Zooming in on protein-RNA interactions : a multi-level workflow to identify interaction partners
Colantoni, Alessio (Istituto Italiano di Tecnologia. Center for Life Nanoscience)
Rupert, Jakob (Istituto Italiano di Tecnologia. Center for Human Technologies)
Vandelli, Andrea (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Tartaglia, Gian Gaetano (Institució Catalana de Recerca i Estudis Avançats)
Zacco, Elsa (Istituto Italiano di Tecnologia. Center for Human Technologies)

Data:	2020
Resum:	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 cat RAPID, 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.
Ajuts:	European Commission 309545 European Commission 855923 European Commission 754490 European Commission 727658 European Commission 825070 Agencia Estatal de Investigación BFU2017-86970-P
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article de revisió ; recerca ; Versió publicada
Matèria:	Clip ; Molecular modelling ; Protein-RNA interaction predictions ; Protein-RNA interaction validation ; Protein-RNA interactions
Publicat a:	Biochemical Society Transactions, Vol. 48, Issue 4 (August 2020) , p. 1529-1543, ISSN 1470-8752

DOI: 10.1042/BST20191059
PMID: 32820806

15 p, 1.1 MB

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