Show Notes
️ Episode 222: snaR-A hijacks splicing to drive proliferation
In this episode of PaperCast Base by Base, we explore This episode examines how the cancer-associated Pol III transcript snaR-A binds core splicing factors, localizes near nuclear speckles, perturbs U2-dependent splicing to increase intron retention, and promotes cell proliferation linked to poorer patient outcomes
Study Highlights:
Proteomic pull-downs and CLIP analyses reveal snaR-A interactions with RNA chaperones (La, ILF3) and multiple splicing factors, with PAR-CLIP and CLIP-qPCR supporting a direct interaction with the U2 snRNP subunit SF3B2. HCR-RNA-FISH and SON TSA-seq place snaR-A in subnuclear foci adjacent to nuclear speckles and show snaR-A gene clusters are speckle-proximal. Functional genomics show snaR-A overexpression increases intron retention while snaR-A depletion reduces intron retention and enhances splicing of transcripts marked by high U2 occupancy and speckle proximity, and snaR-A overexpression selectively reduces SF3B2 protein levels. Phenotypically, snaR-A depletion lowers proliferation in HEK293T cells, snaR-A gene activity correlates with proliferation markers across primary tumors and predicts worse survival, and rescued splicing increases protein abundance for tumor-suppressive targets such as OGFR.
Conclusion:
snaR-A acts as a nuclear antagonist of U2-dependent splicing near speckles, promoting cell proliferation and providing a non-mutational route to splicing dysregulation in cancer
Music:
Enjoy the music based on this article at the end of the episode.
Reference:
Zhou S, Lizarazo S, Chorghade S, Mouli L, Cheng R, KC R, Kalsotra A, Van Bortle K. Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. Nat Commun. 2025;16:10460. https://doi.org/10.1038/s41467-025-65448-x
License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/
Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00
Official website https://basebybase.com
Castos player https://basebybase.castos.com
On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.
Keywords: snaR-A, splicing, SF3B2, intron retention, nuclear speckles
