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Dissecting HIV-1 through RNA interference

Nature Reviews Immunology volume 3, pages 851–858 (2003)Cite this article

Key Points

  • RNA interference (RNAi) is the process by which double-stranded RNA (dsRNA) induces silencing of homologous, endogenous and exogenous genes. This offers a powerful process to regulate gene expression to determine the role of specific proteins in biological processes.

  • The replication of viruses, such as HIV-1, depends on cellular factors that can oppose or enhance virus replication. RNAi can be used to manipulate the expression of these cellular factors to examine their role in virus replication.

  • Several strategies are being developed to introduce interfering RNAs into cells that are normally infected by viruses, so facilitating the study of HIV biology by RNAi.

  • The use of RNAi as a therapeutic approach to virus infections such as AIDS faces several obstacles. However, because of its mechanism of action, RNAi-based therapeutic approaches might prove effective where other antiviral agents in use at present have failed.

Abstract

In cells of organisms, ranging from nematodes to primates, there is a process known as RNA interference (RNAi) that effects the degradation of RNA in a highly sequence-specific manner. Scientists have figured out a way to co-opt elements of the RNAi machinery such that almost any RNA can be targeted for degradation. It is now clear that HIV-1 is fair game for RNAi; viral RNA intermediates have been targeted as well as messenger RNAs for cellular co-factors that are required for replication of HIV-1. The hope is that RNAi can be used not only as a research tool, but also as a therapeutic strategy for infection with HIV-1.

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Figure 1: Gene silencing by RNA interference.
Figure 2: RNA interference susceptible targets in the HIV-1 replication cycle.
Figure 3: Strategies for the expression of interfering RNAs.
Figure 4: Factors affecting susceptibility of HIV-1 to RNA interference.

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References

  1. Napoli, C., Lemieux, C. & Jorgensen, R. Introduction of a chimeric chalcone synthse gene into Petunia results in reversible co-suppression of homologous genes in trans. Plant Cell. 2, 279–289 (1990).

    Article  CAS  Google Scholar 

  2. Lindbo, J. & Dougherty, W. Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts. Virology 189, 725–733 (1992).

    Article  CAS  Google Scholar 

  3. Dougherty, W. et al. RNA-mediated virus resistance in transgenic plants: exploitation of a cellular pathway possibly involved in RNA degradation. Mol. Plant Microbe Interact. 7, 544–552 (1994).

    Article  CAS  Google Scholar 

  4. Angell, S. & Baulcombe, D. Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA. EMBO J. 16, 3675–3684 (1997).

    Article  CAS  Google Scholar 

  5. Guo, S. & Kemphues, K. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81, 611–620 (1995).

    Article  CAS  Google Scholar 

  6. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998). The first to show that double-stranded RNA (dsRNA) promotes the sequence-specific destruction of endogenous RNAs.

    Article  CAS  Google Scholar 

  7. Bernstein, E., Denli, A. & Hannon, G. The rest is silence. RNA 7, 1509–1521 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Hamilton, A. & Baulcombe, D. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286, 950–952 (1999). The first evidence that small ∼25-nucleotide RNAs might be the mediators of post-transcriptional gene silencing mediated by dsRNA.

    Article  CAS  Google Scholar 

  9. Kennerdell, J. & Carthew, R. Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 95, 1017–1026 (1998).

    Article  CAS  Google Scholar 

  10. Tuschl, T., Zamore, P. D., Lehmann, R., Bartel, D. & Sharp, P. Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev. 15, 3191–3197 (1999). The first to describe that long dsRNA is processed to ∼22-nucleotide guide RNAs. This study also showed that messenger RNAs are cleaved at regular intervals in response to dsRNA.

    Article  Google Scholar 

  11. Hammond, S., Bernstein, E., Beach, D. & Hannon, G. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293–296 (2000). Identification of a nuclease activity that targets mRNAs for degradation.

    Article  CAS  Google Scholar 

  12. Elbashir, S. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001). The authors showed that synthetic 21-nucleotide RNA duplexes activate RNA interference (RNAi) in mammalian cell systems.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  14. 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).

    Article  CAS  Google Scholar 

  15. Billy, E., Brondani, V., Zhang, H., Muller, U. & Rilipowicz, 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  17. Sledz, C. A., Holko, M., De Veer, M. J., Silverman, R. H. & Williams, B. R. Activation of the interferon system by short-interfering RNAs. Nature Cell Biol. 5, 834–839 (2003). This paper shows that activation of dsRNA-dependent protein kinase (PKR) is mediated not only by long dsRNA, but also by small interfering (siRNAs).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Novina, C. et al. siRNA-directed inhibition of HIV-1 infection. Nature Med. 8, 681–686 (2002).

    Article  CAS  Google Scholar 

  20. Jacque, J. -M., Triques, K. & Stevenson, M. Modulation of HIV-1 replication by RNAi. Nature 418, 435–438 (2002).

    Article  CAS  Google Scholar 

  21. Coburn, G. & Cullen, B. R. Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J. Virol. 76, 9225–9231 (2002).

    Article  CAS  Google Scholar 

  22. Capodici, J., Kariko, K. & Weissman, D. Inhibition of HIV-1 infection by small interfering RNA-mediated RNA interference. J. Immunol. 169, 5196–5201 (2002).

    Article  Google Scholar 

  23. Park, W. et al. Prevention of HIV-1 infection in human peripheral blood mononuclear cells by specific RNA interference. Nucleic Acids Res. 30, 4830–4835 (2002).

    Article  CAS  Google Scholar 

  24. Surabhi, R. & Gaynor, R. RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type 1 replication. J. Virol. 76, 12963–12973 (2002).

    Article  CAS  Google Scholar 

  25. Yamamoto, T. et al. Double-stranded nef RNA interferes with human immunodeficiency virus type 1 replication. Microbiol. Immunol. 46, 809–817 (2002).

    Article  CAS  Google Scholar 

  26. Hu, W., Myers, C., Kilzer, J., Pfaff, S. & Bushman, F. Inhibition of retroviral pathogenesis by RNA interference. Curr. Biol. 12, 1301–1311 (2002).

    Article  CAS  Google Scholar 

  27. Song, E. et al. Sustained small interfering RNA-mediated human immunodeficiency virus type 1 inhibition in primary macrophages. J. Virol. 77, 7174–7181 (2003).

    Article  CAS  Google Scholar 

  28. Zeng, Y. & Cullen, B. R. RNA interference in human cells is restricted to the cytoplasm. RNA 8, 855–860 (2002).

    Article  CAS  Google Scholar 

  29. 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 (2001).

    Article  CAS  Google Scholar 

  30. Vickers, T. et al. Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem. 279, 7108–7118 (2003).

    Article  Google Scholar 

  31. Qin, X., An, D., Chen, I. & Baltimore, D. Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc. Natl Acad. Sci. USA 100, 183–188 (2003).

    Article  CAS  Google Scholar 

  32. Martinez, M. et al. Suppression of chemokine receptor expression by RNA interference allows for inhibition of HIV-1 replication. AIDS 16, 2385–2390 (2002).

    Article  CAS  Google Scholar 

  33. Garrus, J. E. et al. Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell 107, 55–65 (2001). The first study to use RNAi to validate a role for a cellular co-factor in HIV-1 replication.

    Article  CAS  Google Scholar 

  34. O'Brien, S. & Moore, J. The effect of genetic variation in chemokines and their receptors in HIV transmission and progression to AIDS. Immunol. Rev. 177, 99–111 (2000).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  36. Holen, T., Amarzguioui, M., Wiiger, M., Babaie, E. & Prydz, H. Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res. 30, 1757–1766 (2002).

    Article  CAS  Google Scholar 

  37. Song, E. et al. RNA interference targeting Fas protects mice from fulminant hepatitis. Nature Med. 9, 347–351 (2003).

    Article  CAS  Google Scholar 

  38. McCaffrey, A. et al. RNA interference in adult mice. Nature 418, 38–39 (2002).

    Article  CAS  Google Scholar 

  39. Lewis, D., Hagstrom, J., Loomis, A., Wolff, J. & Herweijer, H. Efficient delivery of siRNA for inhibition of gene expression in postnatal mice. Nature Genet. 32, 107–108 (2002).

    Article  CAS  Google Scholar 

  40. Dykxhoorn, D., Novina, C. & Sharp, P. Killing the messenger: short RNAs that silence gene expression. Nature Rev. Mol. Cell Biol. 4, 457–467 (2003).

    Article  CAS  Google Scholar 

  41. Weinberg, J. B., Matthews, T. J., Cullen, B. R. & Malim, M. H. Productive human immunodeficiency virus type 1 (HIV-1) infection of nonproliferating human monocytes. J. Exp. Med. 174, 1477–1482 (1991).

    Article  CAS  Google Scholar 

  42. Bukrinsky, M. I. et al. Active nuclear import of human immunodeficiency virus type 1 preintegration complexes. Proc. Natl Acad. Sci. USA 89, 6580–6584 (1992).

    Article  CAS  Google Scholar 

  43. Naldini, L. et al. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science 272, 263–267 (1996).

    Article  CAS  Google Scholar 

  44. Xia, H., Mao, Q., Paulson, H. & Davidson, B. siRNA-mediated gene silencing in vitro and in vivo. Nature Biotechnol. 20, 1006–1010 (2002).

    Article  CAS  Google Scholar 

  45. Rubinson, D. et al. A lentivirus-bassed system to functionally silence genes in primary mammalian cells, stem cells, and transgenic mice by RNA interference. Nature Genet. 33, 401–406 (2003).

    Article  CAS  Google Scholar 

  46. Stewart, S. et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 9, 493–501 (2003).

    Article  CAS  Google Scholar 

  47. Tiscornia, G., Singer, O., Ikawa, M. & Verma, I. M. A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc. Natl Acad. Sci. USA 100, 1844–1848 (2003).

    Article  CAS  Google Scholar 

  48. Walker, B. D. & Korber, B. Immune control of HIV: the obstacles of HLA and viral density. Nature Immunol. 2, 473–475 (2001).

    Article  CAS  Google Scholar 

  49. Gitlin, L., Karelsky, S. & Andino, R. Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 25, 430–434 (2002). A paper showing that siRNA-resistant escape mutants of poliovirus emerge rapidly in culture.

    Article  Google Scholar 

  50. McManus, M. et al. Small interfering RNA-mediated gene silencing in T lymphocytes. J. Immunol. 15, 5754–5760 (2002).

    Article  Google Scholar 

  51. Orenstein, J. M., Meltzer, M. S., Phipps, T. & Gendelman, H. E. Cytoplasmic assembly and accumulation of human immunodeficiency virus types 1 and 2 in recombinant human colony-stimulating factor-1-treated human monocytes: an ultrastructural study. J. Virol. 62, 2578–2586 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Raposo, G. et al. Human macrophages accumulate HIV-1 particles in MHC II compartments. Traffic 3, 718–729 (2002).

    Article  CAS  Google Scholar 

  53. Geijtenbeek, T. et al. DC-SIGN, a dendritic cell-specific HIV-1-binding protein that enhances trans-infection of T cells. Cell 100, 587–597 (2000).

    Article  CAS  Google Scholar 

  54. Kwon, D., Gregorio, G., Bitton, N., Hendrickson, W. & Littman, D. DC-SIGN-mediated internalization of HIV is required for trans-enhancement of T cell infection. Immunity 16, 135–144 (2002).

    Article  CAS  Google Scholar 

  55. Smith, B. et al. Persistence of infectious HIV on follicular dendritic cells. J. Immunol. 1, 690–696 (2001).

    Article  Google Scholar 

  56. Palauqui, J., Elmayan, T., Pollien, J. & Vaucheret, H. Systematic acquired silencing: transgene-specific post-transitional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO J 1, 4738–4745 (1997).

    Article  Google Scholar 

  57. Winston, W., Molodowitch, C. & Hunter, C. Systemic RNAi in C. elegans requires the putative transmembrane proteins SID-1. Science 29, 2456–2459 (2002).

    Article  Google Scholar 

  58. Cogoni, C. & Macino, G. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399, 166–169 (1999).

    Article  CAS  Google Scholar 

  59. Dalmay, T., Hamilton, A., Rudd, S., Angell, S. & Baulcombe, D. An RNA-dependent RNA polymerase gene in Arabiopsis is required for posttranscriptional gene silencing mediated by a trangene but not by a virus. Cell 101, 543–553 (2000).

    Article  CAS  Google Scholar 

  60. Lipardi, C., Wei, Q. & Paterson, B. M. RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell 107, 297–307 (2001).

    Article  CAS  Google Scholar 

  61. Sijen, T. et al. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107, 465–476 (2001).

    Article  CAS  Google Scholar 

  62. Stein, P., Svoboda, P., Anger, M. & Schultz, R. M. RNAi: mammalian oocytes do it without RNA-dependent RNA polymerase. RNA 9, 187–192 (2003).

    Article  CAS  Google Scholar 

  63. Cullen, B. R. RNA interference: antiviral defense and genetic tool. Nature Immunol. 3, 597–595 (2002).

    Article  CAS  Google Scholar 

  64. 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).

    Article  CAS  Google Scholar 

  65. Brummelkamp, T. R., Bernards, R. & Agami, R. Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2, 243–247 (2002).

    Article  CAS  Google Scholar 

  66. Miyagishi, M. & Taira, K. U6 promoter–driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells. Nature Biotechnol. 20, 497–500 (2002).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Suite 319, Worcester, 01605, Massachusetts, USA

    Mario Stevenson

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DATABASES

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CCR5

CD4

CD95

CRM1

DICER

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FURTHER INFORMATION

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Glossary

GENOMIC VIRAL RNA

A viral RNA intermediate that is packaged in virus particles and that is converted into a complemetary DNA after introduction into the target cell.

PROVIRUS

A retroviral complementary DNA that is integrated in the chromosomal DNA of the host cell.

NUCLEOCYTOPLASMIC SHUTTLING

The process by which macromolecules, either of host or of exogenous (for example, virus) origin, move between the nucleus and cytoplasm.

FOLLICULAR DENDRITIC CELLS

Cells in the lymph node that present antigens within immune complexes to B cells.

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Stevenson, M. Dissecting HIV-1 through RNA interference. Nat Rev Immunol 3, 851–858 (2003). https://doi.org/10.1038/nri1227

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