Abstract
Long noncoding RNAs (lncRNAs) are RNA transcripts that are at least 200 nucleotides long and lack coding potential, and they have been demonstrated to be involved in a wide range of biological processes. Many lncRNAs, especially those enriched in nucleus, have been found to regulate gene expression at transcriptional level. Regulation of gene transcription by lncRNAs are mainly mediated by transcriptional regulators (TRs) which interact with lncRNAs. LncRNAs can either enhance or suppress TR’s activity, which depends on different mechanism and cellular context. RNA pull-down assay followed by RNA immunoprecipitation is a powerful tool to identify and confirm the specific interaction between TRs and lncRNAs. In this chapter, we illustrate how to perform RNA pull-down and RNA immunoprecipitation to identify TRs that interact with lncRNAs using frozen liver tissues.
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Reference
Guttman M et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223–227. https://doi.org/10.1038/nature07672
Iyer MK et al (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 47:199–208. https://doi.org/10.1038/ng.3192
Hon CC et al (2017) An atlas of human long non-coding RNAs with accurate 5′ ends. Nature 543:199–204. https://doi.org/10.1038/nature21374
Geisler S, Coller J (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 14:699–712. https://doi.org/10.1038/nrm3679
Sun M, Kraus WL (2015) From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 36:25–64. https://doi.org/10.1210/er.2014-1034
Quinodoz S, Guttman M (2014) Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol 24:651–663. https://doi.org/10.1016/j.tcb.2014.08.009
Li P et al (2015) A liver-enriched long non-coding RNA, lncLSTR, regulates systemic lipid metabolism in mice. Cell Metab 21:455–467. https://doi.org/10.1016/j.cmet.2015.02.004
Ruan X, Li P, Cangelosi A, Yang L, Cao H (2016) A long non-coding RNA, lncLGR, regulates hepatic glucokinase expression and glycogen storage during fasting. Cell Rep 14:1867–1875. https://doi.org/10.1016/j.celrep.2016.01.062
Acknowledgment
This work was supported by the Division of Intramural Research of the NHLBI, National Institutes of Health (grants HL006103 and HL006159).
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Ruan, X., Li, P., Cao, H. (2018). Identification of Transcriptional Regulators That Bind to Long Noncoding RNAs by RNA Pull-Down and RNA Immunoprecipitation. In: Raghavachari, N., Garcia-Reyero, N. (eds) Gene Expression Analysis. Methods in Molecular Biology, vol 1783. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7834-2_9
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DOI: https://doi.org/10.1007/978-1-4939-7834-2_9
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