p54nrb associates with the 5′ splice site within large transcription/splicing complexes

The functional coupling of transcription and splicing has been reported both in vivo and in vitro, but the molecular mechanisms governing these interactions remain largely unknown. Here we show that p54nrb, a transcription/splicing factor, associates with the 5′ splice site (SS) within large complexes present in HeLa cell nuclear extracts, in which the hyperphosphorylated form of RNA polymerase II (RNAPIIO) is associated with U1 or U1 and U2 snRNPs. These RNAPIIO–snRNP complexes also contain other transcription/splicing factors, such as PSF and TLS, as well as transcription factors that interact with RNAPIIO during elongation, including P‐TEFb, TAT‐SF1 and TFIIF. The presence of these factors in functional elongation complexes, demonstrated using an immobilized DNA template assay, strongly suggests that the RNAPIIO–snRNP complexes reflect physiologically relevant interactions between the transcription and splicing machineries. Our finding that both p54nrb and PSF, which bind the C‐terminal domain of the largest subunit of RNAPII, can interact directly with the 5′ SS indicates that these factors may mediate contacts between RNAPII and snRNPs during the coupled transcription/splicing process.