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Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions Between Long Noncoding RNAs and RNA-Binding Proteins

  • Je-Hyun YoonEmail author
  • Myriam Gorospe
Part of the Methods in Molecular Biology book series (MIMB, volume 1402)

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.

Key words

CLIP lncRNA RBP Ribonucleoprotein complexes qPCR 

Notes

Acknowledgments

JHY and MG were supported by the National Institute on Aging Intramural Research Program, National Institutes of Health and startup fund from Medical University of South Carolina.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Biochemistry and Molecular BiologyMedical University of South CarolinaCharlestonUSA
  2. 2.Laboratory of Genetics and GenomicsNational Institute on Aging-Intramural Research Program, National Institutes of HealthBaltimoreUSA

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