SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

SOX2 is a master regulator of both pluripotent embryonic stem cells (ESCs) and multipotent neural progenitor cells (NPCs); however, we currently lack a detailed understanding of how SOX2 controls these distinct stem cell populations. Here we show by genome-wide analysis that, while SOX2 bound to a distinct set of gene promoters in ESCs and NPCs, the majority of regions coincided with unique distal enhancer elements, important cis-acting regulators of tissue-specific gene expression programs. Notably, SOX2 bound the same consensus DNA motif in both cell types, suggesting that additional factors contribute to target specificity. We found that, similar to its association with OCT4 (Pou5f1) in ESCs, the related POU family member BRN2 (Pou3f2) co-occupied a large set of putative distal enhancers with SOX2 in NPCs. Forced expression of BRN2 in ESCs led to functional recruitment of SOX2 to a subset of NPC-specific targets and to precocious differentiation toward a neural-like state. Further analysis of the bound sequences revealed differences in the distances of SOX and POU peaks in the two cell types and identified motifs for additional transcription factors. Together, these data suggest that SOX2 controls a larger network of genes than previously anticipated through binding of distal enhancers and that transitions in POU partner factors may control tissue-specific transcriptional programs. Our findings have important implications for understanding lineage specification and somatic cell reprogramming, where SOX2, OCT4, and BRN2 have been shown to be key factors. In mammals, a few thousand transcription factors regulate the differential expression of more than 20,000 genes to specify ~200 functionally distinct cell types during development. How this is accomplished has been a major focus of biology. Transcription factors bind non-coding DNA regulatory elements, including proximal promoters and distal enhancers, to control gene expression. Emerging evidence indicates that transcription factor binding at distal enhancers plays an important role in the establishment of tissue-specific gene expression programs during development. Further, combinatorial binding among groups of transcription factors can further increase the diversity and specificity of regulatory modules. Here, we report the genome-wide binding profile of the HMG-box containing transcription factor SOX2 in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs), and we show that SOX2 occupied a distinct set of binding sites with POU homeodomain family members, OCT4 in ESCs and BRN2 in NPCs. Thus, transitions in SOX2-POU partners may control tissue-specific gene networks. Ultimately, a global analysis detailing the combinatorial binding of transcription factors across all tissues is critical to understand cell fate specification in the context of the complex mammalian genome.