Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

Amy Sebeson,Liqun Xi,Audrey Sigmund,Quanwei Zhang,Jonathan Widom,Ji-Ping Wang,Xiaozhong Wang,Jason Glenn Knott

doi:10.1371/journal.pone.0127214

Abstract

The binding sequence for any transcription factor can be found millions of times within a genome, yet only a small fraction of these sequences encode functional transcription factor binding sites. One of the reasons for this dichotomy is that many other factors, such as nucleosomes, compete for binding. To study how the competition between nucleosomes and transcription factors helps determine a functional transcription factor site from a predicted transcription factor site, we compared experimentally-generated in vitro nucleosome occupancy with in vivo nucleosome occupancy and transcription factor binding in murine embryonic stem cells. Using a solution hybridization enrichment technique, we generated a high-resolution nucleosome map from targeted regions of the genome containing predicted sites and functional sites of Oct4/Sox2 regulation. We found that at Pax6 and Nes, which are bivalently poised in stem cells, functional Oct4 and Sox2 sites show high amounts of in vivo nucleosome displacement compared to in vitro. Oct4 and Sox2, which are active, show no significant displacement of in vivo nucleosomes at functional sites, similar to nonfunctional Oct4/Sox2 binding. This study highlights a complex interplay between Oct4 and Sox2 transcription factors and nucleosomes among different target genes, which may result in distinct patterns of stem cell gene regulation.

Highlights

The binding of transcription factors to DNA is a critical step in the regulation of gene expression
Experimentally-generated profile of nucleosome sequence preferences with a comparison of both predicted and functional transcription factor binding site (TFBS), our results suggest that Oct4 and Sox 2 transcription factors can decrease nucleosome occupancy in vivo at poised genes, but do not alter in vivo nucleosome occupancy at active genes
The advent of ChIP-seq technology greatly facilitated the identification of functional transcription factor binding sites within the genome

Summary

Introduction

The binding of transcription factors to DNA is a critical step in the regulation of gene expression. Transcription factors have specific DNA binding motifs [1, 2], which are found millions of times within the genome. Functional binding sites, identified by occupancy in ChIP experiments, occur with much less frequency. While much work has been done to identify binding motifs for transcription factors as well as to identify binding affinities in vitro [3,4,5,6], these two inputs are not enough to predict whether a binding site is utilized in vivo [3, 7]. Many other factors are involved in this process, such as cooperativity between transcription.

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