title: A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons.
abstract: 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-alpha 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 48 candidates, of which we were able to test 22 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.
authors.affiliation: Department of Biochemistry, University of Oxford, United Kingdom.
authors.forename: Russell S
authors.initials: RS
authors.lastname: Hamilton
authors.forename: Eve
authors.initials: E
authors.lastname: Hartswood
authors.forename: Georgia
authors.initials: G
authors.lastname: Vendra
authors.forename: Cheryl
authors.initials: C
authors.lastname: Jones
authors.forename: Veronique
authors.initials: V
authors.lastname: Van De Bor
authors.forename: David
authors.initials: D
authors.lastname: Finnegan
authors.forename: Ilan
authors.initials: I
authors.lastname: Davis
mesh_terms: D000818:Animals; D001483:Base Sequence; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics*; D049750:Genome, Insect; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009865:Oocytes / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D020079:Terminal Repeat Sequences; D016211:Transforming Growth Factor alpha / Q000235:genetics
chemical_list: D029721:Drosophila Proteins; D012333:RNA, Messenger; D018626:Retroelements; D016211:Transforming Growth Factor alpha; C083730:grk protein, Drosophila