Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

Abstract

Pre-mRNA maturation frequently occurs at the same time and place as transcription by RNA polymerase II. The co-transcriptionality of mRNA processing has permitted the evolution of mechanisms that functionally couple transcription elongation with diverse events that occur on the nascent RNA. This review summarizes the current understanding of the relationship between transcriptional elongation through a chromatin template and co-transcriptional splicing including alternative splicing decisions that affect the expression of most human genes.

Keywords: CTD; RNA polymerase II; alternative splicing; kinetic coupling; transcription elongation.

Figure 1

The mRNA factory model. Coupling of transcription with pre-mRNA processing within a complex that contains both the synthetic and processing machines. Recruitment of RNA processing factors to the transcription elongation complex (TEC) occurs through dynamic interactions with the CTD “landing pad”. According to the CTD code hypothesis , interactions with the CTD are instructed by dynamic phosphorylation of the CTD heptad repeats including Ser2 and Ser5 residues (S2-P and S5-P, red and green dots) in ways that are synched with the transcription cycle. Capping enzyme and the cleavage/polyadenylation (poly(A)) complexes interact directly with S5-P and S2-P CTD isoforms that are enriched at 5’ and 3’ ends of genes respectively. Note that capping factors are detected also at 3’ ends and polyA factors at 5’ ends by ChIP. Whether splicing factors interact directly with the CTD has yet to be confirmed at the structural level. Whether different processing factors can simultaneously localize on the CTD is also not known but it is unlikely to be prohibited on steric grounds. The 7-methyl guanosine cap (7meG) is shown at the 5’ end of the nascent RNA (blue line).

Figure 2

“Window of opportunity” model for kinetic coupling of nascent RNA metabolism with transcription elongation. When upstream and downstream events on the nascent transcript compete, then the upstream site will have a head start, and therefore a competitive advantage. Slow elongation lengthens the window of opportunity for upstream events to occur before they face competition from downstream sites. Competing upstream and downstream sites on the nascent RNA include: A. 3’ splice sites of alternative exons; B. polyadenylation sites; C. RNA binding protein (RBP) recognition sites; D. complementary RNA sequence elements that base pair as the RNA folds. Sites favored by slow and fast elongation are colored in red and green hues respectively.

Figure 3

Splicing-dependent pol II pausing. Commitment to splicing induces pol II pausing close to the 3’ splice site at the start of exons, which have higher nucleosome densities than introns. This pause is accompanied by CTD Ser5 phosphorylation. Pol II pauses with high CTD Ser5 phosphorylation (S2-P). Release from this pause is proposed to be contingent on a splicing-dependent checkpoint being satisfied (grey arrow, lower panel) that may be accompanied by increased CTD Ser2 phosphorylation (S2-P) reminiscent of the switch in CTD phosphorylation that occurs following release from the promoter-proximal pause at transcription start sites. This is a speculative model based on references –, .