Abstract
The accurate and thorough genome-wide detection of adenosine-to-inosine editing, a biologically indispensable process, has proven challenging. Here, we present a discovery pipeline in adult Drosophila, with 3,581 high-confidence editing sites identified with an estimated accuracy of 87%. The target genes and specific sites highlight global biological properties and functions of RNA editing, including hitherto-unknown editing in well-characterized classes of noncoding RNAs and 645 sites that cause amino acid substitutions, usually at conserved positions. The spectrum of functions that these gene targets encompass suggests that editing participates in a diverse set of cellular processes. Editing sites in Drosophila exhibit sequence-motif preferences and tend to be concentrated within a small subset of total RNAs. Finally, editing regulates expression levels of target mRNAs and strongly correlates with alternative splicing.
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Acknowledgements
We wish to thank Y. Vyatkin for help with the bioinformatics analysis, D. Jones for help with SMS, M. Mazaitis for help with figure preparation, R. Bell for help with validations and J. Finch for expert technical assistance. We also would like to thank L. Sugden and members of the Reenan laboratory for helpful discussions. R.A.R. was supported as an Ellison Medical Research Foundation Senior Investigator.
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G.S.L. and R.A.R. designed the experiments. M.R.T., Y.A.S. and G.S.L. conducted the experiments. S.N., D.S., D.A., G.S.L. and P.K. did the bioinformatics analyses. G.S.L., R.A.R., C.E.L., D.S., M.R.T., P.K. and D.A. evaluated the results. R.M. generated mutants by homologous recombination and performed RNA editing analysis. M.R.T., S.N., P.K., G.S.L. and D.A. produced the figures. G.S.L., R.A.R., Y.A.S., C.E.L. and P.K. wrote the manuscript, with contributions from all the authors.
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St Laurent, G., Tackett, M., Nechkin, S. et al. Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila. Nat Struct Mol Biol 20, 1333–1339 (2013). https://doi.org/10.1038/nsmb.2675
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DOI: https://doi.org/10.1038/nsmb.2675
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