title: Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions Between Long Noncoding RNAs and RNA-Binding Proteins.
abstract: Mammalian cells express a wide range of transcripts, some protein-coding RNAs (mRNA) and many noncoding (nc) RNAs. Long (l)ncRNAscan modulates protein expression patterns by regulating gene transcription, pre-mRNA splicing, mRNA export, mRNA degradation, protein translation, and protein ubiquitination. Given the growing recognition that lncRNAs have a robust impact upon gene expression, there is rising interest in elucidating the levels and regulation of lncRNAs. A number of high-throughput methods have been developed recently to map the interaction of lncRNAs and RNA-binding proteins (RBPs). However, few of these approaches are suitable for mapping and quantifying RBP-lncRNA interactions. Here, we describe the recently developed method CLIP-qPCR (cross-linking and immunoprecipitation followed by reverse transcription and quantitative PCR) for mapping and quantifying RBP-lncRNA interactions.
authors.affiliation: Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC, 29425, USA. yoonje@musc.edu.
authors.forename: Je-Hyun
authors.initials: JH
authors.lastname: Yoon
authors.affiliation: Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD, 21224, USA.
authors.forename: Myriam
authors.initials: M
authors.lastname: Gorospe
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques / Q000379:methods; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D062085:RNA, Long Noncoding / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000032:analysis / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D014466:Ultraviolet Rays
chemical_list: D062085:RNA, Long Noncoding; D016601:RNA-Binding Proteins
keywords: CLIP; RBP; Ribonucleoprotein complexes; lncRNA; qPCR