Transcriptional gene silencing is mediated by various epigenetic modifications including DNA methylation, histone modifications and recruitment of binding proteins that reads the methyl and other modification marks. The order in which these modifications occur followed by repressor protein recruitment remains contentious. Here, using purified protein components, we show that mammalian RNA polymerase II (RNA Pol II) is involved in DNA methylation control. DNA (cytosine-5) methyltransferase 1 (DNMT1) colocalizes, directly interacts and binds to the phosphorylated C-terminal repeat domain (CTD) of Rpb1, a major structural subunit of RNA Pol II. The association of RNA Pol II with DNMT1 during transcription enhances DNA methylation, and methylated DNA doesn’t affect in vitro transcription. Addition of methyl CpG binding protein 2 (MeCP2), inhibited in vitro transcription of DNA in a methylation dependent manner, suggesting a possible mechanism for RNA Pol II coupled transcriptional silencing mediated by DNMT1 and MeCP2.