Protein-interaction network analysis reveals the role of Prp19 splicing factor in transcription of both intron-containing and intron-lacking genes

The process of transcription and cotranscriptional mRNA processing are facilitated by myriads of molecular interactions. To elucidate the protein-protein interactions that occur during transcription cycle of RNAPII, we performed mass spectrometry of affinity purified termination complexes from chromatin fraction. Quantitative proteomic analysis revealed interaction of termination factors with TFIIB, TFIID and SAGA complex. Furthermore, all three termination complexes displayed statistically significant interactions with Prp19, Prp43, Sub2, Snu114, Brr2 and Smb1 splicing factors. Since Prp19 consistently emerged as the interactor of both initiation and termination complexes, we affinity-purified the factor and performed mass spectrometry. Prp19 exhibited interactions with subunits of TFIID, CPF complex, and the RSC chromatin remodeling complex. These interactions were observed exclusively in the chromatin context. Since fewer than 4% of yeast genes contain introns, we hypothesized that Prp19 might have a broader splicing-independent role in RNAPII transcription cycle. Auxin-mediated depletion of Prp19 resulted in at least a two-fold decrease in transcription of a subset of both intron-containing and intron-lacking genes. A combination of TFIIB-TBP ChIP and nascent RNA analyses revealed that Prp19 affects assembly of preinitiation complex (PIC) as well as termination step of transcription. Chromatin immunoprecipitation (ChIP) analysis revealed crosslinking of Prp19 to the promoter, coding region and terminator end of both intronic and non-intronic genes. These findings demonstrate that Prp19 has a novel role in transcription and affects multiple steps of RNAPII transcription cycle in budding yeast.