Coupling of transcription and pre-mRNA processing may be in part due to the ability of pol II to bind and "piggyback" some of the processing factors in a complex known as the "mRNA factory" (Bentley 2002). Because this review is focused on splicing, we do not discuss in detail the roles of RNA polymerase II in the coupling of the other pre-mRNA processing reactions and transcription. The C-terminal domain (CTD) of pol II plays a central role in the coupling process: truncation of the CTD causes defects in capping, cleavage/polyadenylation, and splicing (McCracken et al. 1997). The human CTD comprises 52 heptad repeats with the consensus sequence YSPTSPS. Fong and Bentley (2001) found that the CTD C terminus including heptads 27–52 and a unique 10-amino-acid sequence (ISPDDSDEEN) located at the C terminus of heptad 52 supported all three processing reactions but the N terminus supported only capping, concluding that different CTD regions can display different functions in pre-mRNA processing. The heptad repeats alone are not sufficient to support pre-mRNA processing, but the 10-amino-acid C-terminal motif was reported to confer efficient processing capability to pol II with only heptads 1–25 or with 27 consensus heptads (Fong et al. 2003). It was recently reported that different pre-mRNAs might have different dependencies on the number of the CTD repeats as well as the need for the nonrepeated C-terminal sequence for efficient processing (Rosonina and Blencowe 2004). In any case, the C terminus or the repeats might act by binding factors that participate in transcriptions and/or processing directly, in the control of pol II elongation or affecting pol II subnuclear localization. Assignment of a specific role in pre-mRNA processing to the C-terminal sequence seems to be in contradiction with recent findings that this segment might simply act by conferring stability to the CTD. Chapman et al. (2004) found that variants lacking the C-terminal motif suffer proteolytic degradation of the whole CTD in vivo, giving rise to the previously known IIb isoform of the RNA polymerase II large subunit. The abundance and ability to transcribe of this CTD-less isoform vary among the different cell types, which indicates that further investigation is needed to elucidate the apparent contradiction.
Purified phosphorylated RNA pol II is able to activate splicing in vitro (Hirose et al. 1999). Isolated CTD fragments cannot duplicate this effect unless the precursor RNA is recognized via exon definition, that is, it offers to the splicing machinery at least one complete internal exon with its 3'- and 5'-splice sites. CTD does not activate splicing of precursors in which pairs of splice sites are in intronic polarity (Zeng and Berget 2000). These findings support a direct role for the CTD in exon recognition and led to the speculation that the CTD would not only be a landing path for splicing factors but also for bringing closer consecutive exons, which would facilitate spliceosomal assembly (Fig. 2).
Dynamic changes in CTD phosphorylation seem to play significant roles in RNA processing. Consistently, the peptidyl-prolyl isomerase Pin 1, which stimulates CTD phosphorylation by cdc2/cyclin B by affecting CTD structure, was shown to inhibit Pol II-dependent splicing in vitro (Xu et al. 2003).
In addition, the CTD seems to play a role in the nuclear distribution of components of the transcription and splicing machineries. In fact, transcriptional activation of pol II genes increases association of splicing factors to sites of transcription, but this relocalization does not occur if pol II has a truncated C-terminal domain (Misteli and Spector 1999). This is consistent with previous findings that over-expression of CTD-containing large subunits of pol II in mammalian cells induces selective nuclear reorganization of splicing factors (Du and Warren 1997).