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Methods to study RNA–protein interactions

Nature Methodsvolume 16pages225234 (2019) | Download Citation

Abstract

Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through direct interactions with RNA-binding proteins (RBPs). Recent efforts have identified hundreds of new RBPs that lack known RNA-binding domains, thus underscoring the complexity and diversity of RNA–protein complexes. Recent progress has expanded the number of methods for studying RNA–protein interactions in two general categories: approaches that characterize proteins bound to an RNA of interest (RNA-centric), and those that examine RNAs bound to a protein of interest (protein-centric). Each method has unique strengths and limitations, which makes it important to select optimal approaches for the biological question being addressed. Here we review methods for the study of RNA–protein interactions, with a focus on their suitability for specific applications.

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Change history

  • 08 March 2019

    In the version of this paper originally published, three references were accidentally omitted: Schwartz, J. C. et al. Cell Rep. 5, 918–925 (2013); Tundup, S. et al. FEBS Lett. 580, 1285–1293 (2006); and Itri, F. et al. Biochem. Biophys. Res. Commun. 492, 67–73 (2017). The PDF and HTML versions of the paper now include these as references 58, 59, and 60, respectively, and subsequent references have been renumbered accordingly.

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Acknowledgements

We thank members of the Khavari lab for helpful discussions and apologize to colleagues whose work was not cited because of the space limitations of this review. This work was supported by grant 1F32AR072504 to D.F.P., by a USVA Merit Review grant, and by NIAMS/NIH grants AR45192 and AR49737 to P.A.K.

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  1. These authors contributed equally: Muthukumar Ramanathan, Douglas F. Porter.

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  1. Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA

    • Muthukumar Ramanathan
    • , Douglas F. Porter
    •  & Paul A. Khavari
  2. Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA

    • Paul A. Khavari

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Competing interests

The authors declare no competing interests.

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Correspondence to Paul A. Khavari.

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  1. Supplementary Table 1

    RNA library preparation steps.

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https://doi.org/10.1038/s41592-019-0330-1