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 Article
  • Published:

Argonaute proteins: key players in RNA silencing

Nature Reviews Molecular Cell Biology volume 9, pages 22–32 (2008)Cite this article

Key Points

  • The Argonautes represent a highly conserved gene family that is found in almost all eukaryotes and is even found in bacteria and archaea.

  • Many members of the Argonaute gene family are found in the genomes of plants and animals, with an exceptional representation in the nematode Caenorhabditis elegans, which has at least 26 Argonaute genes.

  • Argonaute proteins contain four conserved domains: the N-terminal, PAZ (which is responsible for small RNA binding), Mid and PIWI (which confers catalytic activities) domains.

  • Argonaute proteins associate with small non-coding RNAs (such as small interfering (si)RNAs and microRNAs (miRNAs)) and function in RNA-based silencing mechanisms by altering protein synthesis and affecting RNA stability.

  • Argonaute proteins also contribute to the maintenance of chromosome integrity, are involved in siRNA and miRNA maturation and can even participate in the production of a new class of small non-coding RNAs known as Piwi-interacting (pi)RNAs.

Abstract

During the past decade, small non-coding RNAs have rapidly emerged as important contributors to gene regulation. To carry out their biological functions, these small RNAs require a unique class of proteins called Argonautes. The discovery and our comprehension of this highly conserved protein family is closely linked to the study of RNA-based gene silencing mechanisms. With their functional domains, Argonaute proteins can bind small non-coding RNAs and control protein synthesis, affect messenger RNA stability and even participate in the production of a new class of small RNAs, Piwi-interacting RNAs.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Structural features of Argonaute proteins.
Figure 2: Assembly of the Argonaute–small RNA complex.
Figure 3: Roles of the Argonaute complex in miRNA and RNAi pathways.

Similar content being viewed by others

References

  1. Moussian, B., Schoof, H., Haecker, A., Jurgens, G. & Laux, T. Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J. 17, 1799–1809 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Bohmert, K. et al. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J. 17, 170–180 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Lin, H. & Spradling, A. C. A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development 124, 2463–2476 (1997). References 1–3 are seminal works that originally described the Argonaute gene family.

    CAS  PubMed  Google Scholar 

  4. Dunoyer, P., Himber, C., Ruiz-Ferrer, V., Alioua, A. & Voinnet, O. Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nature Genet. 39, 848–856 (2007).

    Article  CAS  PubMed  Google Scholar 

  5. Zaratiegui, M., Irvine, D. V. & Martienssen, R. A. Noncoding RNAs and gene silencing. Cell 128, 763–776 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Grewal, S. I. & Jia, S. Heterochromatin revisited. Nature Rev. Genet. 8, 35–46 (2007).

    Article  CAS  PubMed  Google Scholar 

  7. Yigit, E. et al. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 127, 747–757 (2006). The first exhaustive study of Argonaute genes in C. elegans . Describes a class of Argonaute proteins that do not contain the important amino acids for endonuclease activity but are still important for the RNAi pathway.

    Article  CAS  PubMed  Google Scholar 

  8. Cerutti, H. & Casas-Mollano, J. A. On the origin and functions of RNA-mediated silencing: from protists to man. Curr. Genet. 50, 81–99 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Ullu, E., Tschudi, C. & Chakraborty, T. RNA interference in protozoan parasites. Cell. Microbiol. 6, 509–519 (2004).

    Article  CAS  PubMed  Google Scholar 

  10. Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002).

    Article  CAS  PubMed  Google Scholar 

  11. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002).

    Article  CAS  PubMed  Google Scholar 

  12. Sigova, A., Rhind, N. & Zamore, P. D. A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe. Genes Dev. 18, 2359–2367 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Yuan, Y. R. et al. Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol. Cell 19, 405–419 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Ma, J. B. et al. Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434, 666–670 (2005). Describes the crystal structure of a PIWI domain in complex with RNA.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Song, J. J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Struct. Biol. 10, 1026–1032 (2003).

    Article  CAS  PubMed  Google Scholar 

  16. Yan, K. S. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468–474 (2003).

    Article  PubMed  CAS  Google Scholar 

  17. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426, 465–469 (2003).

    Article  CAS  PubMed  Google Scholar 

  18. Ma, J. B., Ye, K. & Patel, D. J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318–322 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nature Struct. Mol. Biol. 11, 576–577 (2004). References 18 and 19 report the crystal structure of the PAZ domain in complex with nucleic acids (reference 19) and mini-siRNA (reference 18).

    Article  CAS  Google Scholar 

  20. Parker, J. S., Roe, S. M. & Barford, D. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 23, 4727–4737 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Song, J. J., Smith, S. K., Hannon, G. J. & Joshua-Tor, L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305, 1434–1437 (2004). The first crystal structure of a complete Argonaute protein, revealing its function as the catalytic component of RISC.

    Article  CAS  PubMed  Google Scholar 

  22. Tolia, N. H. & Joshua-Tor, L. Slicer and the argonautes. Nature Chem. Biol. 3, 36–43 (2007).

    Article  CAS  Google Scholar 

  23. Martinez, J. & Tuschl, T. RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev. 18, 975–980 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Schwarz, D. S., Tomari, Y. & Zamore, P. D. The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr. Biol. 14, 787–791 (2004).

    Article  CAS  PubMed  Google Scholar 

  25. Parker, J. S., Roe, S. M. & Barford, D. Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434, 663–666 (2005). Describes the crystal structure of a PIWI domain in complex with RNA.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  27. Kiriakidou, M. et al. An mRNA m(7)G cap binding-like motif within human Ago2 represses translation. Cell 129, 1141–1151 (2007).

    Article  CAS  PubMed  Google Scholar 

  28. Doench, J. G. & Sharp, P. A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504–511 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Haley, B. & Zamore, P. D. Kinetic analysis of the RNAi enzyme complex. Nature Struct. Mol. Biol. 11, 599–606 (2004).

    Article  CAS  Google Scholar 

  30. Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell 115, 787–798 (2003).

    Article  CAS  PubMed  Google Scholar 

  31. 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  PubMed  PubMed Central  Google Scholar 

  32. Miyoshi, K., Tsukumo, H., Nagami, T., Siomi, H. & Siomi, M. C. Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev. 19, 2837–2848 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Rivas, F. V. et al. Purified Argonaute2 and an siRNA form recombinant human RISC. Nature Struct. Mol. Biol. 12, 340–349 (2005). References 32 and 33 describe the minimal RISC: a recombinant Argonaute (human AGO2) associated with siRNA is sufficient for slicer activity.

    Article  CAS  Google Scholar 

  34. Irvine, D. V. et al. Argonaute slicing is required for heterochromatic silencing and spreading. Science 313, 1134–1137 (2006).

    Article  CAS  PubMed  Google Scholar 

  35. Matranga, C., Tomari, Y., Shin, C., Bartel, D. P. & Zamore, P. D. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607–620 (2005). Together with reference 32, describes the contribution of the enzymatic function of Argonaute in the assembly of RISC by cleaving the passenger strand of the siRNA duplex.

    Article  CAS  PubMed  Google Scholar 

  36. Leuschner, P. J., Ameres, S. L., Kueng, S. & Martinez, J. Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep. 7, 314–320 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hutvágner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002).

    Article  PubMed  CAS  Google Scholar 

  38. Gunawardane, L. S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315, 1587–1590 (2007).

    Article  CAS  PubMed  Google Scholar 

  39. Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Meister, G. et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185–197 (2004). This study, together with reference 41, clearly links the slicing activity to Argonautes. It demonstrates that human AGO2 is the only Argonaute in human carrying the nuclease activity, whereas AGO1–AGO4 can bind miRNAs.

    Article  CAS  PubMed  Google Scholar 

  41. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437–1441 (2004). Demonstrates that disruption of specific amino acids found in the cryptic ribonuclease H domain abrogates RISC activity. Also shows that AGO2 is essential for mouse development.

    Article  CAS  PubMed  Google Scholar 

  42. Höck, J. et al. Proteomic and functional analysis of Argonaute-containing mRNA–protein complexes in human cells. EMBO Rep. 8, 1052–1060 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Tahbaz, N. et al. Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep. 5, 189–194 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Behm-Ansmant, I. et al. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 20, 1885–1898 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Till, S. et al. A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain. Nature Struct. Mol. Biol. 14, 897–903 (2007).

    Article  CAS  Google Scholar 

  46. El-Shami, M. et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21, 2539–2544 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Forstemann, K. et al. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3, e236 (2005).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Saito, K., Ishizuka, A., Siomi, H. & Siomi, M. C. Processing of pre-microRNAs by the Dicer-1–Loquacious complex in Drosophila cells. PLoS Biol. 3, e235 (2005).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Jiang, F. et al. Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila. Genes Dev. 19, 1674–1679 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  51. Tomari, Y., Matranga, C., Haley, B., Martinez, N. & Zamore, P. D. A protein sensor for siRNA asymmetry. Science 306, 1377–1380 (2004).

    Article  CAS  PubMed  Google Scholar 

  52. Forstemann, K., Horwich, M. D., Wee, L., Tomari, Y. & Zamore, P. D. Drosophila microRNAs are sorted into functionally distinct Argonaute complexes after production by Dicer-1. Cell 130, 287–297 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  53. Tomari, Y., Du, T. & Zamore, P. D. Sorting of Drosophila small silencing RNAs. Cell 130, 299–308 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Steiner, F. A. et al. Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nature Struct. Mol. Biol. 14, 927–933 (2007).

    Article  CAS  Google Scholar 

  55. Tomari, Y. & Zamore, P. D. Perspective: machines for RNAi. Genes Dev. 19, 517–529 (2005).

    Article  CAS  PubMed  Google Scholar 

  56. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).

    Article  CAS  PubMed  Google Scholar 

  57. Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003).

    Article  CAS  PubMed  Google Scholar 

  58. Okamura, K., Ishizuka, A., Siomi, H. & Siomi, M. C. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 18, 1655–1666 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Tabara, H. et al. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132 (1999). The first report that associated an Argonaute gene with a small non-coding RNA pathway, RNAi.

    Article  CAS  PubMed  Google Scholar 

  60. 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). Identifies the first Argonaute genes that are required for the microRNA pathway.

    Article  CAS  PubMed  Google Scholar 

  61. Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906 (2000).

    Article  CAS  PubMed  Google Scholar 

  62. Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993).

    Article  CAS  PubMed  Google Scholar 

  63. Sijen, T., Steiner, F. A., Thijssen, K. L. & Plasterk, R. H. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315, 244–247 (2007).

    Article  CAS  PubMed  Google Scholar 

  64. Pak, J. & Fire, A. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315, 241–244 (2007).

    Article  CAS  PubMed  Google Scholar 

  65. Vasudevan, S. & Steitz, J. A. AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 128, 1105–1118 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Olsen, P. H. & Ambros, V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216, 671–680 (1999).

    Article  CAS  PubMed  Google Scholar 

  67. Wang, B., Love, T. M., Call, M. E., Doench, J. G. & Novina, C. D. Recapitulation of short RNA-directed translational gene silencing in vitro. Mol. Cell 22, 553–560 (2006).

    Article  CAS  PubMed  Google Scholar 

  68. Humphreys, D. T., Westman, B. J., Martin, D. I. & Preiss, T. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc. Natl Acad. Sci. USA 102, 16961–16966 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Pillai, R. S. et al. Inhibition of translational initiation by Let-7 microRNA in human cells. Science 309, 1573–1576 (2005). Demonstrates that tethering Argonaute proteins to the 3′-UTR region of a mRNA can mimic miRNA translational inhibition, suggesting that miRNAs function to guide Argonautes to mRNAs.

    Article  CAS  PubMed  Google Scholar 

  70. Thermann, R. & Hentze, M. W. Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447, 875–878 (2007).

    Article  CAS  PubMed  Google Scholar 

  71. Chendrimada, T. P. et al. MicroRNA silencing through RISC recruitment of eIF6. Nature 447, 823–828 (2007).

    Article  CAS  PubMed  Google Scholar 

  72. Kim, J. et al. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl Acad. Sci. USA 101, 360–365 (2004).

    Article  CAS  PubMed  Google Scholar 

  73. Nelson, P. T., Hatzigeorgiou, A. G. & Mourelatos, Z. miRNP: mRNA association in polyribosomes in a human neuronal cell line. RNA 10, 387–394 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Nottrott, S., Simard, M. J. & Richter, J. D. Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nature Struct. Mol. Biol. 13, 1108–1114 (2006).

    Article  CAS  Google Scholar 

  75. Maroney, P. A., Yu, Y., Fisher, J. & Nilsen, T. W. Evidence that microRNAs are associated with translating messenger RNAs in human cells. Nature Struct. Mol. Biol. 13, 1102–1107 (2006).

    Article  CAS  Google Scholar 

  76. Petersen, C. P., Bordeleau, M. E., Pelletier, J. & Sharp, P. A. Short RNAs repress translation after initiation in mammalian cells. Mol. Cell 21, 533–542 (2006).

    Article  CAS  PubMed  Google Scholar 

  77. Pillai, R. S., Artus, C. G. & Filipowicz, W. Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA 10, 1518–1525 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Bhattacharyya, S. N., Habermacher, R., Martine, U., Closs, E. I. & Filipowicz, W. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125, 1111–1124 (2006).

    Article  CAS  PubMed  Google Scholar 

  79. Rehwinkel, J. et al. Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol. Cell. Biol. 26, 2965–2975 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Giraldez, A. J. et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75–79 (2006).

    Article  CAS  PubMed  Google Scholar 

  81. Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005).

    Article  CAS  PubMed  Google Scholar 

  82. Farh, K. K. et al. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310, 1817–1821 (2005).

    Article  CAS  PubMed  Google Scholar 

  83. Bagga, S. et al. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122, 553–563 (2005).

    Article  CAS  PubMed  Google Scholar 

  84. Wu, L., Fan, J. & Belasco, J. G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl Acad. Sci. USA 103, 4034–4039 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Valencia-Sanchez, M. A., Liu, J., Hannon, G. J. & Parker, R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20, 515–524 (2006).

    Article  CAS  PubMed  Google Scholar 

  86. Jing, Q. et al. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120, 623–634 (2005).

    Article  CAS  PubMed  Google Scholar 

  87. Kuramochi-Miyagawa, S. et al. Mili, a mammalian member of Piwi family gene, is essential for spermatogenesis. Development 131, 839–849 (2004).

    Article  CAS  PubMed  Google Scholar 

  88. Deng, W. & Lin, H. Miwi, a murine homolog of Piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev. Cell 2, 819–830 (2002).

    Article  CAS  PubMed  Google Scholar 

  89. Cox, D. N., Chao, A. & Lin, H. Piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells. Development 127, 503–514 (2000).

    CAS  PubMed  Google Scholar 

  90. Cox, D. N. et al. A novel class of evolutionarily conserved genes defined by Piwi are essential for stem cell self-renewal. Genes Dev. 12, 3715–3727 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12, 503–514 (2007).

    Article  CAS  PubMed  Google Scholar 

  92. Grivna, S. T., Beyret, E., Wang, Z. & Lin, H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev. 20, 1709–1714 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Watanabe, T. et al. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 20, 1732–1743 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363–367 (2006).

    Article  CAS  PubMed  Google Scholar 

  95. Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006).

    Article  PubMed  Google Scholar 

  96. Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006).

    Article  CAS  PubMed  Google Scholar 

  97. Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006).

    Article  CAS  PubMed  Google Scholar 

  98. Saito, K. et al. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev. 20, 2214–2222 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Houwing, S. et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129, 69–82 (2007).

    Article  CAS  PubMed  Google Scholar 

  100. Pane, A., Wehr, K. & Schupbach, T. Zucchini and Squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev. Cell 12, 851–862 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Brower-Toland, B. et al. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes Dev. 21, 2300–2311 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Hiragami, K. & Festenstein, R. Heterochromatin protein 1: a pervasive controlling influence. Cell. Mol. Life Sci. 62, 2711–2726 (2005).

    Article  CAS  PubMed  Google Scholar 

  103. Noma, K. et al. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nature Genet. 36, 1174–1180 (2004).

    Article  CAS  PubMed  Google Scholar 

  104. Yin, H. & Lin, H. An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 450, 304–308 (2007).

    Article  CAS  PubMed  Google Scholar 

  105. Cerutti, L., Mian, N. & Bateman, A. Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. Trends Biochem. Sci. 25, 481–482 (2000).

    Article  CAS  PubMed  Google Scholar 

  106. Jacobsen, S. E., Running, M. P. & Meyerowitz, E. M. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development 126, 5231–5243 (1999).

    CAS  PubMed  Google Scholar 

  107. Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Borchert, G. M., Lanier, W. & Davidson, B. L. RNA polymerase III transcribes human microRNAs. Nature Struct. Mol. Biol. 13, 1097–1101 (2006).

    Article  CAS  Google Scholar 

  109. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).

    Article  CAS  PubMed  Google Scholar 

  110. Okamura, K., Hagen, J. W., Duan, H., Tyler, D. M. & Lai, E. C. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130, 89–100 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Ruby, J. G., Jan, C. H. & Bartel, D. P. Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83–86 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Yi, R., Qin, Y., Macara, I. G. & Cullen, B. R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17, 3011–3016 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Hutvágner, 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).

    Article  PubMed  Google Scholar 

  115. Kirino, Y. & Mourelatos, Z. Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini. Nature Struct. Mol. Biol. 14, 347–348 (2007).

    Article  CAS  Google Scholar 

  116. Ohara, T. et al. The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated. Nature Struct. Mol. Biol. 14, 349–350 (2007).

    Article  CAS  Google Scholar 

  117. Saito, K. et al. Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi- interacting RNAs at their 3′ ends. Genes Dev. 21, 1603–1608 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Horwich, M. D. et al. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr. Biol. 17, 1265–1272 (2007).

    Article  CAS  PubMed  Google Scholar 

  119. Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911–940 (1999).

    Article  CAS  PubMed  Google Scholar 

  120. Cogoni, C. & Macino, G. Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa. Proc. Natl Acad. Sci. USA 94, 10233–10238 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Catalanotto, C., Azzalin, G., Macino, G. & Cogoni, C. Gene silencing in worms and fungi. Nature 404, 245 (2000).

    Article  CAS  PubMed  Google Scholar 

  122. Lee, D. W., Pratt, R. J., McLaughlin, M. & Aramayo, R. An Argonaute-like protein is required for meiotic silencing. Genetics 164, 821–828 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Mochizuki, K., Fine, N. A., Fujisawa, T. & Gorovsky, M. A. Analysis of a Piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110, 689–699 (2002).

    Article  CAS  PubMed  Google Scholar 

  125. Vazquez, F. et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16, 69–79 (2004).

    Article  CAS  PubMed  Google Scholar 

  126. Vaucheret, H., Vazquez, F., Crete, P. & Bartel, D. P. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 18, 1187–1197 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Zilberman, D., Cao, X. & Jacobsen, S. E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299, 716–719 (2003).

    Article  CAS  PubMed  Google Scholar 

  128. Zheng, X., Zhu, J., Kapoor, A. & Zhu, J. K. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J. 26, 1691–1701 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Hunter, C., Sun, H. & Poethig, R. S. The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr. Biol. 13, 1734–1739 (2003).

    Article  CAS  PubMed  Google Scholar 

  130. Grishok, A., Sinskey, J. L. & Sharp, P. A. Transcriptional silencing of a transgene by RNAi in the soma of C. elegans. Genes Dev. 19, 683–696 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Tijsterman, M., Okihara, K. L., Thijssen, K. & Plasterk, R. H. PPW-1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C. elegans. Curr. Biol. 12, 1535–1540 (2002).

    Article  CAS  PubMed  Google Scholar 

  132. 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). Reports the purification of the RNAi effector nuclease previously described in 2000, revealing Argonaute-2 in the complex.

    Article  CAS  PubMed  Google Scholar 

  133. Janowski, B. A. et al. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nature Struct. Mol. Biol. 13, 787–792 (2006).

    Article  CAS  Google Scholar 

  134. Kim, D. H., Villeneuve, L. M., Morris, K. V. & Rossi, J. J. Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nature Struct. Mol. Biol. 13, 793–797 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to J.-Y. Masson, S. Arthur and members of our laboratories for comments on the manuscript. We would also like to thank L. Joshua-Tor for kindly providing us with the crystal structure of Argonaute protein from Pyrococcus furiosus. G.H. is funded by The Wellcome Trust and European Framework 6 SIROCCO consortium, and M.J.S. receives funding from the Canadian Institutes of Health Research (CIHR) and the Natural Sciences and Engineering Research Council of Canada. G.H. is a Wellcome Trust Career Development fellow and M.J.S. is a CIHR New Investigator.

Author information

Authors and Affiliations

  1. Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK

    Gyorgy Hutvagner

  2. Laval University Cancer Research Centre, Hôtel-Dieu de Québec (CHUQ), Quebec City, G1R 2J6, Québec, Canada

    Martin J. Simard

Authors
  1. Gyorgy Hutvagner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martin J. Simard
    View author publications

    You can also search for this author in PubMed Google Scholar

Related links

Related links

DATABASES

WormBase

rde-1

FURTHER INFORMATION

Gyorgy Hutvagner's homepage

Martin J. Simard's homepage

Glossary

RNA interference

(RNAi). A process by which double-stranded RNA specifically silences the expression of homologous genes through degradation of their cognate mRNA.

microRNA

(miRNA). A non-coding RNA of 21–24 nucleotides, which is processed from an endogenous ∼70-nucleotide hairpin RNA precursor by the RNase-III-type Dicer enzyme. miRNAs are evolutionarily conserved molecules and are thought to have important functions in various biological mechanisms.

Paralogous

The quality of having sequence similarity as a result of gene duplication events that occurred in the same genome. By contrast, orthologous genes or proteins have sequence similarity as a result of gene duplication events that occurred in a different genome.

PAZ domain

A conserved nucleic-acid-binding structure that is found in members of the Dicer and Argonaute protein families.

PIWI domain

A conserved structure that is found in members of the Argonaute protein family. It is structurally similar to ribonuclease H domains and, in at least some cases, has endoribonuclease activity.

RNase H

A class of RNA endonucleases that cleave the RNA strand of a DNA–RNA duplex. Argonaute and Piwi proteins share similar catalytic domain structure and activity with RNase H enzymes but are mostly active on RNA–RNA hybrids.

Dicer

The ribonuclease of the RNase III family that cleaves miRNA precursor (pre-miRNA) and double-stranded RNA molecules into 21–25-nucleotide-long double-stranded RNA with a two-base overhang on the 3′-ends.

OB fold

A common protein domain that is involved in binding nucleic acids.

Small interfering RNA

(siRNA). A short RNA (∼22 nucleotides) that is processed from longer double-stranded RNA during RNAi. These short RNAs hybridize with mRNA targets and confer target specificity to the silencing complexes in which they reside.

Drosha

The RNase III enzyme that is implicated in processing newly transcribed primary miRNA in the nucleus. Drosha cleavage determines the 5′- and 3′-ends of the Dicer substrate (precursor miRNA (pre-miRNA)).

Cap structure

A structure consisting of m7GpppN (in which m7G represents 7-methylguanylate, p represents a phosphate group and N represents any base) that is located at the 5′-end of eukaryotic mRNAs.

RNA-induced silencing complex

(RISC). A multicomponent gene regulatory complex, activated by a small RNA associated with an Argonaute protein, that regulates gene expression mediated by the sequence complementarity between the small RNA and the target mRNA.

rasiRNA

Repeat-associated small interfering RNA that is derived from highly repetitive genomic loci. rasiRNA is involved in heterochromatin silencing in yeast and plants and stellate silencing in D. melanogaster. Metazoan rasiRNAs have similarities to piRNAs because the processing of both classes of small RNAs is independent of Dicer and Drosha.

Piwi-interacting RNAs

(piRNAs). Small ∼31-nucleotide-long RNAs that are processed in a Dicer- and Drosha-independent manner. They associate with Piwi proteins and have a role in transposon silencing in flies. In mammals, they are restricted mostly to male germ cells.

Active strand

The strand of a duplex siRNA or miRNA intermediate that is selected and incorporated into the RISC.

PIWI box

A 40-amino-acid sequence that is located in the C terminus of Piwi-like proteins.

Cytoplasmic processing bodies

(P bodies). Cytoplasmic foci that were first detected by immunostaining with the GW182 antibody. They probably represent protein–RNA aggregates that degrade RNAs by deadenylation and decapping. They also accommodate Argonaute-bound miRNAs and miRNA-targeted RNAs. Cytoplasmic bodies do not form without miRNAs; however, disruption of the P bodies does not affect miRNA-mediated gene regulation.

tasiRNA

Trans-acting small interfering RNAs are plant-specific small RNAs and their maturation involves miRNAs. An Argonaute–miRNA complex cleaves the single-stranded primary transcript, which is further amplified by RNA-dependent RNA polymerases, followed by Dicer-mediated processing of de novo dsRNA molecules. The generated siRNAs are then incorporated into Argonaute complexes and regulate gene expression by cleaving the target RNA.

Passenger strand

The strand of a duplex siRNA or miRNA that is not incorporated into the RISC and is eventually degraded.

Heterochronic phenotypes

Observable characteristics that are related to a specific defect in the developmental timing (that is, larvae that display adult characteristics or an adult animal with larval features).

Exogenous RNAi

A silencing response mediated by exogenous experimentally delivered double-stranded RNA molecules.

Endogenous RNAi

An RNAi response initiated by endogenous double-stranded RNA triggers that are derived from bidirectional transcription of specific loci, or aberrant RNA generated from centromeric regions, transposons and transgenes.

Poly(A) tail

A homopolymeric stretch of usually 25–200 adenine nucleotides that is present at the 3′-end of most eukaryotic mRNAs.

Deadenylation-dependent decapping

Cytoplasmic RNA degradation that starts with the depletion of the poly(A) tail of a mRNA followed by removal of the cap by decapping enzymes. The decapped RNA is degraded by 5′→3′ exonucleases.

Mobile elements

Also known as transposable elements. DNA sequences in the genome that replicate and insert themselves into various positions in the genome.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hutvagner, G., Simard, M. Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9, 22–32 (2008). https://doi.org/10.1038/nrm2321

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm2321

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing