Advertisement

Identification of Transcriptional Regulators That Bind to Long Noncoding RNAs by RNA Pull-Down and RNA Immunoprecipitation

  • Xiangbo Ruan
  • Ping Li
  • Haiming Cao
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1783)

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.

Key words

Long noncoding RNA lncRNA RNA pull-down Transcription regulation RNA-binding proteins 

Notes

Acknowledgment

This work was supported by the Division of Intramural Research of the NHLBI, National Institutes of Health (grants HL006103 and HL006159).

Reference

  1. 1.
    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 CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    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 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    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 CrossRefPubMedGoogle Scholar
  4. 4.
    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 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    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 CrossRefPubMedGoogle Scholar
  6. 6.
    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 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    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 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    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 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Cardiovascular BranchNational Heart, Lung and Blood Institute, NIHBethesdaUSA

Personalised recommendations