The splicing factor U2AF1 contributes to cancer progression through a non-canonical role in translation regulation

Somatic mutations in the spliceosome have emerged in recent years as oncogenes in human cancer. These mutations are in the factors involved in splice site selection, including a missense mutation (Ser34Phe) in a conserved nucleic acid binding domain of the spicing factor U2AF1. This protein plays a critical role in recognition of the 3'-splice site and assembly of the pre-spliceosomal complex. However, the role that this mutation plays in oncogenesis is still unknown. Here, we have uncovered a non-canonical function of U2AF1. PAR-CLIP and RIP data show that U2AF1 directly binds mature mRNA in the cytoplasm and that binding on or near the start codon results in translational repression. This splicing-independent translational regulatory role of U2AF1 is altered by the S34F mutation, leading to elevated translation of hundreds of mRNA, as revealed by polysome profiling. Overall design: PAR-CLIP on Chromatin and Cytoplasmic fractions of Flp-In-293 cells expressing FLAG-HA tagged WT or S34F mutant U2AF1. RIP-Seq was performed from U2AF1 WT,S34F and FS HBECs. To estimate translation efficiency, Ribosomal profiling followed by RNA sequencing of monosome and polysome- associated mRNA was performed from the same cells. Please note that the PAR-CLIP processed data was generated from both replicates (i.e. A and B) and is linked to the corresponding A sample.