Hu Shaohui, Wan Jun, Su Yijing, Song Qifeng, Zeng Yaxue, Nguyen Ha Nam, Shin Jaehoon, Cox Eric, Rho Hee Sool, Woodard Crystal, Xia Shuli, Liu Shuang, Lyu Huibin, Ming Guo-Li, Wade Herschel, Song Hongjun, Qian Jiang, Zhu Heng
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.
Elife. 2013 Sep 3;2:e00726. doi: 10.7554/eLife.00726.
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.
DNA甲基化，尤其是启动子区域的CpG甲基化，通常被认为是一种强大的表观遗传修饰，它会阻止转录因子（TF）的募集，从而导致转录抑制。在此，我们采用基于蛋白质微阵列的方法对整个人类TF家族进行了系统研究，发现了众多具有依赖甲基化CpG（mCpG）的DNA结合活性的纯化TF。有趣的是，一些TF对不同序列的甲基化和未甲基化DNA基序表现出特异性结合活性。为了阐明其潜在机制，我们聚焦于Kruppel样因子4（KLF4），并通过定点诱变将其mCpG结合活性和CpG结合活性解耦。此外，KLF4在体内可结合人类胚胎干细胞中的特定甲基化或未甲基化基序。我们的研究表明，依赖mCpG的TF结合活性是一种普遍现象，并为理解TF在基因转录表观遗传调控中的作用和机制提供了一个新框架。DOI:http://dx.doi.org/10.7554/eLife.00726.001。
