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bioRxiv · 10.1101/2025.06.06.658024

Competing 5' splice sites of SRC1/HEH1 are marked for alternative splicing by U5 and U6 snRNAs during the B to Bact transition of the spliceosome

Mishra, S. K.·Banyal, A. K.·Choudhuri, P.·Pillai, B. R.·Varikkapulakkal, A.
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Abstract

Alternative splicing of precursor-messenger RNA (pre-mRNA) bearing introns with competing and overlapping 5 splice sites (5SS) produces more mRNAs. We investigated the mechanism of this form of alternative splicing by monitoring RNA and protein products of the yeast SRC1/HEH1 gene. Its alternative splicing requires a sixteen-nucleotide pre-mRNA segment spanning the two 5SS. The nucleotides are decoded by U5 and U6 small nuclear RNAs (snRNA), further supported by proteins of the spliceosomal B and Bact complexes. Specific variants of the pre-mRNA segment with recalibrated binding to U5 and U6 snRNAs allowed alternative splicing independently of the trans-acting proteins. Conversely, snRNA variants specified for modified 5SS selection suppressed the splicing defects in the B complex mutants. Further data suggest that alternative splicing from HEH1-type introns containing overlapping and competing 5SS relies on pre-mRNA-snRNA interactions during B to Bact transitions of the spliceosome, supported by proteins that stabilize low-fidelity, high-efficiency conformations.

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Mishra, S. K., Banyal, A. K., Choudhuri, P., Pillai, B. R., Varikkapulakkal, A.. 2025-06-07. Competing 5' splice sites of SRC1/HEH1 are marked for alternative splicing by U5 and U6 snRNAs during the B to Bact transition of the spliceosome. https://doi.org/10.1101/2025.06.06.658024

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