The RBM17/SPF45–SAP30BP interaction is essential for splicing in a subset of human short introns

We recently demonstrated that splicing in a subset of human short introns with a truncated polypyrimidine tract (PPT) depends on RBM17 (SPF45) instead of the known essential splicing factor, U2AF2–U2AF1 (U2AF65–U2AF35). On a truncated PPT, the UHM (U2AF-homology motif) of RBM17 can interact with the ULM (UHM-ligand motif) of SF3B1 (SF3b155) in the U2 snRNP. Fruit fly SAP30BP (HCNGP) is found in spliceosomes assembled on short introns and RBM17 can bind to SAP30BP in yeast two-hybrid assays, suggesting that SAP30BP could be a functional cofactor of RBM17. We show that siRNA-knockdown of SAP30BP specifically represses endogenous, and ectopically expressed, RBM17-dependent splicing, but not conventional U2AF-dependent splicing. Our RNA-Seq data indicate that RBM17 and SAP30BP cooperate for splicing in short introns with a truncated PPT. GST pull-down assays and NMR data reveal the presence of a ULM in SAP30BP that is recognized by the RBM17–UHM. Remarkably, GST pull-down assays with an anti-phospho-SF3B1 antibody suggest that an intermediate interaction between SAP30BP and RBM17 is a prerequisite for RBM17 to be recruited by active phosphorylated SF3B1 in U2 snRNP. We conclude that the RBM17–SAP30BP complex is a constitutive splicing factor and it replaces the U2AF heterodimer for splicing in a subset of human short introns. ### Competing Interest Statement The authors have declared no competing interest.