The Oct4/Sox2 Complex Varies in its Ability to Displace Nucleosomes at Functional Transcription Factor Sites in Murine Embryonic Stem Cells. Mus musculus

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. 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 the ability of Oct4 and Sox2 transcription factors to affect nucleosome occupancy in different ways, which may reflect distinct patterns of stem cell gene regulation. Overall design: BAC-enrichment method sequencing (BEM-seq) of micrococcal nuclease digested in vivo nucleosomes and in vitro nucleosome preferences from murine embryonic stem cells