Utargetome: A targetome prediction tool for modified U1-snRNAs to identify distal-target positions with improved selectivity.

ABSTRACT: The endogenous U1 small nuclear RNA (U1-snRNA) plays a crucial role in splicing initiation through base-pairing to donor splice sites (5'-SSs). Likewise, modified U1s that carry a mutation-adapted 5'-terminal sequence have been demonstrated to rescue exon splicing when this is disrupted by genetic mutations within the 5'-SS. Given the base-pairing flexibility of the endogenous U1, the selectivity of modified U1s requires investigation. We developed a computational pipeline (Utargetome) that considers combinations of mismatches and alternative annealing registers to predict the transcriptome-wide binding sites (or targetome) of a U1. The pipeline accuracy was tested by recapitulating well-established alternative annealing registers and specificity for 5'-SSs in the predicted targetome of th

SUBMITTER: Pigini P 

PROVIDER: S-EPMC12527174 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature