Study of 5mC-DNA, m6A-RNA and RNA-expression in HeLa and EB [RNAseq in HeLa]

The epigenetic marking of DNA, histones, and RNA is central for regulating gene expression in development and disease. On DNA, well-characterized 5-methylcytosine (5mC) controls the chromatin state. On mRNA, the most prevalent internal mark, N6-methyladenosine (m6A), installed by METTL3-METTL14 methyltransferases, regulates RNA metabolism. Recent evidences link RNA modifications with epigenetics, notably by connecting m6A to histone marks. The crosstalk between m6A and DNA methylation, however, remains poorly understood. Here we reveal a direct mechanistic link between m6A and DNA methylation. Our findings indicate a proximal co-occurrence of m6A and 5mC marks at gene body and this contributes to enhanced gene expression. We show that the m6A writer METTL3 regulates intragenic methylation and gene expression. Mechanistically, we evidence a direct binding of METTL3-METTL14 to the 5mC methyltransferase DNMT1 and reveal that chromatin-tethered METTL14 recruits DNMT1 to chromatin. We demonstrate that gene-body 5mC and mRNA-stability-enhancing effect of coding-sequence m6A contribute to increased gene expression. We further substantiate our findings in embryonic stem cells by showing that METTL3 regulates gene-body methylation and expression of key differentiation markers. Altogether, our work establishes a key layer of gene expression regulation, involving a direct mechanistic crosstalk between DNA methylation and RNA methylation machinery.