The U1 snRNP protein U1C and Helix H of U1 snRNA are critical for small molecule splicing modulator function

Kuang, Z.; Li, X.; Tang, Z.; Kosmyna, B.; Shi, S.; Lambert, K.; Zhang, W.; Giovinazzo, J.; Effenberger, K. A.; Sierra, J.; Ying, L.; Barraza, S. J.; Li, W.; Trotta, C. R.; Wang, J.; Zhao, R.

doi:10.1101/2025.08.21.671662

bioRxiv · 10.1101/2025.08.21.671662

The U1 snRNP protein U1C and Helix H of U1 snRNA are critical for small molecule splicing modulator function

Kuang, Z.·Li, X.·Tang, Z.·Kosmyna, B.·Shi, S.·Lambert, K.·Zhang, W.·Giovinazzo, J.·Effenberger, K. A.·Sierra, J.·Ying, L.·Barraza, S. J.·Li, W.·Trotta, C. R.·Wang, J.·Zhao, R.

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Abstract

Risdiplam and branaplam represent two classes of small-molecule splicing modulators that promote U1 snRNP recognition of weak non-canonical GA/GU-containing 5 splice sites (ss). We demonstrated that branaplam enhanced recognition of these 5 ss by reconstituted U1 snRNP in vitro, and that this effect depended on the ZnF domain of U1C and Helix H of U1 snRNA, but not U1A or U1-70K. In cells, depletion of U1C generally reduced compound-induced exon inclusion for most cassette exons. Interestingly, a subset of cassette exons became responsive to compound only upon U1C knockdown, supporting a model in which U1C stabilizes specific conformations at the 5 ss/U1 snRNA interface in a context-dependent manner that can either facilitate or hinder compound binding. Surprisingly, risdiplam shows no effect on weak 5 ss recognition in vitro, suggesting additional cellular factors are required for its activity.

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Kuang, Z., Li, X., Tang, Z., Kosmyna, B., Shi, S., Lambert, K., Zhang, W., Giovinazzo, J., Effenberger, K. A., Sierra, J., Ying, L., Barraza, S. J., Li, W., Trotta, C. R., Wang, J., Zhao, R.. 2025-08-23. The U1 snRNP protein U1C and Helix H of U1 snRNA are critical for small molecule splicing modulator function. https://doi.org/10.1101/2025.08.21.671662

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