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An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine
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An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine
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Journal Article
An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine
2021
Overview
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.
Identifying readers of epigenetic marks is a critical step for understanding the role of epigenetic marks in biology. Here, the authors applied DAPPL, an all-to-all approach to profile the interactions between TFs and epigenetic modified DNA libraries.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ 5-Methylcytosine - analogs & derivatives
/ 5-Methylcytosine - metabolism
/ Binding
/ Cytosine
/ DNA
/ Humanities and Social Sciences
/ Humans
/ Recombinant Proteins - genetics
/ Recombinant Proteins - isolation & purification
/ Recombinant Proteins - metabolism
/ Science
/ Upstream Stimulatory Factors - genetics
