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.