Human U2 snRNA BSL sequence mediates splicing efficiency driven by branchpoint sequence complementarity

To investigate the global effects of perturbing U2 snRNA sequence on splicing and gene expression, we carried out transcriptomic analysis of HEK293T cell lines stably expressing U2 snRNA mutants C28U in the branchpoint interacting stem loop or T34A/ A35C/G36T to create an orthogonal branch point recognition sequence. With both mutants, the expression of many genes is generally repressed, potentially by nonsense mediated decay (NMD) arising from a global decrease in splicing efficiency. However, we also see upregulation of genes important for pre-mRNA processing, translation and protein folding. In several cases, the upregulation of certain genes can be linked to a shift in alternative splicing that favors the productive isoform relative to an NMD-targeted isoform. Overall design: Short-read RNA-seq of HEK293T cell lines engineered for stable expression of empty vector (783) or RNU2-1 expression locus harboring either C28T (U2-C28U), TAG36ACT (U2-UCA) using lentiviral integration