Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II

Abstract

Promoter-proximal pausing by RNA polymerase II (Pol II) ensures both gene-specific regulation and RNA quality control. Structural considerations suggested initiation factor eviction would be required for elongation factor engagement and pausing of transcription complexes. Here we show that selective inhibition of Cdk7—part of TFIIH—increases TFIIE retention, prevents DRB-sensitivity inducing factor (DSIF) recruitment and attenuates pausing in human cells. Pause release depends on Cdk9—cyclin T1 (P-TEFb); Cdk7 is also required for Cdk9-activating phosphorylation and Cdk9-dependent downstream events—Pol II carboxyl-terminal domain Ser2 phosphorylation and histone H2B ubiquitylation—in vivo. Cdk7 inhibition, moreover, impairs Pol II transcript 3′-end formation. Cdk7 thus acts through TFIIE and DSIF to establish and through P-TEFb to relieve barriers to elongation: incoherent feedforward that might create a window to recruit RNA-processing machinery. Therefore, cyclin-dependent kinases govern Pol II handoff from initiation to elongation factors and co-transcriptional RNA maturation.

RNA Polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation

“…In many studies, CDK9 is largely located toward the 5′ end of genes [85][86][87] while the majority of Ser2-P is found to increase toward the 3′ end of genes. While this low Ser2-P signal at CDK9 binding sites could be due to antibody detection issues discussed above, or the activity of a the Ser2 phosphatase FCP1, 88 the identification of CDK12 as a Ser2 kinase helps to resolve this apparent paradox.…”

Functional Role of RNA Polymerase II and P70 S6 Kinase in KCl Withdrawal-induced Cerebellar Granule Neuron Apoptosis

“…Neurons Undergoing Apoptosis Show Increased Expression of CDK7 and CDK9 -Because the elongation by RNA Pol II is regulated by CDK9 and CDK7 (28,32,33,56), we examined whether the neurons undergoing apoptosis show any change in expression of these kinases. Our results show that expression of CDK7 and CDK9 was increased within 4 h after KCl withdrawal, which were inhibited by DRB (Fig.…”

“…The C-terminal domain of Pol II, which is important in linking transcription and mRNA processing, is phosphorylated and activated by the positive transcription elongation factor P-TEFb, a complex of CDK9 and cyclin T (28 -32). In addition to CDK9, CDK7, in association with cyclin H, also plays a role in transcription activation by complexing with transcription factor IIH (TFIIH) (32)(33)(34). The Cdk inhibitors flavopiridol and roscovitine are known to inhibit CDK9 and CDK7 and hinder transcription (35)(36)(37).…”

P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates

“…For example, Cdk7 (the kinase associated with the transcription initiation factor IIH [TFIIH]) and Cdk9 (the catalytic subunit of positive transcription elongation factor b [P-TEFb]) perform essential, nonredundant functions despite their shared substrates and similar distributions on transcribed chromatin (Gomes et al 2006;Larochelle et al 2012). Signaling between TFIIH and PTEFb ensures that they act sequentially; in human cells, the activation of Cdk9 on chromatin, but not its recruitment, requires active Cdk7 ).…”