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iCLIP: Protein-RNA interactions at nucleotide resolution.

Huppertz, I; Attig, J; D'Ambrogio, A; Eastonb, L; Sibley, CR; Sugimoto, Y; Tajnik, M; ... Ule, J; + view all (2014) iCLIP: Protein-RNA interactions at nucleotide resolution. Methods , 65 (3) pp. 274-287. 10.1016/j.ymeth.2013.10.011. Green open access

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Abstract

RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression. Precise knowledge about their binding sites is therefore critical to unravel their molecular function and to understand their role in development and disease. Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) identifies protein-RNA crosslink sites on a genome-wide scale. The high resolution and specificity of this method are achieved by an intramolecular cDNA circularization step that enables analysis of cDNAs that truncated at the protein-RNA crosslink sites. Here, we describe the improved iCLIP protocol and discuss critical optimization and control experiments that are required when applying the method to new RBPs.

Type: Article
Title: iCLIP: Protein-RNA interactions at nucleotide resolution.
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.ymeth.2013.10.011
Publisher version: http://dx.doi.org/10.1016/j.ymeth.2013.10.011
Additional information: ©� 2013 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).
Keywords: RNA, RNA-binding protein, UV crosslinking and immunoprecipitation (CLIP), high-throughput sequencing, iCLIP, post-transcriptional regulation, protein-RNA interaction
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Clinical and Movement Neurosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
URI: http://discovery.ucl.ac.uk/id/eprint/1415709
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