DIS3 dysfunction suppresses altered alternative splicing in cells with the depletion of U2 snRNP component

Precise analysis of DIS3 interactors disclosed in genome-wide siRNA screening revealed enrichment in genes responsible for transcription and processes highly connected to it like splicing and 3’ end formation. Among the strongest positive interactors were components of of SF3a complex and some of SF3b complex. SF3a complex is a substantial integral component of the pre-spliceosome and is required for complex A and B assembly and plays crucial role in initial steps of spliceosome assembly.Transcriptome analysis demonstrated that depletion of SF3A1, one of three SF3a complex components, lead to extensive alterations in multiple classes of alternative splicing events (ASE). Remarkably, the only group of ASE that was reshaped in the presence of DIS3 dysfunction was intron retention. Detailed investigations of transcripts with altered intron retention revealed high enrichment in transcripts coding ribosomal proteins (Rps). To investigate diffrential pre-mRNA splicing, total RNA samples were collected from model cell lines producing either WT or mut DIS3 under tetracyclin induction that were treated with SF3A1 siRNA or control scrambled siRNA. Two replicate samples were prepared for RNA-Seq.