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bioRxiv · 10.1101/2024.06.12.598766

Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts

Smargon, A. A.·Pant, D.·Glynne, S.·Gomberg, T. A.·Yeo, E. W.
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Abstract

Endogenous U small nuclear RNAs (U snRNAs) form RNA-protein complexes responsible for eukaryotic processing of pre-mRNA into mature mRNA. Previous studies have demonstrated the utility of guide-programmable U snRNAs in targeted exon inclusion and exclusion. We investigated whether snRNAs can also enhance conversion of RNA bases over state-of-the-art RNA targeting technologies in human cells. When compared to adenosine deaminase acting on RNA (ADAR)-recruiting circular RNAs, we find that guided A>I snRNAs consistently increase adenosine-to-inosine editing efficiency for genes with higher exon counts, perturb substantially fewer genes in the transcriptome, and localize more persistently to the nucleus where ADAR is expressed. A>I snRNAs can also edit pre-mRNA 3' splice sites to promote splicing changes. Finally, snRNA fusions to H/ACA box snoRNAs (U>{Psi} snRNAs) increase targeted RNA pseudouridylation efficiency. Altogether, our results advance the protein-free RNA base conversion toolbox and enhance minimally invasive RNA targeting technologies to treat genetic diseases.

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Smargon, A. A., Pant, D., Glynne, S., Gomberg, T. A., Yeo, E. W.. 2024-06-13. Small nuclear RNAs enhance protein-free RNA-programmable base conversion on mammalian coding transcripts. https://doi.org/10.1101/2024.06.12.598766

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