remarkably, there were cell type-specific mCpH patterns around methylated CpGs (mCpGs), resulted from preferential methylation at different contexts by DNA methyltransferase (DNMT) 3a and 3b. These DNMTs are differentially expressed in ESCs and brain tissues, resulting in distinct mCpH motifs in these two cell types. Furthermore, in ESCs, DNMT3b interacts with histone H3 tri-methylated at lysine 36 (H3K36me3), resulting in hyper-methylation at CpHs upon actively transcribed genes, including those involved in embryo development. Based on the results, we propose a model to explain the differential establishment of mCpHs in ESCs and neurons, providing insights into the mechanism underlying cell type-specific formation and function of mCpHs.