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

## TL;DR

This study shows that the splicing factor Prp19 also plays a role in RNA polymerase II transcription, affecting both initiation and termination steps.

## Contribution

The paper reveals a novel, splicing-independent role of Prp19 in the transcription cycle of RNAPII in budding yeast.

## Key findings

- Prp19 interacts with TFIID, CPF, and RSC complexes in the chromatin context.
- Depletion of Prp19 reduces transcription of both intron-containing and intron-lacking genes.
- Prp19 affects preinitiation complex assembly and transcription termination.

## Abstract

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.

The classical view of transcription and cotranscriptional RNA processing is that factors involved in these processes have dedicated step-specific functions. Transcription initiation and termination factors are seen as key to the beginning and end of RNA synthesis, while splicing factors are traditionally confined to their role in intron removal during RNA maturation. This seems to be a simplified view of a complex process. The transcription and RNA processing factors participate in broader networks that integrate transcription and RNA processing during eukaryotic gene expression. Here we report the protein interaction network of Prp19 splicing factor, and demonstrate that, in addition to its role in splicing and RNA trafficking, it has a novel, splicing-independent role in the transcription cycle of RNA polymerase II.