The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

Mouse embryonic stem (ES) cells grown in serum exhibit greater heterogeneity in morphology and expression of pluripotency factors than ES cells cultured in defined medium with inhibitors of two kinases (Mek and GSK3), a condition known as 2i postulated to establish a naive ground state. We show that the transcriptome and epigenome profiles of serum- and 2i-grown ES cells are distinct. 2i-treated cells exhibit lower expression of lineage-affiliated genes, reduced prevalence at promoters of the repressive histone modification H3K27me3, and fewer bivalent domains, which are thought to mark genes poised for either up- or downregulation. Nonetheless, serum- and 2i-grown ES cells have similar differentiation potential. Precocious transcription of developmental genes in 2i is restrained by RNA polymerase II promoter-proximal pausing. These findings suggest that transcriptional potentiation and a permissive chromatin context characterize the ground state and that exit from it may not require a metastable intermediate or multilineage priming. º High-resolution genome-wide transcriptome and epigenome of naive pluripotency º Reduced H3K27me3 at promoters and fewer bivalent domains in naive ES cells º Reduced lineage priming and increased RNA polymerase II pausing in the naive state º Naive ES cells show no delay in differentiation Ground state pluripotency is characterized by a permissive chromatin context, but gene expression is not promiscuous due to the high prevalence of promoter-proximal pausing of transcription.