Defining a critical Nanog enhancer using chromatin-focused approaches identifies RNAPII recruitment as required for expression [ATAC-Seq]

Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid reporter assays, rather than within native chromatin. We employed a combination of approaches to investigate the Nanog locus in mouse embryonic stem cells (ESCs) and an associated cis regulatory element (CRE) which may operate as a super-enhancer (SE) or alternative promoter. We establish the element is a SE within chromatin using distance- and orientation-independence as criteria. We next demonstrate this SE regulates Nanog by recruiting and/or initiating RNA Polymerase II. Our work highlights that enhancers likely operate through a diverse set of mechanisms. ATAC-Seq of 2 conditions, 3 replicates of each