ArticleRNA (New York, N.Y.)2009
A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Finishing the egg.Genetics · 2024Article
- High-throughput identification of RNA localization elements in neuronal cells.Nucleic acids research · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Host-transposon interactions: conflict, cooperation, and cooption.Genes & development · 2019Review
- Retrotransposons Mimic Germ Plasm Determinants to Promote Transgenerational Inheritance.Current biology : CB · 2017Article
- Changes of Osvaldo expression patterns in germline of male hybrids between the species Drosophila buzzatii and Drosophila koepferae.Molecular genetics and genomics : MGG · 2015Article
- Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.Nucleic acids research · 2012Article
- RNA:RNA interaction can enhance RNA localization in Drosophila oocytes.RNA (New York, N.Y.) · 2012Article
- Identifying and searching for conserved RNA localisation signals.Methods in molecular biology (Clifton, N.J.) · 2011Article
- Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives.Frontiers in plant science · 2011Article
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Authors and funding
7 authors.
Funding
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.
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