SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns

Abstract

Human pre-mRNA splicing requires the removal of introns with highly variable lengths, from tens to over a million nucleotides. Therefore, mechanisms of intron recognition and splicing are likely not universal. Recently, we reported that splicing in a subset of human short introns with truncated polypyrimidine tracts depends on RBM17 (SPF45), instead of the canonical splicing factor U2AF heterodimer. Here, we demonstrate that SAP30BP, a factor previously implicated in transcriptional control, is an essential splicing cofactor for RBM17. In vitro binding and NMR analyses demonstrate that a U2AF-homology motif (UHM) in RBM17 binds directly to a newly identified UHM-ligand motif (ULM) in SAP30BP. We show that this RBM17-SAP30BP interaction is required to specifically recruit RBM17 to phosphorylated SF3B1 (SF3b155), a U2 snRNP component in active spliceosomes. We propose a unique mechanism for splicing in a subset of short introns, in which SAP30BP guides RBM17 in the assembly of active spliceosomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/522300v4_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@12da1c3org.highwire.dtl.DTLVardef@d71e53org.highwire.dtl.DTLVardef@108160corg.highwire.dtl.DTLVardef@1df7275_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefFukumura et al. discover a general splicing mechanism in a subset of human short introns with truncated polypyrimidine tracts. This splicing reaction is mediated by intermediary RBM17-SAP30BP complex, instead of the known U2AF heterodimer. SAP30BP binding to RBM17 may support RBM17 association with active phosphorylated SF3B1 in U2 snRNP. HighlightsO_LIRBM17 (SPF45) is a splicing factor required for a subset of human short introns C_LIO_LISAP30BP is an essential cofactor, which interacts with RBM17 via UHM-ULM binding C_LIO_LIRBM17 forms a weak complex with SAP30BP before its binding with SF3B1 in U2 snRNP C_LIO_LIRBM17-SAP30BP complex supports RBM17 to be recruited to active phosphorylated SF3B1 C_LI