A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons

Russell Hamilton, Eve Hartswood, Georgia Vendra, Cheryl Jones, Veronique van de Bor, David Finnegan, Ilan Davis

Research output: Contribution to journalArticlepeer-review


mRNA localization is a widespread mode of delivering proteins to their site of function. The embryonic axes in Drosophila are determined in the oocyte, through Dynein dependent transport of gurken/TGF-α mRNA, containing a small localization signal that assigns its destination. A signal with a similar secondary structure, but lacking significant sequence similarity, is present in the I factor retrotransposon mRNA, also transported by Dynein. It is currently unclear whether other mRNAs exist that are localized to the same site using similar signals. Moreover, searches for other genes containing similar elements have not been possible due to a lack of suitable bioinformatics methods for searches of secondary structure elements and the difficulty of experimentally testing all the possible candidates. We have developed a bioinformatics approach for searching across the genome for small RNA elements that are similar to the secondary structures of particular localization signals. We have uncovered 49 candidates, of which we were able to test 23 for their localization potential using injection assays for Dynein mediated RNA localization. We found that G2 and Jockey transposons each contain a gurken / I factor-like RNA stem loop required for Dynein dependent localization to the anterior and dorso-anterior corner of the oocyte. We conclude that I factor, G2 and Jockey are members of a “family” of transposable elements sharing a gurken-like mRNA localization signal and Dynein dependent mechanism of transport. The bioinformatics pipeline we have developed will have broader utility in fields where small RNA signals play important roles.
Original languageEnglish
Pages (from-to)200-207
Number of pages8
Issue number2
Publication statusPublished - Feb 2009


  • transposable elements
  • intracellular RNA localization
  • bioinformatics
  • Drosophila
  • RNA secondary structure
  • Dynein


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