Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome

Eukaryotic nuclear introns have been dichotomously classified into common U2-type introns and rare U12-type introns. Because the highly conserved consensus sequences for the 5' splice site and the branch point are found within all U12-type introns, weighted matrices for these motifs are used for prediction of U12-type introns. However, the U12-type consensus sequences per se are also recognized by the U2-type spliceosome. To better understand how distinct splicing systems recognize their authentic splice sites, we determined the binding sites of splicing factors, U2AF1 and ZRSR2, and found that ZRSR2 binding is mostly limited to U12-type introns. Our results reveal RNA elements contributing to selection of U2-type and U12-type splice sites in a mutually exclusive manner. Overall design: CLIP-seq of endogenous U2AF1 by using anti-U2AF1-antibodies (Bethyl), anti-HA-antibody for HA3-tagged ZRSR2 and IgG controls.