A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells (original) (raw)
- Letter
- Published: 30 April 2006
- Thalie Devosse1,
- Die Wang1,
- Maryam Zamanian-Daryoush1,
- Paul Serbinowski1,
- Rune Hartmann2,
- Takashi Fujita3,
- Mark A Behlke4 &
- …
- Bryan RG Williams1,5
Nature Biotechnology volume 24, pages 559–565 (2006)Cite this article
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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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References
- Marques, J.T. & Williams, B.R. Activation of the mammalian immune system by siRNAs. Nat. Biotechnol. 23, 1399–1405 (2005).
Article CAS Google Scholar - Sledz, C.A., Holko, M., de Veer, M.J., Silverman, R.H. & Williams, B.R. Activation of the interferon system by short-interfering RNAs. Nat. Cell Biol. 5, 834–839 (2003).
Article CAS Google Scholar - Kim, D.H. et al. Interferon induction by siRNAs and ssRNAs synthesized by phage polymerase. Nat. Biotechnol. 22, 321–325 (2004).
Article CAS Google Scholar - Kariko, K., Bhuyan, P., Capodici, J. & Weissman, D. Small interfering RNAs mediate sequence-independent gene suppression and induce immune activation by signaling through toll-like receptor 3. J. Immunol. 172, 6545–6549 (2004).
Article CAS Google Scholar - Persengiev, S.P., Zhu, X. & Green, M.R. Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA 10, 12–18 (2004).
Article CAS Google Scholar - Kim, D.H. et al. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat. Biotechnol. 23, 222–226 (2005).
Article CAS Google Scholar - Peters, K.L., Smith, H.L., Stark, G.R. & Sen, G.C. IRF-3-dependent, NFkappa B- and JNK-independent activation of the 561 and IFN-beta genes in response to double-stranded RNA. Proc. Natl. Acad. Sci. USA 99, 6322–6327 (2002).
Article CAS Google Scholar - Hornung, V. et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat. Med. 11, 263–270 (2005).
Article CAS Google Scholar - Judge, A.D. et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat. Biotechnol. 23, 457–462 (2005).
Article CAS Google Scholar - Ishii, K.J. et al. A Toll-like receptor-independent antiviral response induced by double-stranded B-form DNA. Nat. Immunol. 7, 40–48 (2006).
Article CAS Google Scholar - Stetson, D.B. & Medzhitov, R. Recognition of cytosolic DNA activates an IRF3-dependent innate immune response. Immunity 24, 93–103 (2006).
Article CAS Google Scholar - Yoneyama, M. et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat. Immunol. 5, 730–737 (2004).
Article CAS Google Scholar - Kato, H. et al. Cell type-specific involvement of RIG-I in antiviral response. Immunity 23, 19–28 (2005).
Article CAS Google Scholar - Tanner, N.K. & Linder, P. DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol. Cell 8, 251–262 (2001).
Article CAS Google Scholar - Czauderna, F. et al. Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res. 31, 2705–2716 (2003).
Article CAS Google Scholar - Siolas, D. et al. Synthetic shRNAs as potent RNAi triggers. Nat. Biotechnol. 23, 227–231 (2005).
Article CAS Google Scholar - Rose, S.D. et al. Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res. 33, 4140–4156 (2005).
Article CAS Google Scholar - Cullen, B.R. Transcription and processing of human microRNA precursors. Mol. Cell 16, 861–865 (2004).
Article CAS Google Scholar - Marques, J.T. et al. Down-regulation of p53 by double-stranded RNA modulates the antiviral response. J. Virol. 79, 11105–11114 (2005).
Article CAS Google Scholar - Ambros, V. The functions of animal microRNAs. Nature 431, 350–355 (2004).
Article CAS Google Scholar - Elbashir, S.M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188–200 (2001).
Article CAS Google Scholar - Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001).
Article CAS Google Scholar - Caplen, N.J., Parrish, S., Imani, F., Fire, A. & Morgan, R.A. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc. Natl. Acad. Sci. USA 98, 9742–9747 (2001).
Article CAS Google Scholar - Manche, L., Green, S.R., Schmedt, C. & Mathews, M.B. Interactions between double-stranded RNA regulators and the protein kinase DAI. Mol. Cell. Biol. 12, 5238–5248 (1992).
Article CAS Google Scholar - Levy, D.E. & Marie, I.J. RIGging an antiviral defense–it's in the CARDs. Nat. Immunol. 5, 699–701 (2004).
Article CAS Google Scholar - Zhang, W. et al. Inhibition of respiratory syncytial virus infection with intranasal siRNA nanoparticles targeting the viral NS1 gene. Nat. Med. 11, 56–62 (2005).
Article CAS Google Scholar - Palliser, D. et al. An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection. Nature 439, 89–94 (2006).
Article CAS Google Scholar - Carpick, B.W. et al. Characterization of the solution complex between the interferon-induced, double-stranded RNA-activated protein kinase and HIV-I trans-activating region RNA. J. Biol. Chem. 272, 9510–9516 (1997).
Article CAS Google Scholar
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
- 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 - Department of Molecular Biology, University of Aarhus, Aarhus, DK-8000, Denmark
Rune Hartmann - Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
Takashi Fujita - Integrated DNA Technologies, Inc., Coralville, 52241, Iowa, USA
Mark A Behlke - Monash Institute of Medical Research, Monash University, 246 Clayton Road, Clayton, VIC. 3168, Melbourne, Australia
Bryan RG Williams
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Correspondence toBryan RG Williams.
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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
- Received: 09 December 2005
- Accepted: 22 March 2006
- Published: 30 April 2006
- Issue Date: 01 May 2006
- DOI: https://doi.org/10.1038/nbt1205
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