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Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference

  • Protocol
Functional Analysis of Long Non-Coding RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2254))

Abstract

CRISPR-mediated interference (CRISPRi), a robust and specific system for programmably repressing transcription, provides a versatile tool for systematically characterizing the function of long noncoding RNAs (lncRNAs). When used with highly parallel, lentiviral pooled screening approaches, CRISPRi enables the targeted knockdown of tens of thousands of lncRNA-expressing loci in a single screen. Here we describe the use of CRISPRi to target lncRNA loci in a pooled screen, using cell growth and proliferation as an example of a phenotypic readout. Considerations for custom lncRNA-targeting libraries, alternative phenotypic readouts, and orthogonal validation approaches are also discussed.

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Author information

Authors and Affiliations

  1. Department of Neurological Surgery, University of California, San Francisco, CA, USA

    S. John Liu & Daniel A. Lim

  2. Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA

    S. John Liu & Daniel A. Lim

  3. Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA

    Max A. Horlbeck & Jonathan S. Weissman

  4. Howard Hughes Medical Institute, University of California, San Francisco, CA, USA

    Max A. Horlbeck & Jonathan S. Weissman

  5. California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA, USA

    Max A. Horlbeck & Jonathan S. Weissman

  6. Center for RNA Systems Biology, University of California, San Francisco, CA, USA

    Max A. Horlbeck & Jonathan S. Weissman

  7. San Francisco Veterans Affairs Medical Center, University of California, San Francisco, CA, USA

    Daniel A. Lim

Authors
  1. S. John Liu
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  2. Max A. Horlbeck
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  3. Jonathan S. Weissman
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  4. Daniel A. Lim
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Corresponding author

Correspondence to Daniel A. Lim .

Editor information

Editors and Affiliations

  1. Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MA, USA

    Haiming Cao

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Liu, S.J., Horlbeck, M.A., Weissman, J.S., Lim, D.A. (2021). Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference. In: Cao, H. (eds) Functional Analysis of Long Non-Coding RNAs. Methods in Molecular Biology, vol 2254. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1158-6_20

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  • DOI: https://doi.org/10.1007/978-1-0716-1158-6_20

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1157-9

  • Online ISBN: 978-1-0716-1158-6

  • eBook Packages: Springer Protocols

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