Multiple P-TEFbs cooperatively regulate the release of promoter-proximally paused RNA polymerase II

Abstract

The association of DSIF and NELF with initiated RNA Polymerase II (Pol II) is the general mechanism for inducing promoter-proximal pausing of Pol II. However, it remains largely unclear how the paused Pol II is released in response to stimulation. Here, we show that the release of the paused Pol II is cooperatively regulated by multiple P-TEFbs which are recruited by bromodomain-containing protein Brd4 and super elongation complex (SEC) via different recruitment mechanisms. Upon stimulation, Brd4 recruits P-TEFb to Spt5/DSIF via a recruitment pathway consisting of Med1, Med23 and Tat-SF1, whereas SEC recruits P-TEFb to NELF-A and NELF-E via Paf1c and Med26, respectively. P-TEFb-mediated phosphorylation of Spt5, NELF-A and NELF-E results in the dissociation of NELF from Pol II, thereby transiting transcription from pausing to elongation. Additionally, we demonstrate that P-TEFb-mediated Ser2 phosphorylation of Pol II is dispensable for pause release. Therefore, our studies reveal a co-regulatory mechanism of Brd4 and SEC in modulating the transcriptional pause release by recruiting multiple P-TEFbs via a Mediator- and Paf1c-coordinated recruitment network.

Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation

“…This study identified a mutual dependence of Paf1C and P-TEFb with respect to their recruitment to/retention on active chromatin [16], an observation consistent with a positive feedback model in which Paf1C promotes pause release by regulating the chromatin association of P-TEFb both directly and via Paf1C-dependent histone modifications (see below) [56]. Another report postulates the existence of at least four unique P-TEFb-containing super elongation complexes (SECs), each with distinct targets for CDK9 activity [17]. Paf1C is critical for the recruitment of two of these SEC subtypes.…”

“…In recent years, new roles for Paf1C have been identified in processes predominantly found in metazoans, particularly in the regulation of promoter-proximal pausing [15–17]. Studies in metazoans and in fission yeast have also advanced our understanding of previously characterized Paf1C functions, such as the maintenance of heterochromatin and the regulation of alternative cleavage and polyadenylation of mRNAs [18–21].…”

“…Several recent studies have identified Paf1C as a factor that regulates promoter proximal pausing [16, 17, 56]. One genome-wide survey of Pol II and Paf1C occupancy in human monocytic leukemia (THP1) cells indicated that Paf1C promotes release from pausing at > 5,800 genes [16] (Figure 2A).…”

“…Because the interaction between Paf1C and CDK12 is stronger than that between CDK12 and Pol II [16], it is possible that Paf1C is important for transferring CDK12 to elongating Pol II. A recent report suggests that Ser2P occurs downstream of pause release [17], suggesting that Paf1C’s role in pause release may relate more to its interactions with P-TEFb [16, 17], which targets numerous pausing factors, than to its involvement in CDK12 recruitment.…”

Role of Host Factors on the Regulation of Tat-Mediated HIV-1 Transcription

“…Brd4 binds acetylated H3/H4 histones near cellular promoters, enabling P-TEFb to contact the Mediator complex and promote P-TEFb-dependent transcription [93, 94]. To be noted, the Mediator complex, but not the Mediator CDK8 module, can interact with Tat and be recruited by the intermediate of the MED14 subunit to induce TMT [95].…”