A Conditional Role of U2AF in Splicing of Introns with Unconventional Polypyrimidine Tracts

Abstract

Recognition of polypyrimidine (Py) tracts typically present between the branch point and the 3′ splice site by the large subunit of the essential splicing factor U2AF is a key early step in pre-mRNA splicing. Diverse intronic sequence arrangements exist, however, including 3′ splice sites lacking recognizable Py tracts, which raises the question of how general the requirement for U2AF is for various intron architectures. Our analysis of fission yeast introns in vivo has unexpectedly revealed that whereas introns lacking Py tracts altogether remain dependent on both subunits of U2AF, introns with long Py tracts, unconventionally positioned upstream of branch points, are unaffected by U2AF inactivation. Nevertheless, mutation of these Py tracts causes strong dependence on the large subunit U2AF⁵⁹. We also find that Py tract diversity influences the requirement for the conserved C-terminal domain of U2AF⁵⁹ (RNA recognition motif 3), which has been implicated in protein-protein interactions with other splicing factors. Together, these results suggest that in addition to Py tract binding by U2AF, supplementary mechanisms of U2AF recruitment and 3′ splice site identification exist to accommodate diverse intron architectures, which have gone unappreciated in biochemical studies of model pre-mRNAs.

SUPPLEMENTAL MATERIAL

We thank Dick McIntosh and DeWight Williams for help with the yeast work, Erin Peden for help with computational analysis, Chris Webb, Jo Ann Wise, Judith Potashkin, and Tokio Tani for plasmids, strains, and reagents, and Tom Blumenthal, Dick McIntosh, Juan Valcárcel, Joaquin Espinosa, Greg Odorizzi, Jens Lykke-Andersen, Mark Robida, and Rajesh Gaur for helpful discussions and critical reading of the manuscript.

This work was supported in part by grants from the American Cancer Society, the Keck Foundation, and the National Institutes of Health to R.S.