The idea that RNAP II, and specifically the CTD of its largest subunit, participates in mRNA processing was unexpected and controversial just a few years ago, but now seems quite solidly established. In part because it's the simplest of the processing reactions, the case is tightest, and the details best understood, for capping: Biochemical and genetic data support a direct, functionally significant interaction between capping enzyme and a specifically phosphorylated form of the CTD that results in an allosteric activation of capping, and this mechanism seems conserved from yeast to humans. But the evidence that RNAP II, via the CTD, actively functions in splicing and polyadenylation is nearly as compelling. In both these cases, the evidence so far comes largely from biochemical and cell biological studies, and principally from vertebrate systems. In keeping with the greater complexity of these two reactions, it is less clear exactly how the CTD functions. In both, though, it appears that it can act directly, independent of transcription. RNAP II functions very early in the splicing reaction, likely by interacting, directly or indirectly, with key splicing factors to facilitate splice site recognition. The CTD interacts with polyadenylation factors and can play a required role in the cleavage reaction. But beyond that, the mechanisms are unclear, and an important goal now is to elucidate the molecular mechanisms involved. It will be interesting, for example, to learn if there are similarities in how the CTD works in capping, splicing, and 3'-end formation.
Aside from mechanism, a significant issue will concern the importance of these interactions to gene regulation. A number of factors suggest that targeting the transcription-processing link should provide an important avenue of regulation. For example, given the large number of kinases that can phosphorylate the CTD and the enormous number of potential sites, the possibility that differential CTD phosphorylation might influence the constellation of factors associated with it, which could in turn influence alternative processing events, is attractive. The observations that polyadenylation factors can associate with the transcription pre-initiation complex, and that promoter structure can influence alternative splicing patterns, suggest that events that occur at the promoter might help dictate subsequent processing efficiency. For example, could sequence-specific DNA binding proteins, or perhaps transcriptional coactivators, contribute to recruitment of distinct processing factors to promoter-bound RNAP II? It will be critical now to obtain biochemical and/or genetic evidence that some of the potential regulators we have described here indeed function in gene control.
The implications of the transcriptosome theory have the potential to be far reaching. But first we must learn if transcriptosomes are found generally throughout metazoa, and whether they do indeed reflect preassembled, organized sites of transcription and processing. If so, is this an essential pathway of mRNA synthesis? Or might it be designed, for example, to enhance the efficiency with which certain highly expressed mRNAs are produced? Whatever the answers to these and other questions, it is remarkable how cell biology, biochemistry, and in some cases genetics are all providing evidence that processes within the cell nucleus are coordinated to a remarkable and unanticipated degree. The coming decade promises to be a fascinating one for understanding the role that RNA polymerase II plays in orchestrating these events, and the significance of this integration to the mechanisms and regulation of gene expression.