Letter | Published:

Modulation of HIV-1 replication by RNA interference

Naturevolume 418pages435438 (2002) | Download Citation



RNA interference (RNAi) is the process by which double-stranded RNA (dsRNA) directs sequence-specific degradation of messenger RNA in animal and plant cells1,2. In mammalian cells, RNAi can be triggered by 21-nucleotide duplexes of small interfering RNA (siRNA)3. Here we describe inhibition of early and late steps of HIV-1 replication in human cell lines and primary lymphocytes by siRNAs targeted to various regions of the HIV-1 genome. We demonstrate that synthetic siRNA duplexes or plasmid-derived siRNAs inhibit HIV-1 infection by specifically degrading genomic HIV-1 RNA, thereby preventing formation of viral complementary-DNA intermediates. These results demonstrate the utility of RNAi for modulating the HIV replication cycle and provide evidence that genomic HIV-1 RNA, as it exists within a nucleoprotein reverse-transcription complex, is amenable to siRNA-mediated degradation.

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  1. 1

    Sharp, P. A. RNA interference—2001. Genes Dev. 15, 485–490 (2001)

  2. 2

    Hutvagner, G. & Zamore, P. D. RNAi: nature abhors a double-strand. Curr. Opin. Genet. Dev. 12, 225–232 (2002)

  3. 3

    Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001)

  4. 4

    Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998)

  5. 5

    Zamore, P. D., Tuschl, T., Sharp, P. A. & Bartel, D. P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25–33 (2000)

  6. 6

    Elbashir, S. M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188–200 (2001)

  7. 7

    Hammond, S. M., Bernstein, E., Beach, D. & Hannon, G. J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293–296 (2000)

  8. 8

    Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001)

  9. 9

    Nykanen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309–321 (2001)

  10. 10

    Caplen, N. J., Fleenor, J., Fire, A. & Morgan, R. A. dsRNA-mediated gene silencing in cultured Drosophila cells: a tissue culture model for the analysis of RNA interference. Gene 252, 95–105 (2000)

  11. 11

    Ui-Tei, K., Zenno, S., Miyata, Y. & Saigo, K. Sensitive assay of RNA interference in Drosophila and Chinese hamster cultured cells using firefly luciferase gene as target. FEBS Lett. 479, 79–82 (2000)

  12. 12

    Welker, R., Harris, M., Cardel, B. & Krausslich, H. G. Virion incorporation of human immunodeficiency virus type 1 Nef is mediated by a bipartite membrane-targeting signal: analysis of its role in enhancement of viral infectivity. J. Virol. 72, 8833–8840 (1998)

  13. 13

    Kimpton, J. & Emerman, M. Detection of replication-competent and pseudotyped human immunodeficiency virus with a sensitive cell line on the basis of activation of an integrated β-galactosidase gene. J. Virol. 66, 2232–2239 (1992)

  14. 14

    Bitko, V. & Barik, S. Phenotypic silencing of cytoplasmic genes using sequence-specific double-stranded short interfering RNA and its application in the reverse genetics of wild type negative-strand RNA viruses. BMC Microbiol. 1, 34–45 (2001)

  15. 15

    Li, Y. et al. Molecular characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: Identification of replication-competent and -defective viral genomes. J. Virol. 65, 3973–3985 (1991)

  16. 16

    Moore, J. & Stevenson, M. New targets for inhibitors of HIV-1 replication. Nature Rev. Mol. Cell Biol. 1, 40–49 (2000)

  17. 17

    Bitko, V. & Barik, S. An endoplasmic reticulum-specific stress-activated caspase (caspase-12) is implicated in the apoptosis of A549 epithelial cells by respiratory syncytial virus. J. Cell Biochem. 80, 441–454 (2001)

  18. 18

    Wang, M. B. & Waterhouse, P. M. High-efficiency silencing of a β-glucuronidase gene in rice is correlated with repetitive transgene structure but is independent of DNA methylation. Plant Mol. Biol. 43, 67–82 (2000)

  19. 19

    Varshawesley, S. et al. Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581–590 (2001)

  20. 20

    Dornburg, R. & Pomerantz, R. J. HIV-1 gene therapy: promise for the future. Adv. Pharmacol. 49, 229–261 (2000)

  21. 21

    Ketting, R. F., Haverkamp, T. H., van Luenen, H. G. & Plasterk, R. H. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99, 133–141 (1999)

  22. 22

    Tabara, H., Hill, R. J., Mello, C. C., Priess, J. R. & Kohara, Y. pos-1 encodes a cytoplasmic zinc-finger protein essential for germline specification in C. elegans. Development 126, 1–11 (1999)

  23. 23

    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)

  24. 24

    Billy, E., Brondani, V., Zhang, H., Muller, U. & Filipowicz, W. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc. Natl Acad. Sci. USA 98, 14428–14433 (2001)

  25. 25

    Paddison, P. J., Caudy, A. A. & Hannon, G. J. Stable suppression of gene expression by RNAi in mammalian cells. Proc. Natl Acad. Sci. USA 99, 1443–1448 (2002)

  26. 26

    Yang, S., Tutton, S., Pierce, E. & Yoon, K. Specific double-stranded RNA interference in undifferentiated mouse embryonic stem cells. Mol. Cell. Biol. 21, 7807–7816 (2001)

  27. 27

    Sharkey, M. et al. Persistence of episomal HIV-1 infection intermediates in patients on highly active antiretroviral therapy. Nature Med. 6, 76–81 (2000)

  28. 28

    Brichacek, B. & Stevenson, M. Quantitative competitive RNA PCR for quantitation of virion associated HIV-1 RNA. Methods 12, 294–299 (1997)

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We thank A. Mann for research support, C. Mello and P. Zamore for discussions, B. Mellor for preparation of the figures, and T. Pinkos for manuscript preparation. We also acknowledge assay support provided by the University of Massachusetts Center for AIDS Research. HIVYU-2 was obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), from B. Hahn and G. Shaw. This study was supported by grants from the NIH and the Jenner Foundation to M.S.

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  1. Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 373 Plantation Street, Massachusetts, 01605, USA

    • Jean-Marc Jacque
    • , Karine Triques
    •  & Mario Stevenson


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The authors declare that they have no competing financial interests.

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Correspondence to Mario Stevenson.

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