Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

Publication date: 13 June 2017
Source:Cell Reports, Volume 19, Issue 11
Author(s): Judith F. Kribelbauer, Oleg Laptenko, Siying Chen, Gabriella D. Martini, William A. Freed-Pastor, Carol Prives, Richard S. Mann, Harmen J. Bussemaker
Although DNA modifications play an important role in gene regulation, the underlying mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of transcription factor binding to DNA modification in vitro using massively parallel sequencing. Feature-based modeling quantifies the effect of cytosine methylation (⁵mC) on binding free energy in a position-specific manner. Application to the human bZIP proteins ATF4 and C/EBPβ and three different Pbx-Hox complexes shows that ⁵mCpG can both increase and decrease affinity, depending on where the modification occurs within the protein-DNA interface. The TF paralogs tested vary in their methylation sensitivity, for which we provide a structural rationale. We show that ⁵mCpG can also enhance in vitro p53 binding and provide evidence for increased in vivo p53 occupancy at methylated binding sites, correlating with primed enhancer histone marks. Our results establish a powerful strategy for dissecting the epigenomic modulation of protein-DNA interactions and their role in gene regulation.

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Teaser

Kribelbauer et al. present a high-throughput method for quantifying the in vitro sensitivity of TF binding to epigenetic DNA modifications. Application to p53 tetramers shows that cytosine methylation can either increase or decrease binding affinity, depending on where the modification occurs within the binding interface. These effects persist in vivo.


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