iCLIP: protein-RNA interactions at nucleotide resolution

Huppertz, I.; Attig, J.; D'Ambrogio, A.; Easton, L. E.; Sibley, C. R.; Sugimoto, Y.; Tajnik, M.; Konig, J.; Ule, J.

doi:10.1016/j.ymeth.2013.10.011

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iCLIP: protein-RNA interactions at nucleotide resolution

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Huppertz, I.
Huppertz – RNA-Binding Proteins in Metabolism and Ageing, Max Planck Research Groups, Max Planck Institute for Biology of Ageing, Max Planck Society;

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https://www.ncbi.nlm.nih.gov/pubmed/24184352
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Citation

Huppertz, I., Attig, J., D'Ambrogio, A., Easton, L. E., Sibley, C. R., Sugimoto, Y., et al. (2013). iCLIP: protein-RNA interactions at nucleotide resolution. Methods, 65(3), 274-87. doi:10.1016/j.ymeth.2013.10.011.

Cite as: https://hdl.handle.net/21.11116/0000-000B-83F6-B

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.