title: Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons.
abstract: The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3'ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing.
authors: University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK.
authors: Jana
authors: J
authors: Kralovicova
authors: University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK igvo@soton.ac.uk.
authors: Igor
authors: I
authors: Vorechovsky
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D005091:Exons; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D007438:Introns; D021122:Protein Subunits / Q000235:genetics* / Q000378:metabolism; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism; D022821:RNA Splice Sites; D000068103:Serine-Arginine Splicing Factors / Q000235:genetics* / Q000378:metabolism; D000072668:Splicing Factor U2AF / Q000235:genetics* / Q000378:metabolism
chemical_list: D021122:Protein Subunits; D012322:RNA Precursors; D022821:RNA Splice Sites; C491388:SRSF3 protein, human; D000072668:Splicing Factor U2AF; D000068103:Serine-Arginine Splicing Factors