Ground state conditions induce rapid reorganization of core pluripotency factor binding that precede global epigenetic reprogramming

Mouse embryonic stem cells (mESCs) cultured under serum/LIF conditions exhibit heterogeneous expression of pluripotency-associated factors that can be overcome by two inhibitors (2i) of the MEK and GSK3 pathway, respectively. Several studies have shown that the “ground state” induced by 2i is characterized by global hypomethylation and specific transcriptional profiles, but little is known about the contributing effectors. Here we show that 2i conditions rapidly alter the global binding landscape of OCT4, SOX2 and NANOG. The dynamic binding influences enhancer activity and shows enrichment for regulators linked to Wnt and Erk signaling. Epigenomic characterization provided limited insights to the immediate transcriptional dynamics suggesting these are likely more secondary effects. Likewise, knock-out of the PRC2 component EED to prevent H3K27me3 deposition had minimal effect on the transcriptome, rendering it largely dispensable for continued repression of bivalent genes and de novo silencing in 2i.