Pause, play, repeat: CDKs push RNAP II's buttons

Abstract

Cyclin-dependent kinases (CDKs) play a central role in governing eukaryotic cell division. It is becoming clear that the transcription cycle of RNA polymerase II (RNAP II) is also regulated by CDKs; in metazoans, the cell cycle and transcriptional CDK networks even share an upstream activating kinase, which is itself a CDK. From recent chemical-genetic analyses we know that CDKs and their substrates control events both early in transcription (the transition from initiation to elongation) and late (3' end formation and transcription termination). Moreover, mutual dependence on CDK activity might couple the "beginning" and "end" of the cycle, to ensure the fidelity of mRNA maturation and the efficient recycling of RNAP II from sites of termination to the transcription start site (TSS). As is the case for CDKs involved in cell cycle regulation, different transcriptional CDKs act in defined sequence on multiple substrates. These phosphorylations are likely to influence gene expression by several mechanisms, including direct, allosteric effects on the transcription machinery, co-transcriptional recruitment of proteins needed for mRNA-capping, splicing and 3' end maturation, dependent on multisite phosphorylation of the RNAP II C-terminal domain (CTD) and, perhaps, direct regulation of RNA-processing or histone-modifying machinery. Here we review these recent advances, and preview the emerging challenges for transcription-cycle research.

Keywords: RNA polymerase II; RNA-processing; TFIIH; chemical genetics; cyclin-dependent kinase; positive transcription elongation factor b; promoter-proximal pausing; termination; transcription.

Figure 1. Transcriptional CDK networks of metazoans and yeast. In metazoans, the TFIIH-associated kinase Cdk7 directly activates Cdk9, catalytic subunit of P-TEFb. Still to be determined: the identity of a Cdk7-activating kinase active during transcription, and whether Cdk7 also activates Cdk12 and/or Cdk13. In both budding and fission yeast, the job of activating all transcriptional CDKs falls to a single-subunit CAK (Cak1 or Csk1, respectively). Substrate phosphorylation by transcriptional CDKs is conserved among eukaryotes; indicated preferences for different positions within the CTD repeats are based on an amalgamation of biochemical and genetic data, but in most cases have not been rigorously determined. The larger number of substrates shown for metazoan CDKs reflects either lack of conservation of individual substrates in yeast (e.g., NELF) or simply the fact that specific CDK-substrate relationships have not been tested (e.g., TFIIE with any CDK, or Spt5 with Kin28).

Figure 2. RNAP II CTD-binding preference of factors implicated in co-transcriptional events. The phosphorylation state of the RNAP II CTD changes during the transcription cycle, to promote recruitment of proteins responsible for histone modification and maturation of the nascent RNA transcript.^, Different factors can bind the CTD in 1) either unphosphorylated or phosphorylated form, 2) with a preference for the modified CTD but without discrimination among the phosphorylated positions, or 3) with phosphosite-specificity, as indicated in key at top left. Schematic at bottom shows distribution of total RNAP II (solid line) and RNAP II phosphorylated at Ser5 (P-Ser5) or Ser2 (P-Ser2) (dashed lines), along a typical metazoan gene.