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Methods to study RNA–protein interactions

Nature Methods volume 16, pages 225–234 (2019)Cite this article

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An Author Correction to this article was published on 08 March 2019

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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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Fig. 1: Schematic representation of RNA-centric methods.
Fig. 2: Subway map of CLIP protocols, from immunoprecipitation to PCR.

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  • 08 March 2019

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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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Supplementary Table 1

RNA library preparation steps.

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Ramanathan, M., Porter, D.F. & Khavari, P.A. Methods to study RNA–protein interactions. Nat Methods 16, 225–234 (2019). https://doi.org/10.1038/s41592-019-0330-1

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