Pausing of RNA polymerase II regulates mammalian developmental potential. Mus musculus

The remarkable capacity for pluripotency and self-renewal in embryonic stem cells (ESCs) requires a finely-tuned transcriptional circuitry wherein the genes and pathways that initiate differentiation are suppressed, but poised to respond rapidly to developmental signals. To elucidate transcriptional control in mouse ESCs in the naïve, ground state, we defined the distribution of engaged RNA polymerase II (Pol II) at high-resolution. We find that promoter-proximal pausing of Pol II is widespread at genes encoding signaling molecules that control ESC proliferation, differentiation and metabolism, but is not enriched at developmental control genes. Accordingly, ablation of the primary pause-inducing factor, NELF, causes proliferation defects, early embryonic lethality and dysregulation of critical ESC signaling pathways. Moreover, loss of NELF in ESCs causes resistance to cell fate commitment through dramatic attenuation of FGF/ERK activity. This work thus uncovers an unanticipated role for NELF-mediated pausing in establishing the responsiveness of ESCs to developmental cues. Overall design: RNA-seq, GRO-seq, and Start-RNA-seq from mouse embryonic stem cells (mESCs). For RNA-seq, two biological replicates are included for each of two treatment conditions; control, and 4-hydroxytamoxifen (4OHT) treated to ablate expression of NELF-B. For GRO-seq, data from two biological replicates of untreated mESCs are included. For Start-RNA-seq, three biological replicates are included for each of two treatment conditions; control and 4OHT.