Pre-mRNA Processing and the CTD of RNA Polymerase II: The Tail That Wags the Dog?

The studies described herein foster an expanded view of cellular functions of the CTD of RNA polymerase II. The biogenesis of mRNA in mammalian cells can now be seen as a set of coordinated processes (see Figure 1Figure 1), with the CTD participating not only in the activation of transcription, but also as the foundation of an “RNA factory” (McCracken et al. 1997xMcCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S.D., Wickens, M., and Bentley, D.L. Nature. 1997; 385: 357–361Crossref | PubMed | Scopus (633)See all ReferencesMcCracken et al. 1997). At the level of resolution afforded by currently available data, it cannot be discerned whether this factory comprises an ordered assembly line or simply provides the necessary processing machinery in proximity to the site of RNA synthesis. In either case, the localization of this machinery may have significant ramifications for regulation of gene expression.Figure 1Schematic Representation of the Association of Pre-mRNA Processing Factors with the Carboxy-Terminal Domain (CTD) of Transcriptionally Engaged RNA Polymerase IIPotential physical and functional interactions between splicing, polyadenylation, and elongation factors are indicated by double-headed arrows.View Large Image | View Hi-Res Image | Download PowerPoint SlideAlthough splicing in vivo can occur cotranscriptionally, this is not obligatory since some introns are not removed until after the RNA has been released from the chromosome (Wetterberg et al. 1996xWetterberg, I., Bauren, G., and Wieslander, L. RNA. 1996; 2: 641–651PubMedSee all ReferencesWetterberg et al. 1996). Yet in vitro studies suggest that association with the CTD is maintained during the catalytic steps of splicing even when polymerase is not engaged in the synthesis of the splicing substrate. At what point are spliceosomes released from the CTD in vivo? Do processing factors dissociate from the CTD as they associate with nascent pre-mRNA, or might a polymerase molecule be committed to its newly synthesized pre-mRNA transcript until processing is complete, even after transcription has terminated? Can multiple spliceosomes assemble on a single CTD simultaneously, or must each intron be spliced in succession? What might be the significance for alternative splicing? Might microheterogeneous control of CTD phosphorylation and, thereby, factor binding play a role in splicing regulation? The answers to these questions will require detailed characterization of the molecular connections between the spliceosome and the CTD and dissection of the precise role of the CTD in spliceosome assembly and function.It is attractive to consider the mRNA factory as a highly integrated machine. For example, intercommunication between splicing and polyadenylation factors (e.g.,Lutz et al. 1996xLutz, C.S., Murthi, K.G.K., Schek, N., O'Connor, P.J., Manley, J., and Alwine, J.C. Genes Dev. 1996; 10: 325–337Crossref | PubMedSee all ReferencesLutz et al. 1996), facilitated by their colocalization, may allow the coordinated selection of splice junctions and cleavage/polyadenylation sites. The apparent role of the CTD in transcriptional activation raises the possibility that the specificity or efficiency of processing may be determined in part by promoter-specific factors, or that association with processing factors in turn may influence initiation. Promoter-dependent selection of snRNA versus mRNA 3′-end formation pathways (Dahlberg and Lund 1988xSee all ReferencesDahlberg and Lund 1988), for example, conceivably could be mediated by CTD-bound factors. Accumulating evidence implicates the CTD as a target for control of transcriptional elongation, whether through modulation of its phosphorylation state or its association with specific factors. An exciting corollary is that signals from the processing machinery may be propagated through the CTD to coordinate the continued elongation of a transcript with its processing, providing a form of mRNA surveillance or “quality control.” Such a mechanism could lie at the heart of the observed coupling between 3′-end processing and transcript termination, as proposed by McCracken et al. 1997xMcCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S.D., Wickens, M., and Bentley, D.L. Nature. 1997; 385: 357–361Crossref | PubMed | Scopus (633)See all ReferencesMcCracken et al. 1997. A similar coupling mechanism could signal pausing or termination of transcription in response to delays or errors in spliceosome assembly or function. These signals might be relayed through factors like the yeast Nrd1 protein or related mammalian SR-like proteins. Clearly, researchers investigating RNA Pol II transcription and those studying pre-mRNA processing will both contribute to this unfolding picture. With their combined efforts, a “grand unified theory” of mRNA biogenesis may soon be at hand.