Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity

Nucleic Acids Res. 2013 Nov;41(20):9438-60. doi: 10.1093/nar/gkt702. Epub 2013 Aug 13.


Despite studies that have investigated the interactions of double-stranded RNA-binding proteins like Staufen with RNA in vitro, how they achieve target specificity in vivo remains uncertain. We performed RNA co-immunoprecipitations followed by microarray analysis to identify Staufen-associated mRNAs in early Drosophila embryos. Analysis of the localization and functions of these transcripts revealed a number of potentially novel roles for Staufen. Using computational methods, we identified two sequence features that distinguish Staufen's target transcripts from non-targets. First, these Drosophila transcripts, as well as those human transcripts bound by human Staufen1 and 2, have 3' untranslated regions (UTRs) that are 3-4-fold longer than unbound transcripts. Second, the 3'UTRs of Staufen-bound transcripts are highly enriched for three types of secondary structures. These structures map with high precision to previously identified Staufen-binding regions in Drosophila bicoid and human ARF1 3'UTRs. Our results provide the first systematic genome-wide analysis showing how a double-stranded RNA-binding protein achieves target specificity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions*
  • Animals
  • Cytoskeletal Proteins / metabolism*
  • Drosophila / embryology
  • Drosophila / genetics
  • Drosophila Proteins / metabolism*
  • Genome, Insect
  • Humans
  • Nucleic Acid Conformation
  • RNA, Double-Stranded / chemistry
  • RNA, Double-Stranded / metabolism
  • RNA, Messenger / analysis
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / metabolism*


  • 3' Untranslated Regions
  • Cytoskeletal Proteins
  • Drosophila Proteins
  • RNA, Double-Stranded
  • RNA, Messenger
  • RNA-Binding Proteins
  • STAU1 protein, human
  • stau protein, Drosophila