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RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods pp 491–521Cite as

RNA–Protein Interactions: An Overview

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1097))

Abstract

RNA binding proteins (RBPs) are key players in the regulation of gene expression. In this chapter we discuss the main protein–RNA recognition modes used by RBPs in order to regulate multiple steps of RNA processing. We discuss traditional and state-of-the-art technologies that can be used to study RNAs bound by individual RBPs, or vice versa, for both in vitro and in vivo methodologies. To help highlight the biological significance of RBP mediated regulation, online resources on experimentally verified protein–RNA interactions are briefly presented. Finally, we present the major tools to computationally infer RNA binding sites according to the modeling features and to the unsupervised or supervised frameworks that are adopted. Since some RNA binding site search algorithms are derived from DNA binding site search algorithms, we discuss the commonalities and novelties introduced to handle both sequence and structural features uniquely characterizing protein–RNA interactions.

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Acknowledgements

The preparation of this chapter was partially supported by a Canadian Institute of Health Research grant to Quaid Morris (MOP-93671) and by an Italian Autonomous Province of Trento grant to Angela Re.

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Authors and Affiliations

  1. University of Trento, Mattarello, Italy

    Angela Re

  2. Technical University of Denmark, Lyngby, Denmark

    Tejal Joshi & Eleonora Kulberkyte

  3. The Donnelly Centre, University of Toronto, Toronto, Canada

    Quaid Morris

  4. Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

    Christopher T. Workman

  5. Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark

    Christopher T. Workman

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  1. Angela Re
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  2. Tejal Joshi
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  3. Eleonora Kulberkyte
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  4. Quaid Morris
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  5. Christopher T. Workman
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Editors and Affiliations

  1. Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

    Jan Gorodkin

  2. University of Washington Dept. Computer Science & Engineering, Seattle, Washington, USA

    Walter L. Ruzzo

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Re, A., Joshi, T., Kulberkyte, E., Morris, Q., Workman, C.T. (2014). RNA–Protein Interactions: An Overview. In: Gorodkin, J., Ruzzo, W. (eds) RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Methods in Molecular Biology, vol 1097. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-709-9_23

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  • DOI: https://doi.org/10.1007/978-1-62703-709-9_23

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