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Mol. Cell. Biol. doi:10.1128/MCB.00627-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

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

Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA

^* To whom correspondence should be addressed. Email: rsingh{at}colorado.edu.

	Abstract

Recognition of polypyrimidine-tracts (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 from biochemical studies on model pre-mRNAs.