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RNA motifs and combinatorial prediction of interactions, stability and localization of noncoding RNAs

Nature Structural & Molecular Biology volume 25, pages 1070–1076 (2018)Cite this article

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Abstract

Although the number of documented noncoding RNAs (ncRNAs) is rapidly increasing, knowledge of their molecular function is lagging behind. The identification of specific RNA motifs that mediate transcript stability, interactions and localization may aid in the prediction of these features in new transcripts and may have potential implications for ncRNA function. Here, we review RNA motifs, focusing on four recent studies identifying nuclear-retention motifs, and discuss the limited specificity of short-RNA motifs and the resulting challenge for effective functional prediction. Future approaches may succeed by integrating combinatorial and cooperative effects of additional partially sequence-based properties.

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Fig. 1: Screening for RNA localization motifs.
Fig. 2: Combinatorial determinants of RNA-motif function.

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Acknowledgements

S.D. is supported by the Deutsche Forschungsgemeinschaft (German Research Foundation), Di1421/7-1.

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Authors and Affiliations

  1. Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Minakshi Gandhi, Maiwen Caudron-Herger & Sven Diederichs

  2. German Academic Exchange Service (DAAD), Bonn, Germany

    Minakshi Gandhi

  3. Helmholtz International Graduate School for Cancer Research (HIGS), Heidelberg, Germany

    Minakshi Gandhi & Sven Diederichs

  4. Division of Cancer Research, Department of Thoracic Surgery, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK)–Partner Site, Freiburg, Germany

    Sven Diederichs

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Correspondence to Sven Diederichs.

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Gandhi, M., Caudron-Herger, M. & Diederichs, S. RNA motifs and combinatorial prediction of interactions, stability and localization of noncoding RNAs. Nat Struct Mol Biol 25, 1070–1076 (2018). https://doi.org/10.1038/s41594-018-0155-0

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