A comprehensive proteomic analysis of the human spliceosome (Zhou et al. 2002; for review, see Jurica and Moore 2003) reveals that at least 30 out of the 145 spliceosomal proteins are either known or candidate participants in the coupling between splicing and other gene expression steps. For instance, the transcription cofactor TAT-SF1 (see below) and the transcription factors CA150, XAB2, and SKIP are present in the spliceosome. On the other hand, the promoter itself could be responsible for recruiting splicing factors, such as SR proteins, to the site of transcription, possibly through transcription factors that bind the promoter or the transcriptional enhancers. Some proteins display a dual function; acting in both processes as is the case of a transcriptional activator of the human papilloma virus (Lai et al. 1999), or the thermogenic coactivator PGC-1. Interestingly, PGC-1 can affect alternative splicing, but only when it is recruited to complexes that interact with gene promoters (Monsalve et al. 2000). The product of the WT-1 gene, which is essential for normal kidney development, could also be involved in both transcription and splicing. Although generally considered a transcription factor, WT1 isoforms that include three amino acids, KTS, interact with the essential splicing factor U2AF65 in vitro (Davies et al. 1998). Another example of dual function is the transcription/splicing factor p54nrb, which associates with the 5'-splice site within large complexes in HeLa cells together with the hyperphosphorylated form of RNA pol II and U1 or U1 and U2 snRNPs. These macromolecular complexes also contain other transcription/splicing factors, such as PSF and TLS, as well as factors known to control elongation, such as P-TEFb, TAT-SF1, and TFIIF (Kameoka et al. 2004). Other proteins, such as SAF-B, which mediate chromatin attachment to the nuclear matrix, have been implicated in the coupling of transcription and pre-mRNA splicing (Nayler et al. 1998). The RNA polymerase itself could be responsible for recruiting these proteins, perhaps through its CTD. Three proteins carrying WW and/or FF domains, and whose activities might be related to the coupling between transcription and splicing, were found to bind specifically to phosphorylated CTD: (1) the yeast splicing factor Prp40 (Morris and Greenleaf 2000); (2) Ess1, a yeast peptidyl prolyl isomerase, proposed to act in cis/trans protein isomerizations that could play a crucial role in the recognition of CTD by other proteins (Myers et al. 2001); and (3) CA150, a human nuclear factor implicated in transcriptional elongation (Carty et al. 2000). Other candidates to function in the coupling of splicing and transcription are a group of proteins known as SCAFs (SR-like CTD associated factors). These are CTD-interacting proteins that, similarly to SR proteins, contain an RS domain and an RNA-binding domain (Yuryev et al. 1996). The fact that SR-like proteins interact with the CTD might not be related to splicing. Indeed, SR and SR-like proteins have been implicated in other coupling events. For instance, the yeast poly(A)+ RNA-binding proteins Gbp2 and Hrb1, which resemble members of the SR family, specifically bind to the TREX (transcription/export) complex, which couples transcription elongation to the nuclear export of mRNAs. TREX-bound Gbp2 and Hrb1 could be then transferred from the TREX complex to the nascent pre-mRNA during transcription (Hurt et al. 2004). It is claimed that cotranscriptional recruitment of these mRNA-binding proteins might increase export efficiency to ensure their later function as part of the mRNP in the cytoplasm.
A summary of protein factors that are candidates for linking transcription and splicing is presented in Table 1. As a general remark, although evidence of CTD recruitment of processing factors explains satisfactorily the coupling of transcription with capping and cleavage/polyadenylation, evidence for a link between recruitment and splicing is still circumstantial and needs further investigation.