Ribozymes pp 287-301 | Cite as

Long Non-coding RNA Depletion Using Self-Cleaving Ribozymes

  • Alex C. Tuck
  • Marc BühlerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2167)


Some long non-coding RNA (lncRNA) genes encode a functional RNA product, whereas others act as DNA elements or via the act of transcription. We describe here a ribozyme-based approach to deplete an endogenous lncRNA in mouse embryonic stem cells, with minimal disruption of its gene. This enables the role of the lncRNA product to be tested.

Key words

Ribozyme RNA Genome editing lncRNA Long non-coding RNA lincRNA 



This work was supported by the Wellcome Trust [WT103977]; the Swiss National Science Foundation National Centres of Competence in Research RNA & Disease [141735]; and the Friedrich Miescher Institute for Biomedical Research, which is supported by the Novartis Research Foundation.


  1. 1.
    Guttman M, Amit I, Garber M et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223–227CrossRefGoogle Scholar
  2. 2.
    Grote P, Wittler L, Hendrix D et al (2013) The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cel 24:206–214CrossRefGoogle Scholar
  3. 3.
    Latos PA, Pauler FM, Koerner MV et al (2012) Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338:1469–1472CrossRefGoogle Scholar
  4. 4.
    Paralkar VR, Taborda CC, Huang P et al (2016) Unlinking an lncRNA from its associated cis element. Mol Cel 62:104–110CrossRefGoogle Scholar
  5. 5.
    Tuck AC, Natarajan KN, Rice GM et al (2018) Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions. Life Sci Alliance 1:e201800124CrossRefGoogle Scholar
  6. 6.
    Leucci E, Vendramin R, Spinazzi M et al (2016) Melanoma addiction to the long non-coding RNA SAMMSON. Nature 531:518–522CrossRefGoogle Scholar
  7. 7.
    Engreitz JM, Haines JE, Perez EM et al (2016) Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539:452–455CrossRefGoogle Scholar
  8. 8.
    Liu SJ, Horlbeck MA, Cho SW et al (2016) CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells. Science 355:aah7111CrossRefGoogle Scholar
  9. 9.
    Knuckles P, Carl SH, Musheev M et al (2017) RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding. Nat Struct Mol Biol 24:561–569CrossRefGoogle Scholar
  10. 10.
    Flemr M, Bühler M (2015) Single-Step Generation of Conditional Knockout Mouse Embryonic Stem Cells. Cell Rep 12:709–716CrossRefGoogle Scholar
  11. 11.
    Camblong J, Beyrouthy N, Guffanti E et al (2009) Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 23:1534–1545CrossRefGoogle Scholar
  12. 12.
    Nomura Y, Zhou L, Miu A et al (2013) Controlling mammalian gene expression by allosteric hepatitis Delta virus ribozymes. ACS Synth Biol 2:684–689CrossRefGoogle Scholar
  13. 13.
    Yen L, Svendsen J, Lee J-S et al (2004) Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431:471CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2021

Authors and Affiliations

  1. 1.Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
  2. 2.University of BaselBaselSwitzerland

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