title: DNA methylation presents distinct binding sites for human transcription factors.
abstract: DNA methylation, especially CpG methylation at promoter regions, has been generally considered as a potent epigenetic modification that prohibits transcription factor (TF) recruitment, resulting in transcription suppression. Here, we used a protein microarray-based approach to systematically survey the entire human TF family and found numerous purified TFs with methylated CpG (mCpG)-dependent DNA-binding activities. Interestingly, some TFs exhibit specific binding activity to methylated and unmethylated DNA motifs of distinct sequences. To elucidate the underlying mechanism, we focused on Kruppel-like factor 4 (KLF4), and decoupled its mCpG- and CpG-binding activities via site-directed mutagenesis. Furthermore, KLF4 binds specific methylated or unmethylated motifs in human embryonic stem cells in vivo. Our study suggests that mCpG-dependent TF binding activity is a widespread phenomenon and provides a new framework to understand the role and mechanism of TFs in epigenetic regulation of gene transcription. DOI:http://dx.doi.org/10.7554/eLife.00726.001.
authors.affiliation: Department of Pharmacology and Molecular Sciences , Johns Hopkins University School of Medicine , Baltimore , United States ; Center for High-Throughput Biology , Johns Hopkins University School of Medicine , Baltimore , United States.
authors.forename: Shaohui
authors.initials: S
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Wan
authors.forename: Yijing
authors.initials: Y
authors.lastname: Su
authors.forename: Qifeng
authors.initials: Q
authors.lastname: Song
authors.forename: Yaxue
authors.initials: Y
authors.lastname: Zeng
authors.forename: Ha Nam
authors.initials: HN
authors.lastname: Nguyen
authors.forename: Jaehoon
authors.initials: J
authors.lastname: Shin
authors.forename: Eric
authors.initials: E
authors.lastname: Cox
authors.forename: Hee Sool
authors.initials: HS
authors.lastname: Rho
authors.forename: Crystal
authors.initials: C
authors.lastname: Woodard
authors.forename: Shuli
authors.initials: S
authors.lastname: Xia
authors.forename: Shuang
authors.initials: S
authors.lastname: Liu
authors.forename: Huibin
authors.initials: H
authors.lastname: Lyu
authors.forename: Guo-Li
authors.initials: GL
authors.lastname: Ming
authors.forename: Herschel
authors.initials: H
authors.lastname: Wade
authors.forename: Hongjun
authors.initials: H
authors.lastname: Song
authors.forename: Jiang
authors.initials: J
authors.lastname: Qian
authors.forename: Heng
authors.initials: H
authors.lastname: Zhu
mesh_terms: D001665:Binding Sites; D018899:CpG Islands; D019175:DNA Methylation; D006801:Humans; D000090062:Kruppel-Like Factor 4; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D014157:Transcription Factors
keywords: DNA methylation; Human; epigenetics; protein microarray; protein-DNA interactions; transcription factors; transcription regulation