An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine

• Type of Material: Article
• Authors: Guang Song, Johns Hopkins University; Gouhua Wang, Harbin Institute of Technology; Ximei Luo, Harbin Institute of Technology; Ying Cheng, Emory University; Qifeng Song, Johns Hopkins University; Jun Wan, Johns Hopkins University; Cedric Moore, Johns Hopkins University; Hongjun Song, University of Pennsylvania; Peng Jin, Emory University; Jiang Qian, Johns Hopkins University; Heng Zhu, Johns Hopkins University
• Language: English
• Date: 2021-02-04
• Publisher: NATURE RESEARCH
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2021
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1038/s41467-021-20950-w
• Title of Journal or Parent Work: NATURE COMMUNICATIONS
• Volume: 12
• Issue: 1
• Start Page: 795
• End Page: 795
• Keywords: Multidisciplinary Sciences; Science & Technology - Other Topics; Science & Technology
• Research Categories: Health Sciences, Pharmacology; Biology, Neuroscience; Computer Science

Abstract

Epigenetic modifications of DNA play important roles in many biological processes. Identifying readers of these epigenetic marks is a critical step towards understanding the underlying mechanisms. Here, we present an all-to-all approach, dubbed digital affinity profiling via proximity ligation (DAPPL), to simultaneously profile human TF-DNA interactions using mixtures of random DNA libraries carrying different epigenetic modifications (i.e., 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine) on CpG dinucleotides. Many proteins that recognize consensus sequences carrying these modifications in symmetric and/or hemi-modified forms are identified. We further demonstrate that the modifications in different sequence contexts could either enhance or suppress TF binding activity. Moreover, many modifications can affect TF binding specificity. Furthermore, symmetric modifications show a stronger effect in either enhancing or suppressing TF-DNA interactions than hemi-modifications. Finally, in vivo evidence suggests that USF1 and USF2 might regulate transcription via hydroxymethylcytosine-binding activity in weak enhancers in human embryonic stem cells.