Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners

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• dc.contributor.author Colantoni, Alessio
• dc.contributor.author Rupert, Jakob
• dc.contributor.author Vandelli, Andrea
• dc.contributor.author Tartaglia, Gian Gaetano
• dc.contributor.author Zacco, Elsa
• dc.date.accessioned 2020-10-26T10:17:51Z
• dc.date.available 2020-10-26T10:17:51Z
• dc.date.issued 2020
• dc.description.abstract Interactions between proteins and RNA are at the base of numerous cellular regulatory and functional phenomena. The investigation of the biological relevance of non-coding RNAs has led to the identification of numerous novel RNA-binding proteins (RBPs). However, defining the RNA sequences and structures that are selectively recognised by an RBP remains challenging, since these interactions can be transient and highly dynamic, and may be mediated by unstructured regions in the protein, as in the case of many non-canonical RBPs. Numerous experimental and computational methodologies have been developed to predict, identify and verify the binding between a given RBP and potential RNA partners, but navigating across the vast ocean of data can be frustrating and misleading. In this mini-review, we propose a workflow for the identification of the RNA binding partners of putative, newly identified RBPs. The large pool of potential binders selected by in-cell experiments can be enriched by in silico tools such as catRAPID, which is able to predict the RNA sequences more likely to interact with specific RBP regions with high accuracy. The RNA candidates with the highest potential can then be analysed in vitro to determine the binding strength and to precisely identify the binding sites. The results thus obtained can furthermore validate the computational predictions, offering an all-round solution to the issue of finding the most likely RNA binding partners for a newly identified potential RBP.
• dc.description.sponsorship The research leading to this work has been supported by European Research Council (RIBOMYLOME_309545 and ASTRA_855923), by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754490 and under projects IASIS_727658 and INFORE_825080, by the Spanish Ministry of Economy and Competitiveness BFU2017-86970-P as well as the collaboration with Peter St. George-Hyslop financed by the Wellcome Trust.
• dc.format.mimetype application/pdf
• dc.identifier.citation Colantoni A, Rupert J, Vandelli A, Tartaglia GG, Zacco E. Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners. Biochem Soc Trans. 2020; 48(4):1529-43. DOI: 10.1042/BST20191059
• dc.identifier.doi http://dx.doi.org/10.1042/BST20191059
• dc.identifier.issn 0300-5127
• dc.identifier.uri http://hdl.handle.net/10230/45576
• dc.language.iso eng
• dc.publisher Portland Press
• dc.relation.ispartof Biochem Soc Trans. 2020; 48(4):1529-43
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/855923
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86970-P
• dc.rights © 2020 The Author(s). This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Clip
• dc.subject.keyword Molecular modelling
• dc.subject.keyword Protein-RNA interaction predictions
• dc.subject.keyword Protein–RNA interaction validation
• dc.subject.keyword Protein–RNA interactions
• dc.title Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion