GSE64171
The effects of cytosine methylation on general transcription factors
DNA methylation (mC) on CpG sites is the most common epigenetic modification.  Recently methylation on non-CpG context was found to widely occur on genomic DNA.  However, how non-CpG methylation influences DNA/protein interaction and regulates transcription is unknown.  Using single-molecule assays, we studied the interactions of transcription factors (TFs) GR, ER and BMAL1-CLOCK with methylated or unmethylated cognate DNA binding sequences.  The results demonstrated that these TFs interact with methylated DNA discriminatively.  We then performed BisChIP-seq with GR and BMAL1-CLOCK in HEK-293T cells and showed that they can recognize and bind to the methylated sites within chromatin.  The effects of non-CpG methylation on transcriptional regulation were validated by in vitro transcription assays with correlated RNA level, and further studied mechanistically by crystallographic analyses and molecular dynamics simulations.  We conclude that the non-CpG methylation of DNA provides another general mechanism for regulating gene expression through affecting TFs binding affinity. Overall design: In order to verify that TFs can bind to and distinguish the methylated and unmethylated DNA in vivo, we performed bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) for two TFs - GR and BMAL1-CLOCK in HEK-293T cells.  The experiment revealed that both GR and BMAL1-CLOCK could distinguish between the methylated and the unmethylated sites in cells.