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  iCLIP: protein-RNA interactions at nucleotide resolution

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.

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Huppertz, I.1, Author           
Attig, J., Author
D'Ambrogio, A., Author
Easton, L. E., Author
Sibley, C. R., Author
Sugimoto, Y., Author
Tajnik, M., Author
Konig, J., Author
Ule, J., Author
Affiliations:
1Huppertz – RNA-Binding Proteins in Metabolism and Ageing, Max Planck Research Groups, Max Planck Institute for Biology of Ageing, Max Planck Society, ou_3444906              

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Free keywords: Binding Sites DNA, Circular/chemistry/genetics Gene Expression Regulation *Gene Library HeLa Cells High-Throughput Nucleotide Sequencing Humans Immunoprecipitation/*methods Protein Binding RNA/*chemistry/genetics RNA-Binding Proteins/*chemistry/genetics Ultraviolet Rays High-throughput sequencing Post-transcriptional regulation Protein-RNA interaction Rna RNA-binding protein UV crosslinking and immunoprecipitation (CLIP) iCLIP
 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.

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 Dates: 2014-02-012013-10-25
 Publication Status: Issued
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 Rev. Type: -
 Identifiers: Other: 24184352
DOI: 10.1016/j.ymeth.2013.10.011
ISSN: 1095-9130 (Electronic)1046-2023 (Linking)
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Title: Methods
Source Genre: Journal
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Pages: - Volume / Issue: 65 (3) Sequence Number: - Start / End Page: 274 - 87 Identifier: -