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


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

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Correspondence to Sven Diederichs.

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Unrelated to this work, S.D. is a co-owner of siTOOLs Biotech GmbH, Martinsried, Germany.

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