siRNA-directed inhibition of HIV-1 infection

A Corrigendum to this article was published on 01 November 2003


RNA interference silences gene expression through short interfering 21–23-mer double-strand RNA segments that guide mRNA degradation in a sequence-specific fashion. Here we report that siRNAs inhibit virus production by targeting the mRNAs for either the HIV-1 cellular receptor CD4, the viral structural Gag protein or green fluorescence protein substituted for the Nef regulatory protein. siRNAs effectively inhibit pre- and/or post-integration infection events in the HIV-1 life cycle. Thus, siRNAs may have potential for therapeutic intervention in HIV-1 and other viral infections.

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Figure 1: CD4-siRNA inhibits HIV-1 entry and infection in Magi-CCR5 cells.
Figure 2: p24-siRNA inhibits viral replication in HeLa-CD4 cells.
Figure 3: 3Time course of silencing HIV-1 gene expression and inhibition of viral replication in H9 T cells.
Figure 4: siRNA-directed silencing of viral gene expression in HeLa-CD4 cells in established HIV-1 infection.
Figure 5: siRNA-directed silencing of viral gene expression after integration.
Figure 6: Model for pathways of RNA interference for inhibition of productive HIV-1 infection.


  1. 1

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

    CAS  Article  Google Scholar 

  2. 2

    Zamore, P.D. RNA interference: listening to the sound of silence. Nature Struct. Biol. 8, 746–750 (2001).

    CAS  Article  Google Scholar 

  3. 3

    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).

    CAS  Article  Google Scholar 

  4. 4

    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).

    CAS  Article  Google Scholar 

  5. 5

    Tabara, H. et al. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132 (1999).

    CAS  Article  Google Scholar 

  6. 6

    Jones, A.R. & Schedl, T. Mutations in gld-1, a female germ cell-specific tumor suppressor gene in Caenorhabditis elegans, affect a conserved domain also found in Src-associated protein Sam68. Genes Dev. 9, 1491–1504 (1995).

    CAS  Article  Google Scholar 

  7. 7

    Gaudet, J., Van der Elst, I. & Spence, A.M. Post-transcriptional regulation of sex determination in Caenorhabditis elegans: widespread expression of the sex-determining gene fem-1 in both sexes. Mol. Biol. Cell 7, 1107–1121 (1996).

    CAS  Article  Google Scholar 

  8. 8

    Pal-Bhadra, M., Bhadra, U. & Birchler, J.A. Cosuppression of nonhomologous transgenes in Drosophila involves mutually related endogenous sequences. Cell 99, 35–46 (1999).

    CAS  Article  Google Scholar 

  9. 9

    Ratcliff, F., Harrison, B.D. & Baulcombe, D.C. A similarity between viral defense and gene silencing in plants. Science 276, 1558–1560 (1997).

    CAS  Article  Google Scholar 

  10. 10

    Waterhouse, P.M., Wang, M.-B. & Lough, T. Gene silencing as an adaptive defence against viruses. Nature 411, 834–842 (2001).

    CAS  Article  Google Scholar 

  11. 11

    Kumar, M. & Carmichael, G.G. Antisense RNA: function and fate of duplex RNA in cells of higher eukaryotes. Microbiol. Mol. Biol. Rev. 62, 1415–1434 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Stark, G.R., Kerr, I.M., Williams, B.R., Silverman, R.H. & Schreiber, R.D. How cells respond to interferons. Annu. Rev. Biochem. 67, 227–264 (1998).

    CAS  Article  Google Scholar 

  13. 13

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

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Elbashir, S.M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877–6888 (2001).

    CAS  Article  Google Scholar 

  15. 15

    Klatzmann, D. et al. T-lymphocyte T4 molecule behaves as the receptor for human retrovirus LAV. Nature 312, 767–768 (1984).

    CAS  Article  Google Scholar 

  16. 16

    Maddon, P.J. et al. The T4 gene encodes the AIDS virus receptor and is expressed in the immune system and the brain. Cell 47, 333–348 (1986).

    CAS  Article  Google Scholar 

  17. 17

    Chackerian, B., Long, E.M., Luciw, P.A. & Overbaugh, J. HIV-1 co-receptors participates in post-entry stages of the virus replication cycle and function in SIV infection. J. Virol. 71, 3932–3939 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18

    Pavlakis, G.N., Schwartz, S., D'Agostino, D.M. & Felber, B.K. Structure, splicing, and regulation of expression of HIV-1: a model for the general organization of lentiviruses and other complex retroviruses. in Annual Review of AIDS Research. (eds. Kennedy, R., Wong-Staal, F. & Koff, W.C.) 41–63 (Marcel Dekker, New York, 1991).

    Google Scholar 

  19. 19

    Kim, S., Byrn, R., Groopman, J. & Baltimore, D. Temporal aspects of DNA and RNA synthesis during human immunodeficiency virus infection: evidence for differential gene expression. J. Virol. 63, 3708–3713 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Wu, Y. & Marsh, J.W. Selective transcription and modulation of resting T cell activity by preintegrated HIV DNA. Science 293, 1503–1506 (2001).

    CAS  Article  Google Scholar 

  21. 21

    Page, K.A., Liegler, T. & Feinberg, M.B. Use of a green fluorescent protein as a marker for human immunodeficiency virus type 1 infection. AIDS Res. Hum. Retroviruses 13, 1077–1081 (1997).

    CAS  Article  Google Scholar 

  22. 22

    Samson, M. et al. Resistance to HIV-1 infection in caucasian individualos bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382, 722–725 (1996).

    CAS  Article  Google Scholar 

  23. 23

    Liu, R. et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86, 367–377 (1996).

    CAS  Article  Google Scholar 

  24. 24

    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. 34, 1–11 (2001).

    Google Scholar 

  25. 25

    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).

    CAS  Article  Google Scholar 

  26. 26

    Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R. & Hannon, G.J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150 (2001).

    CAS  Article  Google Scholar 

  27. 27

    Zapp, M.L. & Green, M.R. Sequence-specific RNA binding by the HIV-1 Rev protein. Nature 342, 714–716 (1989).

    CAS  Article  Google Scholar 

  28. 28

    Malim, M.H. et al. HIV-1 structural gene expression requires binding of the Rev trans- activator to its RNA target sequence. Cell 60, 675–683 (1990).

    CAS  Article  Google Scholar 

  29. 29

    Cochrane, A.W., Chen, C.H. & Rosen, C.A. Specific interaction of the human immunodeficiency virus Rev protein with a structured region in the env mRNA. Proc. Natl. Acad. Sci. USA 87, 1198–1202 (1990).

    CAS  Article  Google Scholar 

  30. 30

    Brummelkamp, T.R., Bernards, R. & Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550–553 (2002).

    CAS  Article  Google Scholar 

  31. 31

    Paddison, P.J., Caudy, A.A., Bernstein, E., Hannon, G.J. & Conklin, D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948–958 (2002).

    CAS  Article  Google Scholar 

  32. 32

    Sui, G. et al. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 5515–5520 (2002).

    CAS  Article  Google Scholar 

  33. 33

    Yu, J.-Y., DeRuiter, S.L. & Turner, D.L. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 6047–6052 (2002).

    CAS  Article  Google Scholar 

  34. 34

    Paul, C.P., Good, P.D., Winer, I. & Engelke, D.R. Effective expression of small interfering RNA in human cells. Nature Biotech. 20, 505–508 (2002).

    CAS  Article  Google Scholar 

  35. 35

    McManus, M.T., Petersen, C.P., Haines, B.B., Chen, J. & Sharp, P.A. Gene silencing using micro-RNA designed hairpins. RNA 8, 1–9 (2002).

    Article  Google Scholar 

  36. 36

    Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001).

    CAS  Article  Google Scholar 

  37. 37

    Hutvagner, G. et al. A cellular function for the RNA-interference enzyme DICER in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001).

    CAS  Article  Google Scholar 

  38. 38

    Ketting, R.F. et al. DICER function in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654–2659 (2001).

    CAS  Article  Google Scholar 

  39. 39

    Rougvie, A.E. Control of developmental timing in animals. Nature Rev. Genet. 2, 690–701 (2001).

    CAS  Article  Google Scholar 

  40. 40

    Banerjee, D. & Slack, F. Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression. Bioessays 24, 119–129 (2002).

    CAS  Article  Google Scholar 

  41. 41

    Dorman, N. & Lever, A.M. RNA-based gene therapy for HIV infection. HIV Med 2, 114–122 (2001).

    CAS  Article  Google Scholar 

  42. 42

    James, H.A. & Gibson, I. The therapeutic potential of ribozymes. Blood 91, 371–382 (1998).

    CAS  PubMed  Google Scholar 

  43. 43

    Lee, N.S. et al. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotech. 20, 500–505 (2002).

    CAS  Article  Google Scholar 

  44. 44

    Shankar, P., Xu, Z. & Lieberman, J. Viral-specific cytotoxic T lymphocytes lyse human immunodeficiency virus-infected primary T lymphocytes by the granule exocytosis pathway. Blood 94, 3084–3093 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45

    Ratner, L. et al. Complete nucleotide sequences of functional clones of the AIDS virus. AIDS Res. Hum. Retroviruses 3, 57–69 (1987).

    CAS  Article  Google Scholar 

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We thank V. François-Bongarçon for help and technical assistance; H. Cargill for help with Fig. 6; and J. Doench for helpful discussions and comments. The following reagents were obtained through the AIDS Research and Reference Reagent Program Division of AIDS, NIAID, NIH: HeLaT4+ and T4pMV7 were provided by R. Axel, pR7-GFP was provided by K. Page and M. Feinberg and Magi-CCR5 was provided by J. Overbaugh. This work was supported by grants NIH F32 AI10523 (to C.D.N.), NIH T32-GM07748 (to M.F.M.), NIH AI 35502 (to R.G.C.), NIH AI 45306 (to P.S.) and NIH MERIT grant R37-GM34277, NCI grant PO1-CA42063 and partially by NCI Cancer Center Support (Core) grant P30-CA14051 (to P.A.S.).

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Correspondence to Premlata Shankar or Phillip A. Sharp.

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The authors of this paper have applied for a patent that will be owned by the Massachusetts Institute of Technology. It is possible that in the future the authors will receive royalties from this patent.

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Novina, C., Murray, M., Dykxhoorn, D. et al. siRNA-directed inhibition of HIV-1 infection. Nat Med 8, 681–686 (2002).

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