PAF1 regulation of promoter-proximal pause release via enhancer activation

Abstract

Gene expression in metazoans is regulated by RNA Polymerase II (Pol II) promoter-proximal pausing and its release. Previously, we identified that Pol II-associated factor 1 (PAF1) modulates the release of paused Pol II into productive elongation. Here, we find that PAF1 occupies transcriptional enhancers and restrains hyperactivation of a subset of these enhancers. Enhancer activation as the result of PAF1 loss releases Pol II from paused promoters of nearby PAF1 target genes. Knockout of PAF1-regulated enhancers attenuates the release of paused Pol II on PAF1 target genes without major interference in the establishment of pausing at their cognate promoters. Thus, a subset of enhancers can primarily modulate gene expression by controlling the release of paused Pol II in a PAF1-dependent manner.

Enhancers predominantly regulate gene expression in vivo via transcription initiation

“…Although our data suggest that changes in gene expression are predominantly driven by changes in initiation of transcription, others have proposed that enhancers regulate gene expression via changes in Pol II pausing (Chen et al 2017;Ghavi-Helm et al 2014;Liu et al 2013;Schaukowitch et al 2014). To help resolve this dichotomy, we investigated the role that enhancers play in regulating promoter proximal transcription by studying the well characterized enhancer clusters, which meet the current criteria of superenhancers and regulate the α-and β-globin genes (Bender et al 2012;Gariglio, Bellard, and Chambon 1981;Lee et al 2015;Sawado et al 2003;Vernimmen 2014).…”

“…Inhibition of CDK9 causes the pausing index to increase, and this has been interpreted as evidence for regulation of transcriptional pausing (Gressel et al 2017;Jonkers, Kwak, and Lis 2014;Rahl et al 2010). Consequently, changes in the pausing index have been used to suggest that pausing is a key regulatory step in the transcription cycle (Adelman and Lis 2012;Chen, Smith, and Shilatifard 2018;Jonkers and Lis 2015) and that this is regulated by enhancers (Chen et al 2017;Gao et al 2018;Ghavi-Helm et al 2014;Liu et al 2013;Schaukowitch et al 2014). Clearly this interpretation depends on whether the promoter-proximal peak of Pol II observed in ChIP experiments reflects initiation, pausing, or both (Ehrensberger, Kelly, and Svejstrup 2013).…”

Molecular mechanisms driving transcriptional stress responses

“…Whether the role of HSF1 at enhancers is to induce eRNA production, reach to paused Pol II at the promoter-proximal region, or to increase the local concentration of transcriptional regulators in the connected promoter–enhancer hubs, remains to be shown. However, previous results have demonstrated that Pol II pause-release can be triggered from enhancers 87–89 , and that HSF1 contributes to the transcriptional induction as well as to the recruitment of transcription machinery and chromatin modifiers 47,70–73,75 . All of these features of HSF1 activity could be exploited at enhancers.…”

The essential and multifunctional TFIIH complex

“…Pol II pausing may have evolved in part to ensure that nascent transcripts are appropriately 5'‐capped prior to the transition to productive elongation . TFIIH‐dependent phosphorylation of the pol II CTD also enhances PAF1 complex association, and the PAF1 complex has been shown by the Roeder and Shilatifard labs to control pol II promoter‐proximal pausing in human cells …”

“…119,120 TFIIH-dependent phosphorylation of the pol II CTD also enhances PAF1 complex association, 96 and the PAF1 complex has been shown by the Roeder and Shilatifard labs to control pol II promoter-proximal pausing in human cells. [121][122][123] Elongation, RNA processing, and termination…”