Developing a software suite to analyze the interplay between nucleosome arrangement, DNA methylation and transcription factor binding

Abstract

We have developed a software suite for the biophysical analysis of high-throughput sequencing experiments, and applied it to the interplay between nucleosome positioning, DNA methylation and transcription factor binding during ES cell differentiation. DNA cytosine methylation (5mC) and hydroxymethylation (5hmC) are among the most important epigenetic marks. The interplay of 5mC/5hmC marks, the arrangement of nucleosomes and transcription factors (TFs) links DNA methylation with cellular gene expression programs but the underlying mechanisms are poorly understood. Here, we analyzed nucleosome positioning, DNA methylation and TF binding in conjunction with additional dinucleosome occupancy maps. Our study provides a novel quantitative description for the relations between DNA methylation/demethylation, TF binding and nucleosome occupancy changes.