The effects of cytosine methylation on general transcription factors

Abstract

DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.

High throughput screening identifies SOX2 as a Super Pioneer Factor that inhibits DNA methylation maintenance at its binding sites

“…On the other hand, N-MYC was reported to bind to hypermethylated regions in neuroblastoma cell lines, although binding sites in this study were depleted of the E-box CACGTG that was used in our study 57 . While GR was previously shown to bind methylated cytosines in non-CG context, its effect on DNA methylation was not assessed 58 . Finally, SOX9 and SOX17 have low expression levels in ESCs, but seem to behave as PPFs and SPFs in these cells: while low expression levels may be sufficient for this activity, it cannot be excluded that the motifs chosen might also be recognized and bound by other SOX family members.…”

Epigenetics and Trained Immunity

“…First, 5mc is mechanistically interpreted by proteins possessing the methyl-CpG-binding domain, which, in turn, recruit transcriptional repressors and chromatin remodeling complexes to establish transcriptionally incompetent chromatin (43). Second, 5mc can physically modulate the binding of TFs to gene regulatory elements (52). On the other hand, 5mc regulates gene splicing, transcriptional elongation, and distal regulatory activities of highly transcribed genes (53).…”

DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices

“…It is an inheritable chemical modification that regulates gene transcription [1]. The mechanism of this regulation is either by binding of dedicated proteins that serve as a reader of the epigenetic state [2], or by modulating the assembly of the transcription machinery directly [3]. Understanding the mechanisms through which DNA methylation influences gene expression is an active research field due to the growing evidence of its relation to human development and disease, and in particular aging [4], environmental response [5], and cancer [6].…”