Abstract
Mammalian cells express a wide range of transcripts, some protein-coding RNAs (mRNA), and many noncoding (nc) RNAs. Long (l)ncRNAs can modulate 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 (crosslinking and immunoprecipitation followed by reverse transcription and quantitative PCR) for mapping and quantifying interactions of lncRNAs with canonical and non-canonical RBPs.
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Acknowledgments
J.-H.C. was supported by the Holing Cancer Center’s Fellowship Program sponsored by the Abney Foundation at Medical university of South Carolina. J.W.L. and K.-Y.M. were supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2019R1C1C1002886). J.-H.Y. was supported by Medical university of South Carolina.
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Cho, JH., Lee, J.W., Yoon, JH., Min, KW. (2021). Crosslinking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions of Long Noncoding RNAs with Canonical and Non-canonical RNA-Binding Proteins. In: Zhang, L., Hu, X. (eds) Long Non-Coding RNAs. Methods in Molecular Biology, vol 2372. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1697-0_2
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DOI: https://doi.org/10.1007/978-1-0716-1697-0_2
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