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Conclusions and perspectives
- On the importance of being co-transcriptional


Co-transcriptional RNA processing is probably the consequence both of the relatively fast kinetics of processing reactions compared with the relatively long time that it takes to synthesize an entire pre-mRNA and of direct binding of some RNA processing factors to the transcriptional machinery. Capping of the 5' end is specified by the direct binding of capping enzymes to the Pol II CTD and is not dependent on signals within the nascent RNA substrate. Thus, in spite of the speed of the capping reactions, it is essential that capping is co-transcriptional. Although polyadenylation and splicing are similarly stimulated by the CTD, these processes depend on signals within the nascent RNA to which essential transacting factors bind. Because transcription termination depends on polyadenylation signals and factors, transcription and polyadenylation are tightly coupled. Association of polyadenylation factors with Pol II probably enhances the efficiency of polyadenylation, but cleavage and poly(A) addition can clearly occur post-transcriptionally. Pre-mRNA splicing is both co- and post-transcriptional, and the kinetics of splicing factor binding, spliceosome assembly and transcription rate probably combine to determine which splicing events occur before termination. Despite much speculation concerning the potential utility of physical links between the transcription and splicing machineries, evidence supporting such a model is surprisingly lacking. Thus, the importance of co-transcriptional splicing has yet to be established, and outstanding questions as to the mechanisms of splicing factor recruitment and the regulation of alternative splice site selection remain. Given the existing evidence for transcription units as gene expression `factories', it is clear that Pol II is not the only engineer on duty; specific signals within nascent RNA and the interplay between the kinetics of transcription and processing are important parts of the blueprint for assembling distinct sets of machinery.

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