Protein-interaction network analysis reveals the role of Prp19 splicing factor in transcription of both intron-containing and intron-lacking genes
Katherine Dwyer, Mary-Ann Essak, Ahlam Awada, Zuzer Dhoondia, Athar Ansari
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.
Introduction
In the complex landscape of eukaryotic gene expression, the process of transcription by RNA polymerase II is intricately linked to the processing of nascent mRNA by capping, splicing, and cleavage-polyadenylation [1,2]. The processing of mRNA predominantly occur cotranscriptionally.
Materials and method
Yeast strains and primers
All yeast strains used in this study are listed in Table A in S1 File. All PCR primers used in this study are listed in Table B in S1 File.
Results
Our previous work revealed that the interaction of TFIIB with termination factors is crucial for promoter-terminator communication through gene looping and plays a pivotal role in transcription termination [45]. Interestingly, TFIIB and the Rat1 termination factor also exhibit interactions with several splicing factors in the chromatin context [21,25].
Discussion
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 respectively, while splicing factors are traditionally confined to their role in intron removal during RNA maturation.
Acknowledgments
We thank Dr. Markus Friedrich of WSU for critically reading the manuscript and for sharing valuable comments. We thank Dr. Marc Gartenberg for kindly providing plasmids for making Prp19-AID strain. We thank lab members Emma Fidler, Kasun Rathnasinghe, Isabella Nadeau and Kyle Kilgore for their useful help.
Citation: Dwyer K, Essak M-A, Awada A, Dhoondia Z, Ansari A (2026) Protein-interaction network analysis reveals the role of Prp19 splicing factor in transcription of both intron-containing and intron-lacking genes. PLoS Genet 22(2): e1012051. https://doi.org/10.1371/journal.pgen.1012051
Editor: Marnie E. Blewitt, Walter and Eliza Hall Institute of Medical Research, AUSTRALIA
Received: April 9, 2025; Accepted: February 8, 2026; Published: February 20, 2026
Copyright: © 2026 Dwyer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting information files. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD061187 and 10.6019/PXD061187. Statistical source data is provided with this article. The GRO-Seq data have been deposited in the NCBI database. The NCBI Geo accession number is GSE294484. All yeast strains are available upon request to the corresponding author.
Funding: This work was supported by the grant (Grant #1R01GM146803-05) from National Institute of General Medical Sciences to AA (Athar Ansari). KD received support of a Chemistry Biology Interface (CBI) predoctoral fellowship (Grant #T32GM142519) and Rumble fellowship from WSU. AA (Ahlam Awada) received UROP undergraduate research fellowship from WSU. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
