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CLIP: A method for identifying protein-RNA interaction sites in living cells

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dc.contributor.authorUle, J.
dc.contributor.authorJensen, K.
dc.contributor.authorMele, A.
dc.contributor.authorDarnell, R.
dc.date.issued2005
dc.descriptionhttp://www.elsevier.com/wps/find/journaldescription.cws_home/622914/description#description
dc.description.abstractNucleic-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.
dc.description.statementofresponsibilityJernej Ule, Kirk Jensen, Aldo Mele and Robert B. Darnell
dc.identifier.citationMethods, 2005; 37(4):376-386
dc.identifier.doi10.1016/j.ymeth.2005.07.018
dc.identifier.issn1046-2023
dc.identifier.issn1095-9130
dc.identifier.orcidJensen, K. [0000-0002-2084-1734]
dc.identifier.urihttp://hdl.handle.net/2440/27584
dc.language.isoen
dc.publisherAcademic Press Inc Elsevier Science
dc.source.urihttps://doi.org/10.1016/j.ymeth.2005.07.018
dc.subjectCLIP
dc.subjectUV cross-linking
dc.subjectImmunoprecipitation
dc.subjectNova
dc.subjectProtein–RNA binding
dc.titleCLIP: A method for identifying protein-RNA interaction sites in living cells
dc.typeJournal article
pubs.publication-statusPublished

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