title: Genome-wide identification of alternatively spliced mRNA targets of specific RNA-binding proteins.
abstract: BACKGROUND
  Alternative splicing plays an important role in generating molecular and functional diversity in multi-cellular organisms. RNA binding proteins play crucial roles in modulating splice site choice. The majority of known binding sites for regulatory proteins are short, degenerate consensus sequences that occur frequently throughout the genome. This poses an important challenge to distinguish between functionally relevant sequences and a vast array of those occurring by chance.
  
  
  RESULTS
  Here we have used a computational approach that combines a series of biological constraints to identify uridine-rich sequence motifs that are present within relevant biological contexts and thus are potential targets of the Drosophila master sex-switch protein Sex-lethal (SXL). This strategy led to the identification of one novel target. Moreover, our systematic analysis provides a starting point for the molecular and functional characterization of an additional target, which is dependent on SXL activity, either directly or indirectly, for regulation in a germline-specific manner.
  
  
  CONCLUSIONS
  This approach has successfully identified previously known, new, and potential SXL targets. Our analysis suggests that only a subset of potential SXL sites are regulated by SXL. Finally, this approach should be directly relevant to the large majority of splicing regulatory proteins for which bonafide targets are unknown.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado, United States of America.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Robida
authors.forename: Andrew
authors.initials: A
authors.lastname: Rahn
authors.forename: Ravinder
authors.initials: R
authors.lastname: Singh
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001665:Binding Sites; D015152:Blotting, Northern; D019295:Computational Biology; D029721:Drosophila Proteins / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D016678:Genome; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D029721:Drosophila Proteins; D016601:RNA-Binding Proteins; C067777:Sxl protein, Drosophila