MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1

Downie Ruiz Velasco, Angela; Parsons, Aimee L.; Heatley, Matthew C.; Martin, Athena R.G.; Smart, Alfredo D.; Shah, Niraj; Jopling, Catherine L.

Abstract

In animals, microRNA (miRNA) biogenesis begins with cotranscriptional cleavage of the primary (pri-)miRNA by the Microprocessor complex. Cotranscriptional splicing has been shown to influence Microprocessor cleavage when miRNAs are hosted in introns of protein-coding pri-miRNAs, but the impact of splicing on production of miRNAs hosted in long non-coding (lnc)RNAs is largely unknown. Here, we investigated the role of splicing in the biogenesis of miR-122, an lncRNA-hosted, highly expressed, medically important, liver-specific miRNA. We found that splicing inhibition by the SF3B1 inhibitor pladienolide B (PlaB) led to strong and rapid reduction in transcription of endogenous, but not plasmid-encoded, pri-miR-122, resulting in reduced production of mature miR-122. To allow detection of rapid changes in miRNA biogenesis despite the high stability of mature miRNAs, we used SLAMseq to globally quantify the effects of short-term splicing inhibition on miRNA synthesis. We observed an overall decrease in biogenesis of mature miRNAs following PlaB treatment. Surprisingly, miRNAs hosted in exons and introns were similarly affected. Together, this study provides new insights into the emerging role of splicing in transcription, demonstrating novel biological importance in promotion of miR-122 biogenesis from an lncRNA, and shows that SF3B1 is important for global miRNA biogenesis.

Citation

Downie Ruiz Velasco, A., Parsons, A. L., Heatley, M. C., Martin, A. R., Smart, A. D., Shah, N., & Jopling, C. L. (2024). MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1. Nucleic Acids Research, 52(15), 9210-9229. https://doi.org/10.1093/nar/gkae505

• Journal Article Type: Article
• Acceptance Date: Jun 6, 2024
• Online Publication Date: Jun 17, 2024
• Publication Date: Aug 27, 2024
• Deposit Date: Jun 17, 2024
• Publicly Available Date: Jun 17, 2024
• Journal: Nucleic Acids Research
• Print ISSN: 0305-1048
• Electronic ISSN: 1362-4962
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 52
• Issue: 15
• Article Number: gkae505
• Pages: 9210-9229
• DOI: https://doi.org/10.1093/nar/gkae505
• Public URL: https://nottingham-repository.worktribe.com/output/36288265
• Publisher URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae505/7694274