title: 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.
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.|State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China.
authors.forename: Jianshi
authors.initials: J
authors.lastname: Jin
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.|State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China.
authors.forename: Tengfei
authors.initials: T
authors.lastname: Lian
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.|Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
authors.forename: Chan
authors.initials: C
authors.lastname: Gu
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.|State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Yu
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.|Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
authors.forename: Yi Qin
authors.initials: YQ
authors.lastname: Gao
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.|State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China.
authors.forename: Xiao-Dong
authors.initials: XD
authors.lastname: Su
mesh_terms: D001483:Base Sequence; D001921:Brain / Q000254:growth & development / Q000378:metabolism; D056926:CLOCK Proteins / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000378:metabolism; D005260:Female; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D006801:Humans; D007231:Infant, Newborn; D008156:Luciferases / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D056004:Molecular Dynamics Simulation; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D000072417:Protein Domains; D011965:Receptors, Glucocorticoid / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D011965:Receptors, Glucocorticoid; D014157:Transcription Factors; D003596:Cytosine; D008156:Luciferases; D056926:CLOCK Proteins