Competition for the conserved branch point sequence influences physiological outcomes in pre-mRNA splicing

Recognition of the intron branch point during spliceosome assembly is a multistep process that can influence mRNA structure and levels. A branch point sequence motif UACUAAC is variably conserved in eukaryotic genomes, but in some organisms, more than one protein can recognize it. Here, we show that SF1 and Quaking (QKI) compete for a subset of intron branch sites with the sequence ACUAA in mammalian cells. SF1 activates exon inclusion through this sequence, but QKI represses the inclusion of alternatively spliced exons with this intron branch point sequence. Using mutant reporters derived from a natural intron with two branch site-like sequences, we find that when either branch point sequence is mutated, the other is utilized; however, when both are present, neither is used due to high-affinity binding and strong splicing repression by QKI. QKI occupancy at the dual branch site directly prevents SF1 binding and the subsequent recruitment of spliceosome-associated factors. Finally, ectopic expression of QKI in budding yeast (which lacks QKI) is lethal, at least in part due to widespread splicing repression. In conclusion, QKI can function as a splicing repressor by directly competing with SF1/BBP for a subset of branch point sequences that closely mirror its high-affinity binding site.