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

RNA
Russell S HamiltonIlan Davis

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 requi...Continue Reading

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Citations

Feb 22, 2012·RNA·Eve HartswoodDavid J Finnegan
Nov 16, 2010·Trends in Genetics : TIG·Justin P Blumenstiel
May 20, 2009·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Mark G BeckettArthur Trew
Sep 5, 2019·Genes & Development·Rachel L CosbyCédric Feschotte

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