A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells (original) (raw)

Nature Biotechnology volume 24, pages 559–565 (2006)Cite this article

Abstract

Nonspecific effects triggered by small interfering RNAs (siRNAs) complicate the use of RNA interference (RNAi) to specifically downregulate gene expression1,2,3,4,5. To uncover the basis of these nonspecific activities, we analyzed the effect of chemically synthesized siRNAs on mammalian double-stranded RNA (dsRNA)-activated signaling pathways. siRNAs ranging from 21 to 27 nucleotides (nt) in length activated the interferon system when they lacked 2-nt 3′ overhangs, a characteristic of Dicer products. We show that the recognition of siRNAs is mediated by the RNA helicase RIG-I and that the presence of 3′ overhangs impairs its ability to unwind the dsRNA substrate and activate downstream signaling to the transcription factor IRF-3. These results suggest a structural basis for discrimination between microRNAs that are endogenous Dicer products, and nonself dsRNAs such as by-products of viral replication. These findings will enable the rational design of siRNAs that avoid nonspecific effects or, alternatively, that induce bystander effects to potentially increase the efficacy of siRNA-based treatments of viral infections or cancer.

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Acknowledgements

We would like to thank Patricia Stanhope-Baker, Michelle Holko, Anthony Sadler and Mark Whitmore for helpful comments and Patricia Kessler and Scott D. Rose for valuable assistance. We are also grateful to Michael Gale Jr. for providing the sequences for DDX58 primers, James Finke and Patricia Rayman, Joe DiDonato and the DiDonato laboratory, Ganes Sen and the Sen laboratory and Yan Xu for providing reagents. This work was supported by National Institutes of Health grants RO1 AI34039 and PO1 CA 62220.

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Authors and Affiliations

  1. Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, 44195, Ohio, USA
    Joao Trindade Marques, Thalie Devosse, Die Wang, Maryam Zamanian-Daryoush, Paul Serbinowski & Bryan RG Williams
  2. Department of Molecular Biology, University of Aarhus, Aarhus, DK-8000, Denmark
    Rune Hartmann
  3. Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
    Takashi Fujita
  4. Integrated DNA Technologies, Inc., Coralville, 52241, Iowa, USA
    Mark A Behlke
  5. Monash Institute of Medical Research, Monash University, 246 Clayton Road, Clayton, VIC. 3168, Melbourne, Australia
    Bryan RG Williams

Authors

  1. Joao Trindade Marques
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  2. Thalie Devosse
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  3. Die Wang
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  4. Maryam Zamanian-Daryoush
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  5. Paul Serbinowski
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  6. Rune Hartmann
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  7. Takashi Fujita
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  8. Mark A Behlke
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  9. Bryan RG Williams
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Corresponding author

Correspondence toBryan RG Williams.

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Competing interests

M.A.B. is employed by Integrated DNA Technologies Inc. (IDT), which offers oligonucleotides for sale similar to the ones described in the manuscript. IDT is not, however, a publicly traded company and the author does not own any equity in IDT.

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Marques, J., Devosse, T., Wang, D. et al. A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells.Nat Biotechnol 24, 559–565 (2006). https://doi.org/10.1038/nbt1205

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