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Specific Gene Silencing Using RNAi in Cell Culture

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Neurodegeneration

Part of the book series: Methods in Molecular Biology ((MIMB,volume 793))

Abstract

RNA interference (RNAi) is a conserved cellular mechanism in most eukaryotes that can mediate specific gene silencing. Since its discovery in 1998, rapid progress has been made in understanding its basic mechanism and its application in research and drug discovery. In recent years, the application of RNAi in research, including research in neurodegeneration, has expanded rapidly such that it has become a regular tool for reverse genetics in cultured cells in many labs. However, an incomplete understanding of the RNAi mechanism and worries about its pitfalls still intimidate many others. Here, we present a streamlined and simple protocol for the design and implementation of an RNAi experiment in cultured cells, aiming to enable those who are inexperienced with RNAi to apply this powerful method in their research, particularly in the field of neurodegeneration.

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References

  1. Mello, C. C., and Conte, D. (2004) Revealing the world of RNA interference. Nature. 431, 338–342.

    Article  PubMed  CAS  Google Scholar 

  2. Tomari, Y., and Zamore, P. D. (2005) Perspective: machines for RNAi. Genes Dev. 19, 517–529.

    CAS  Google Scholar 

  3. Xia, X., Zhou, H., Huang, Y., and Xu, Z. (2006) Allele-specific RNAi selectively silences mutant SOD1 and achieves significant therapeutic benefit in vivo. Neurobiol. Dis. 23, 578–586.

    Article  PubMed  CAS  Google Scholar 

  4. Qiu, L., Wang, H., Xia, X., Zhou, H., and Xu, Z. (2008) A construct with fluorescent indicators for conditional expression of miRNA. BMC Biotechnology. 8, 77.

    Article  PubMed  Google Scholar 

  5. Pei, Y., and Tuschl, T. (2006) On the art of identifying effective and specific siRNAs. Nat Meth. 3, 670–676.

    Article  CAS  Google Scholar 

  6. Birmingham, A., Anderson, E., Sullivan, K., Reynolds, A., Boese, Q., Leake, D., Karpilow, J., and Khvorova, A. (2007) A protocol for designing siRNAs with high functionality and specificity. Nat. Protocols. 2, 2068–2078.

    Article  CAS  Google Scholar 

  7. Hornung, V., Guenthner-Biller, M., Bourquin, C., Ablasser, A., Schlee, M., Uematsu, S., Noronha, A., Manoharan, M., Akira, S., de Fougerolles, A., Endres, S., and Hartmann, G. (2005) Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat. Med. 11, 263–270. Epub 2005 Feb 2020.

    Google Scholar 

  8. Judge, A. D., Sood, V., Shaw, J. R., Fang, D., McClintock, K., and MacLachlan, I. (2005) Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotech. 23, 457–462.

    Article  CAS  Google Scholar 

  9. Lan, T., Putta, M. R., Wang, D., Dai, M., Yu, D., Kandimalla, E. R., and Agrawal, S. (2009) Synthetic oligoribonucleotides-containing secondary structures act as agonists of Toll-like receptors 7 and 8. Biochemical and Biophysical Research Communications. 386, 443–448.

    Article  PubMed  CAS  Google Scholar 

  10. Borchert, G. M., Lanier, W., and Davidson, B. L. (2006) RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol. 13, 1097–1101.

    Article  PubMed  CAS  Google Scholar 

  11. Zhou, H., Xia, X. G., and Xu, Z. (2005) An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi. Nucl. Acids Res. 33, e62.

    Google Scholar 

  12. Cashman, N. R., Durham, H. D., Blusztajn, J. K., Oda, K., Tabira, T., Shaw, I. T., Dahrouge, S., and Antel, J. P. (1992) Neuroblastoma x spinal cord (NSC) hybrid cell lines resemble developing motor neurons. Dev Dyn. 194, 209–221.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This work has been supported by RO1 NS048145 and R21 NS062230-01.

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Correspondence to Zuoshang Xu .

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© 2011 Springer Science+Business Media, LLC

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Yang, C., Qiu, L., Xu, Z. (2011). Specific Gene Silencing Using RNAi in Cell Culture. In: Manfredi, G., Kawamata, H. (eds) Neurodegeneration. Methods in Molecular Biology, vol 793. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-328-8_30

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  • DOI: https://doi.org/10.1007/978-1-61779-328-8_30

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-327-1

  • Online ISBN: 978-1-61779-328-8

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