RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases

Abstract

The transition between initiation and productive elongation during RNA Polymerase II (Pol II) transcription is a well-appreciated point of regulation across many eukaryotes. Elongating Pol II is modified by phosphorylation of serine 2 (Ser2) on its carboxy terminal domain (CTD) by two kinases, Bur1/Ctk1 in yeast and Cdk9/Cdk12 in metazoans. Here, we discuss the roles and regulation of these kinases and their relationship to Pol II elongation control, and focus on recent data from work in C. elegans that point out gaps in our current understand of transcription elongation.

Keywords: Bur1; C. elegans; Cdk12; Cdk9; Ctk1; P-TEFb; RNA Polymerase II; Serine 2; elongation; transcription.

Figure 1. Ser2 kinases in eukaryotic transcriptional elongation regulation. (A) Loss of Bur1/CDK9 or Ctk1/Lsk1/CDK12 activity results in different effects on Ser2-P levels in yeast vs. metazoans. While Ctk1/Lsk1 are responsible for the majority of Ser2-P in yeast S. cerevisae and S. pombe, both CDK9 and CDK12 significantly contribute to Ser2-P levels in Drosophila and huamans. Importantly, loss of Cdk9 in metazoans results in complete loss of Ser2-P suggesting it is required upstream of CDK12 activity. Finally, while Bur1 and CDK9 are largely essential proteins (S. cerevisae bur1 mutants are extremely slow growing), Ctk1/Lsk1 is not essential in yeast. (B) Transcription elongation is not a rate-limiting step of gene expression in organisms without NELF homologs, including yeast. In these organisms, the kinases Bur1/CDK9 and Ctk1/CDK12 are recruited through general mechanisms to phosphorylate Ser2 of the Pol II CTD and SPT5. These phosphorylation marks enhance recruitment of other Pol II elongation associated factors such as RNA processing factors and chromatin remodelers. (C) In organisms that contain the NELF complex, such as Drosophila and mammals, the transition from Pol II initiation to elongation is a regulated step of gene expression. Here, DSIF (SPT4/SPT5) mediates NELF binding to the Pol II complex, “pausing” Pol II and preventing productive elongation. Regulated recruitment of CDK9 and Cyclin T results in the release of this pause. CDK9 phosphorylates the Pol II CTD on Ser2, SPT5, and NELF. Downstream of this regulated step, the CDK12 complex further phosphorylates the Pol II CTD.

Figure 2. Ser2 kinases in C. elegans transcriptional elongation regulation. (A) Loss of CDK-9 or CDK-12 activity results in different effects on Ser2-P levels in the C. elegans germline vs. soma (compare with Fig. 1A). While CDK-12 is responsible for the bulk of Ser2-P in the germline, both CDK-9 and CDK-12 regulate Ser2-P levels in the soma. Importantly, loss of CDK-9 in the soma results in complete loss of Ser2-P, suggesting it is required upstream of CDK-12 activity. Finally, while both CDK-9 and CDK-12 are essential for somatic development, only CDK-9 is essential for germline development. (B) As an analogy to eukaryotic organisms that do not have a NELF homolog, transcription elongation may not be a rate-limiting step of gene expression in the germline. Because CDK-9 is essential in the germline, it may target SPT-5 or other factors, though it is not required for phosphorylation of Ser2 on the Pol II CTD. (C) In the soma, the transition from Pol II initiation to elongation can be a regulated step of gene expression. Here, DSIF (SPT4/SPT5) alone or in combination with an additional pausing factor (PF) may regulate a 5′ check point prior to productive Pol II elongation. Regulated recruitment of CDK9 and Cyclin T through transcription factors and possibly phosphorylation of pausing factors may release Pol II from this check point. At the same time, CDK9 phosphorylates the Pol II CTD on Ser2 and may phosphorylate the SPT5 CTR. Downstream of this regulated step, the CDK12 complex further phosphorylates the Pol II CTD.