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Type: Journal article
Title: CLIP: A method for identifying protein-RNA interaction sites in living cells
Author: Ule, J.
Jensen, K.
Mele, A.
Darnell, R.
Citation: Methods, 2005; 37(4):376-386
Publisher: Academic Press Inc Elsevier Science
Issue Date: 2005
ISSN: 1046-2023
Statement of
Jernej Ule, Kirk Jensen, Aldo Mele and Robert B. Darnell
Abstract: Nucleic-acid binding proteins constitute nearly one-fourth of all functionally annotated human genes. Genome-wide analysis of protein–nucleic acid contacts has not yet been performed for most of these proteins, restricting attempts to establish a comprehensive understanding of protein function. UV cross-linking is a method typically used to determine the position of direct interactions between proteins and nucleic acids. We have developed the cross-linking and immunoprecipitation assay, which exploits the covalent protein–nucleic acid cross-linking to stringently purify a specific protein–RNA complex using immunoprecipitation followed by SDS–PAGE separation. In this way, the vast majority of non-specific contaminating RNA, which can bind to co-immunoprecipitated proteins or beads, can be removed. Here, we present an improved protocol that performs RNA linker ligation before the SDS–PAGE step, and describe its application to the specific purification and amplification of RNA ligands of Nova in neurons.
Keywords: CLIP
UV cross-linking
Protein–RNA binding
DOI: 10.1016/j.ymeth.2005.07.018
Appears in Collections:Aurora harvest 2
Molecular and Biomedical Science publications

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