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Tuning the Expression of Long Noncoding RNA Loci with CRISPR Interference

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RNA-Chromatin Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2161))

Abstract

Long noncoding RNAs (lncRNAs) have emerged as important regulators of gene expression networks. Over 50,000 lncRNA loci have been annotated in the human genome, but only a subset has been involved in regulation of key cellular processes, organismal development, and diseases. Hence, the functional role for the majority of the lncRNA genes remains unknown. With the recent developments of different CRISPR/Cas9 technologies, the function of lncRNAs can now be examined. CRISPR interference (CRISPRi) is one of these methods that can be used to inhibit the expression of any genomic locus including lncRNAs. This system utilizes catalytically inactive (d)Cas9 fused to KRAB repression domain and single guide RNA against targeted genomic locus. Since CRISPRi has negligible off-target effects and does not involve changes in the underlying genomic DNA sequence, it represents a valuable addition to the existing armamentarium used to investigate lncRNA biology.

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Acknowledgments

I would like to thank Jasmin Mangei and Valentina Quarantotti for critically reading the manuscript. I also thank Richard Grenfell from the FACS Core Facility at the CRUK Cambridge Institute for help with the FACS sorting, and Alasdair Russel for providing us with the pHIV-Zsgreen vector. This work was supported by Cancer Research UK (C14303/A17197 to Fanni Gergely and Duncan Odom; A24455 to Fanni Gergely, and A20412 to Duncan Odom). We also acknowledge the support of the University of Cambridge, the Wellcome Trust (WT202878; Duncan Odom), European Research Council (615584; Duncan Odom), and Hutchison Whampoa Limited.

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  1. Lovorka Stojic

    Present address: Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK

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  1. Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, London, UK

    Lovorka Stojic

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  1. Lovorka Stojic
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Correspondence to Lovorka Stojic .

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  1. Department for Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark

    Ulf Andersson Vang Ørom

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Stojic, L. (2020). Tuning the Expression of Long Noncoding RNA Loci with CRISPR Interference. In: Ørom, U. (eds) RNA-Chromatin Interactions. Methods in Molecular Biology, vol 2161. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0680-3_1

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  • DOI: https://doi.org/10.1007/978-1-0716-0680-3_1

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  • Publisher Name: Humana, New York, NY

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