Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review
  • Published:

Gene Therapy Progress and Prospects. Downregulating gene expression: the impact of RNA interference

Abstract

The control and maintenance of gene expression is critical for cell development and differentiation. Over the last 2 years, our understanding of the role of RNA as a regulator of gene expression has significantly increased. Small RNA molecules are key elements of a machinery that trigger chromosomal modifications, post-transcriptional gene silencing and protein translational blockade depending on the source, the RNA and the nature of the interaction with the target nucleic acid. Currently, the best characterized of this group of RNA-mediated gene regulation pathways is the post-transcriptional gene silencing mechanism known as RNA interference. RNAi is triggered by double-stranded RNA (dsRNA), which induces the formation of a ribonucleoprotein complex that mediates sequence-specific cleavage of the transcript cognate with the input dsRNA. RNAi has been adapted as a functional genomics tool and it has potential as a therapeutic approach. This review will summarize our current understanding of the RNAi mechanism and the various applications of RNAi-based technologies.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1

Similar content being viewed by others

References

  1. Hammond SM et al. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 2001; 293: 1146–1150.

    Article  CAS  Google Scholar 

  2. Martinez J et al. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 2002; 110: 563–574.

    Article  CAS  Google Scholar 

  3. Mourelatos Z et al. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 2002; 16: 720–728.

    Article  CAS  Google Scholar 

  4. Hutvagner G, Zamore PD . A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002; 297: 2056–2060.

    Article  CAS  Google Scholar 

  5. Doi N et al. Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Curr Biol 2003; 13: 41–46.

    Article  CAS  Google Scholar 

  6. Caudy AA, Myers M, Hannon GJ, Hammond SM . Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev 2002; 16: 2491–2496.

    Article  CAS  Google Scholar 

  7. Ishizuka A, Siomi MC, Siomi H . A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev 2002; 16: 2497–2508.

    Article  CAS  Google Scholar 

  8. Schwarz DS, Hutvagner G, Haley B, Zamore PD . Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell 2002; 10: 537–548.

    Article  CAS  Google Scholar 

  9. Schwarz DS et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003; 115: 199–208.

    Article  CAS  Google Scholar 

  10. Khvorova A, Reynolds A, Jayasena SD . Functional siRNAs and miRNAs exhibit strand bias. Cell 2003; 115: 209–216.

    Article  CAS  Google Scholar 

  11. Bernstein E, Caudy AA, Hammond SM, Hannon GJ . Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001; 409: 363–366.

    Article  CAS  Google Scholar 

  12. Elbashir SM, Lendeckel W, Tuschl T . RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 2001; 15: 188–200.

    Article  CAS  Google Scholar 

  13. Yang D, Lu H, Erickson JW . Evidence that processed small dsRNAs may mediate sequence-specific mRNA degradation during RNAi in Drosophila embryos. Curr Biol 2000; 10: 1191–1200.

    Article  CAS  Google Scholar 

  14. Liu Q et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 2003; 301: 1921–1925.

    Article  CAS  Google Scholar 

  15. Elbashir SM et al. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 2001; 20: 6877–6888.

    Article  CAS  Google Scholar 

  16. Caudy AA et al. A micrococcal nuclease homologue in RNAi effector complexes. Nature 2003; 425: 411–414.

    Article  CAS  Google Scholar 

  17. Elbashir SM et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001; 411: 494–498.

    Article  CAS  Google Scholar 

  18. Caplen NJ et al. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 2001; 98: 9742–9747.

    Article  CAS  Google Scholar 

  19. Billy E et al. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci USA 2001; 98: 14428–14433.

    Article  CAS  Google Scholar 

  20. Sijen T et al. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 2001; 107: 465–476.

    Article  CAS  Google Scholar 

  21. Winston WM, Molodowitch C, Hunter CP . Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science 2002; 295: 2456–2459.

    Article  CAS  Google Scholar 

  22. Feinberg EH, Hunter CP . Transport of dsRNA into cells by the transmembrane protein SID-1. Science 2003; 301: 1545–1547.

    Article  CAS  Google Scholar 

  23. Volpe T et al. RNA interference is required for normal centromere function in fission yeast. Chromosome Res 2003; 11: 137–146.

    Article  CAS  Google Scholar 

  24. Reinhart BJ, Bartel DP . Small RNAs correspond to centromere heterochromatic repeats. Science 2002; 297: 1831.

    Article  CAS  Google Scholar 

  25. Hall IM et al. Establishment and maintenance of a heterochromatin domain. Science 2002; 297: 2232–2237.

    Article  CAS  Google Scholar 

  26. Hall IM, Noma K, Grewal SI . RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc Natl Acad Sci USA 2003; 100: 193–198.

    Article  CAS  Google Scholar 

  27. Verdel A et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 2004; 303: 672–676.

    Article  CAS  Google Scholar 

  28. Sijen T, Plasterk RH . Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 2003; 426: 310–314.

    Article  CAS  Google Scholar 

  29. Lippman Z et al. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 2003; 1: E67.

    Article  Google Scholar 

  30. Schramke V, Allshire R . Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 2003; 301: 1069–1074.

    Article  CAS  Google Scholar 

  31. 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 2001; 106: 23–34.

    Article  CAS  Google Scholar 

  32. Hutvagner G et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 2001; 293: 834–838.

    Article  CAS  Google Scholar 

  33. Ketting RF et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 2001; 15: 2654–2659.

    Article  CAS  Google Scholar 

  34. Knight SW, Bass BL . A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 2001; 293: 2269–2271.

    Article  CAS  Google Scholar 

  35. Bernstein E et al. Dicer is essential for mouse development. Nat Genet 2003; 35: 215–217.

    Article  CAS  Google Scholar 

  36. Doench JG, Petersen CP, Sharp PA . siRNAs can function as miRNAs. Genes Dev 2003; 17: 438–442.

    Article  CAS  Google Scholar 

  37. Zeng Y, Yi R, Cullen BR . MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc Natl Acad Sci USA 2003; 100: 9779–9784.

    Article  CAS  Google Scholar 

  38. Paddison PJ et al. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 2002; 16: 948–958.

    Article  CAS  Google Scholar 

  39. Brummelkamp TR, Bernards R, Agami R . A system for stable expression of short interfering RNAs in mammalian cells. Science 2002; 296: 550–553.

    Article  CAS  Google Scholar 

  40. Paddison PJ, Caudy AA, Hannon GJ . Stable suppression of gene expression by RNAi in mammalian cells. Proc Natl Acad Sci USA 2002; 99: 1443–1448.

    Article  CAS  Google Scholar 

  41. Brummelkamp TR, Bernards R, Agami R . Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2002; 2: 243–247.

    Article  CAS  Google Scholar 

  42. Aza-Blanc P et al. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell 2003; 12: 627–637.

    Article  CAS  Google Scholar 

  43. Williams NS et al. Identification and validation of genes involved in the pathogenesis of colorectal cancer using cDNA microarrays and RNA interference. Clin Cancer Res 2003; 9: 931–946.

    CAS  PubMed  Google Scholar 

  44. Kamath RS et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003; 421: 231–237.

    Article  CAS  Google Scholar 

  45. Lum L et al. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 2003; 299: 2039–2045.

    Article  CAS  Google Scholar 

  46. Kiger A et al. A functional genomic analysis of cell morphology using RNA interference. J Biol 2003; 2: 27.

    Article  CAS  Google Scholar 

  47. Paddison PJ et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 2004; 428: 427–431.

    Article  CAS  Google Scholar 

  48. Berns K et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 2004; 428: 431–437.

    Article  CAS  Google Scholar 

  49. Mousses S et al. RNAi microarray analysis in cultured mammalian cells. Genome Res 2003; 13: 2341–2347.

    Article  CAS  Google Scholar 

  50. Kumar R, Conklin DS, Mittal V . High-throughput selection of effective RNAi probes for gene silencing. Genome Res 2003; 13: 2333–2340.

    Article  CAS  Google Scholar 

  51. Hemann MT et al. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat Genet 2003; 33: 396–400.

    Article  CAS  Google Scholar 

  52. Hasuwa H, Kaseda K, Einarsdottir T, Okabe M . Small interfering RNA and gene silencing in transgenic mice and rats. FEBS Lett 2002; 532: 227–230.

    Article  CAS  Google Scholar 

  53. Tiscornia G, Singer O, Ikawa M, Verma IM . A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc Natl Acad Sci USA 2003; 100: 1844–1848.

    Article  CAS  Google Scholar 

  54. Carmell MA et al. Germline transmission of RNAi in mice. Nat Struct Biol 2003; 10: 147.

    Article  Google Scholar 

  55. Rubinson DA et al. A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat Genet 2003; 33: 401–406.

    Article  CAS  Google Scholar 

  56. Kunath T et al. Transgenic RNA interference in ES cell-derived embryos recapitulates a genetic null phenotype. Nat Biotechnol 2003; 21: 559–561.

    Article  CAS  Google Scholar 

  57. Hommel JD et al. Local gene knockdown in the brain using viral-mediated RNA interference. Nat Med 2003; 9: 1539–1544.

    Article  CAS  Google Scholar 

  58. Calegari F et al. Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNA. Proc Natl Acad Sci USA 2002; 99: 14236–14240.

    Article  CAS  Google Scholar 

  59. Yang D et al. Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc Natl Acad Sci USA 2002; 99: 9942–9947.

    Article  CAS  Google Scholar 

  60. Myers JW, Jones JT, Meyer T, Ferrell Jr JE . Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat Biotechnol 2003; 21: 324–328.

    Article  CAS  Google Scholar 

  61. Kawasaki H, Suyama E, Iyo M, Taira K . siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cells. Nucleic Acids Res 2003; 31: 981–987.

    Article  CAS  Google Scholar 

  62. Sen G, Wehrman TS, Myers JW, Blau HM . Restriction enzyme-generated siRNA (REGS) vectors and libraries. Nat Genet 2004; 36: 183–189.

    Article  CAS  Google Scholar 

  63. Shirane D et al. Enzymatic production of RNAi libraries from cDNAs. Nat Genet 2004; 36: 190–196.

    Article  CAS  Google Scholar 

  64. Reynolds A et al. Rational siRNA design for RNA interference. Nat Biotechnol 2004; 22: 326–330.

    Article  CAS  Google Scholar 

  65. Ui-Tei K et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res 2004; 32: 936–948.

    Article  CAS  Google Scholar 

  66. Whither RNAi? Nat Cell Biol 2003; 5: 489–490.

  67. Lassus P, Rodriguez J, Lazebnik Y . Confirming specificity of RNAi in mammalian cells. Sci STKE 2002; 147: PL13.

    Google Scholar 

  68. Vickers TA et al. Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J Biol Chem 2003; 278: 7108–7118.

    Article  CAS  Google Scholar 

  69. Aoki Y et al. RNA interference may be more potent than antisense RNA in human cancer cell lines. Clin Exp Pharmacol Physiol 2003; 30: 96–102.

    Article  CAS  Google Scholar 

  70. Miyagishi M, Hayashi M, Taira K . Comparison of the suppressive effects of antisense oligonucleotides and siRNAs directed against the same targets in mammalian cells. Antisense Nucleic Acid Drug Dev 2003; 13: 1–7.

    Article  CAS  Google Scholar 

  71. Hemmings-Mieszczak M et al. Independent combinatorial effect of antisense oligonucleotides and RNAi-mediated specific inhibition of the recombinant rat P2X3 receptor. Nucleic Acids Res 2003; 31: 2117–2126.

    Article  CAS  Google Scholar 

  72. Sledz CA et al. Activation of the interferon system by short-interfering RNAs. Nat Cell Biol 2003; 5: 834–839.

    Article  CAS  Google Scholar 

  73. Bridge AJ et al. Induction of an interferon response by RNAi vectors in mammalian cells. Nat Genet 2003; 34: 263–264.

    Article  CAS  Google Scholar 

  74. Jackson AL et al. Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 2003; 21: 635–637.

    Article  CAS  Google Scholar 

  75. Miller VM et al. Allele-specific silencing of dominant disease genes. Proc Natl Acad Sci USA 2003; 100: 7195–7200.

    Article  CAS  Google Scholar 

  76. Xia H, Mao Q, Paulson HL, Davidson BL . siRNA-mediated gene silencing in vitro and in vivo. Nat Biotechnol 2002; 20: 1006–1010.

    Article  CAS  Google Scholar 

  77. Lee NS et al. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 2002; 20: 500–505.

    Article  CAS  Google Scholar 

  78. Lewis DL et al. Efficient delivery of siRNA for inhibition of gene expression in postnatal mice. Nat Genet 2002; 32: 107–108.

    Article  CAS  Google Scholar 

  79. McCaffrey AP et al. RNA interference in adult mice. Nature 2002; 418: 38–39.

    Article  CAS  Google Scholar 

  80. Song E et al. RNA interference targeting Fas protects mice from fulminant hepatitis. Nat Med 2003; 9: 347–351.

    Article  CAS  Google Scholar 

  81. Zender L et al. Caspase 8 small interfering RNA prevents acute liver failure in mice. Proc Natl Acad Sci USA 2003.

  82. Wang J et al. Fas siRNA reduces apoptotic cell death of allogeneic-transplanted hepatocytes in mouse spleen. Transplant Proc 2003; 35: 1594–1595.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Caplen, N. Gene Therapy Progress and Prospects. Downregulating gene expression: the impact of RNA interference. Gene Ther 11, 1241–1248 (2004). https://doi.org/10.1038/sj.gt.3302324

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/sj.gt.3302324

Keywords

This article is cited by

Search

Quick links