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Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila

Nature Structural & Molecular Biology volume 20, pages 1333–1339 (2013)Cite this article

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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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Figure 1: Detection and measurement of editing sites with SMS.
Figure 2: Separation of true Drosophila editing sites from artifacts.
Figure 3: Biological properties of Drosophila editing sites.
Figure 4: Conservation of genomically encoded amino acids changed as a result of nonsynonymous editing.
Figure 5: Global biological properties of edited transcripts.

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Sequence Read Archive

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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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Author notes

  1. Rachel Maloney

    Present address: Present address: Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,

Authors and Affiliations

  1. Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA

    Georges St Laurent, Yiannis A Savva, Rachel Maloney & Robert A Reenan

  2. St. Laurent Institute, Cambridge, Massachusetts, USA

    Georges St Laurent, Michael R Tackett, Sergey Nechkin, Dmitry Shtokalo & Philipp Kapranov

  3. A.P. Ershov Institute of Informatics Systems, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia

    Sergey Nechkin & Dmitry Shtokalo

  4. State Research Center of Virology and Biotechnology 'Vector', Novosibirsk, Russia

    Denis Antonets

  5. Department of Applied Mathematics, Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA

    Charles E Lawrence

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Contributions

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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Correspondence to Robert A Reenan.

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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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