The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells

The RNA polymerase II (RNAPII) associated factor 1 complex (Paf1C) plays critical roles in modulating the release of paused RNAPII into productive elongation. However, regulation of Paf1C-mediated promoter-proximal pausing is complex and context dependent. In fact, in cancer cell lines opposing models of Paf1Cs’ role in RNAPII pause-release control have been proposed. Here we show that the Paf1C positively regulates RNAPII pause-release at both protein-coding genes and at enhancers in mouse embryonic stem cells (mESC). Our analyses reveal extensive Paf1C binding at mESC enhancers, in particular at super enhancers. Importantly, Paf1C occupancy correlates with the strength of enhancer activity. Depletion of Paf1C attenuates the expression of genes regulated by targeted enhancers and affects RNAPII Ser2 phosphorylation at the binding sites, suggesting that mESC self-renewal depends on Paf1C-mediated positive regulation of pluripotency enhancers. RNA-Seq transcriptome profiling of murine ES-E14 and NIH-3T3 cells, as well as ChIP-Seq based examination of Ctr9 binding sites and H3K27ac histone modifications in both cell lines.