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Knocking Down Long Noncoding RNAs Using Antisense Oligonucleotide Gapmers

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Gapmers

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2176))

Abstract

Long noncoding RNAs (lncRNAs) are a class of RNA with 200 nucleotides or longer that are not translated into protein. lncRNAs are highly abundant; a study estimates that at least four times more lncRNAs are typically present than coding RNAs in humans. However, function of more than 95% of human lncRNAs are still unknown. Synthetic antisense oligonucleotides called gapmers are powerful tools for lncRNA loss-of-function studies. Gapmers contain a central DNA part, which activates RNase H-mediated RNA degradation, flanked by modified oligonucleotides, such as 2′-O-methyl RNA (2′OMe), 2′-O-methoxyethyl RNA (2′MOE), constrained ethyl nucleosides (cEt), and locked nucleic acids (LNAs). In contrast to siRNA or RNAi-based methods, antisense oligonucleotide gapmer-based knockdown is often more effective against nuclear-localized lncRNA targets, since RNase H is mainly localized in nuclei. As such, gapmers are also potentially a powerful tool for therapeutics targeting lncRNAs in various diseases, including cancer, cardiovascular diseases, lung fibrosis, and neurological/neuromuscular diseases. This chapter will discuss the development and applications of gapmers for lncRNA loss-of-function studies and tips to design effective antisense oligonucleotides.

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Acknowledgments

This work is supported by Muscular Dystrophy Canada, the Friends of Garrett Cumming Research Fund, HM Toupin Neurological Science Research Fund, Canadian Institutes of Health Research (CIHR), Alberta Innovates: Health Solutions (AIHS), Canada Foundation for Innovation (CFI), Alberta Advanced Education and Technology, and Women and Children’s Health Research Institute (WCHRI).

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Authors and Affiliations

  1. Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada

    Rika Maruyama & Toshifumi Yokota

  2. The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada

    Toshifumi Yokota

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  1. Rika Maruyama
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  2. Toshifumi Yokota
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Correspondence to Toshifumi Yokota .

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Editors and Affiliations

  1. Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada

    Toshifumi Yokota

  2. Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada

    Rika Maruyama

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Maruyama, R., Yokota, T. (2020). Knocking Down Long Noncoding RNAs Using Antisense Oligonucleotide Gapmers. In: Yokota, T., Maruyama, R. (eds) Gapmers. Methods in Molecular Biology, vol 2176. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0771-8_3

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  • DOI: https://doi.org/10.1007/978-1-0716-0771-8_3

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