Cancer-Associated Substitutions in RNA Recognition Motifs of PUF60 and U2AF65 Reveal Residues Required for Correct Folding and 3′ Splice-Site Selection

U2AF65 (U2AF2) and PUF60 (PUF60) are splicing factors important for recruitment of the U2 small nuclear ribonucleoprotein to lariat branch points and selection of 3 ' splice sites (3 ' ss). Both proteins preferentially bind uridine-rich sequences upstream of 3 ' ss via their RNA recognition motifs (RRMs). Here, we examined 36 RRM substitutions reported in cancer patients to identify variants that alter 3 ' ss selection, RNA binding and protein properties. Employing PUF60- and U2AF65-dependent 3 ' ss previously identified by RNA-seq of depleted cells, we found that 43% (10/23) and 15% (2/13) of independent RRM mutations in U2AF65 and PUF60, respectively, conferred splicing defects. At least three RRM mutations increased skipping of internalU2AF2(similar to 9%, 2/23) orPUF60(similar to 8%, 1/13) exons, indicating that cancer-associated RRM mutations can have bothcis- andtrans-acting effects on splicing. We also report residues required for correct folding/stability of each protein and map functional RRM substitutions on to existing high-resolution structures of U2AF65 and PUF60. These results identify new RRM residues critical for 3 ' ss selection and provide relatively simple tools to detect clonal RRM mutations that enhance the mRNA isoform diversity.