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Slicer and the Argonautes

Abstract

Though they started out as somewhat mysterious components of the RNAi effector complexes, Argonaute proteins have since taken center stage in RNAi gene silencing. They interact with small RNAs to effect gene silencing in all RNAi-related pathways known so far. We will review the dramatic advances in our understanding of the role of the Argonautes in RNAi through studies of their structure and function.

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Figure 1: Pathways of post-transcriptional gene silencing.
Figure 2: The crystal structure of Argonaute from P. furiosus.
Figure 3: The three clades of the Argonautes.
Figure 4: Model for the role of slicing in TGS in S. pombe.

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References

  1. 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).

    Article  CAS  PubMed  Google Scholar 

  2. Yekta, S., Shih, I.H. & Bartel, D.P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594–596 (2004).

    Article  CAS  PubMed  Google Scholar 

  3. Liu, J. et al. A role for the P-body component GW182 in microRNA function. Nat. Cell Biol. 7, 1261–1266 (2005).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Pillai, R.S. et al. Inhibition of translational initiation by Let-7 microRNA in human cells. Science 309, 1573–1576 (2005).

    Article  CAS  PubMed  Google Scholar 

  5. Rossi, J.J. RNAi and the P-body connection. Nat. Cell Biol. 7, 643–644 (2005).

    Article  CAS  PubMed  Google Scholar 

  6. Sen, G.L. & Blau, H.M. Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat. Cell Biol. 7, 633–636 (2005).

    Article  CAS  PubMed  Google Scholar 

  7. Wassenegger, M., Heimes, S., Riedel, L. & Sanger, H.L. RNA-directed de novo methylation of genomic sequences in plants. Cell 76, 567–576 (1994).

    Article  CAS  PubMed  Google Scholar 

  8. 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 

  9. Pal-Bhadra, M., Bhadra, U. & Birchler, J.A. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell 9, 315–327 (2002).

    Article  CAS  PubMed  Google Scholar 

  10. 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).

    Article  CAS  PubMed  Google Scholar 

  11. Caudy, A.A. et al. A micrococcal nuclease homologue in RNAi effector complexes. Nature 425, 411–414 (2003).

    Article  CAS  PubMed  Google Scholar 

  12. Caudy, A.A., Myers, M., Hannon, G.J. & Hammond, S.M. Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev. 16, 2491–2496 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Ishizuka, A., Siomi, M.C. & Siomi, H. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev. 16, 2497–2508 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. 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).

    Article  CAS  PubMed  Google Scholar 

  15. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437–1441 (2004).

    Article  CAS  PubMed  Google Scholar 

  16. 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 

  17. 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 

  18. Wintersberger, U. Ribonucleases H of retroviral and cellular origin. Pharmacol. Ther. 48, 259–280 (1990).

    Article  CAS  PubMed  Google Scholar 

  19. 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 

  20. 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 

  21. Meister, G. et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185–197 (2004).

    Article  CAS  PubMed  Google Scholar 

  22. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R. & Tuschl, T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563–574 (2002).

    Article  CAS  PubMed  Google Scholar 

  23. 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 

  24. Rivas, F.V. et al. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat. Struct. Mol. Biol. 12, 340–349 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Rand, T.A., Ginalski, K., Grishin, N.V. & Wang, X. Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc. Natl. Acad. Sci. USA 101, 14385–14389 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Song, J.J. & Joshua-Tor, L. Argonaute and RNA–getting into the groove. Curr. Opin. Struct. Biol. 16, 5–11 (2006).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  28. 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 

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

    Article  PubMed  CAS  Google Scholar 

  30. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nat. Struct. Mol. Biol. 11, 576–577 (2004).

    Article  CAS  PubMed  Google Scholar 

  31. 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 

  32. Haren, L., Ton-Hoang, B. & Chandler, M. Integrating DNA: transposases and retroviral integrases. Annu. Rev. Microbiol. 53, 245–281 (1999).

    Article  CAS  PubMed  Google Scholar 

  33. Kennedy, A.K., Haniford, D.B. & Mizuuchi, K. Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: insights from phosphorothioate stereoselectivity. Cell 101, 295–305 (2000).

    Article  CAS  PubMed  Google Scholar 

  34. Krakowiak, A., Owczarek, A., Koziolkiewicz, M. & Stec, W.J. Stereochemical course of Escherichia coli RNase H. ChemBioChem 3, 1242–1250 (2002).

    Article  CAS  PubMed  Google Scholar 

  35. Steitz, T.A. & Steitz, J.A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA 90, 6498–6502 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Nowotny, M., Gaidamakov, S.A., Crouch, R.J. & Yang, W. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121, 1005–1016 (2005).

    Article  CAS  PubMed  Google Scholar 

  37. Lovell, S., Goryshin, I.Y., Reznikoff, W.R. & Rayment, I. Two-metal active site binding of a Tn5 transposase synaptic complex. Nat. Struct. Biol. 9, 278–281 (2002).

    Article  CAS  PubMed  Google Scholar 

  38. Baumberger, N. & Baulcombe, D.C. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. USA 102, 11928–11933 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Qi, Y., Denli, A.M. & Hannon, G.J. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol. Cell 19, 421–428 (2005).

    Article  CAS  PubMed  Google Scholar 

  40. Qi, Y. et al. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443, 1008–1012 (2006).

    Article  PubMed  Google Scholar 

  41. 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 

  42. 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 

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

    Article  CAS  PubMed  Google Scholar 

  44. 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 

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

    Article  CAS  PubMed  Google Scholar 

  46. Carmell, M.A., Xuan, Z., Zhang, M.Q. & Hannon, G.J. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16, 2733–2742 (2002).

    Article  CAS  PubMed  Google Scholar 

  47. 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 

  48. 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).

    CAS  PubMed  Google Scholar 

  49. Reddien, P.W., Oviedo, N.J., Jennings, J.R., Jenkin, J.C. & Sanchez Alvarado, A. SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells. Science 310, 1327–1330 (2005).

    Article  CAS  PubMed  Google Scholar 

  50. Schmidt, E.E., Hanson, E.S. & Capecchi, M.R. Sequence-independent assembly of spermatid mRNAs into messenger ribonucleoprotein particles. Mol. Cell. Biol. 19, 3904–3915 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. 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 

  52. Kuramochi-Miyagawa, S. et al. Two mouse piwi-related genes: miwi and mili. Mech. Dev. 108, 121–133 (2001).

    Article  CAS  PubMed  Google Scholar 

  53. 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 

  54. 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 

  55. 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 

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

    Article  CAS  PubMed  Google Scholar 

  57. 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 

  58. Yigit, E. et al. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell (in the press).

  59. 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 

  60. Vastenhouw, N.L. et al. A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Curr. Biol. 13, 1311–1316 (2003).

    Article  CAS  PubMed  Google Scholar 

  61. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. 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 

  64. 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 

  65. Stark, A., Brennecke, J., Russell, R.B. & Cohen, S.M. Identification of Drosophila MicroRNA targets. PLoS Biol. 1, E60 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Hall, T.M. Structure and function of argonaute proteins. Structure 13, 1403–1408 (2005).

    Article  CAS  PubMed  Google Scholar 

  67. Preall, J.B. & Sontheimer, E.J. RNAi: RISC gets loaded. Cell 123, 543–545 (2005).

    Article  CAS  PubMed  Google Scholar 

  68. 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).

    Article  CAS  PubMed  Google Scholar 

  69. Rand, T.A., Petersen, S., Du, F. & Wang, X. Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123, 621–629 (2005).

    Article  CAS  PubMed  Google Scholar 

  70. 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 

  71. Haley, B., Tang, G. & Zamore, P.D. In vitro analysis of RNA interference in Drosophila melanogaster. Methods 30, 330–336 (2003).

    Article  CAS  PubMed  Google Scholar 

  72. Ming, D., Wall, M.E. & Sanbonmatsu, K.Y. Domain motions in Argonaute, the catalytic engine of RNA interference. PLoS Comput. Biol. (in the press).

  73. Gregory, R.I., Chendrimada, T.P., Cooch, N. & Shiekhattar, R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123, 631–640 (2005).

    Article  CAS  PubMed  Google Scholar 

  74. Allshire, R.C., Nimmo, E.R., Ekwall, K., Javerzat, J.P. & Cranston, G. Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9, 218–233 (1995).

    Article  CAS  PubMed  Google Scholar 

  75. Partridge, J.F., Scott, K.S., Bannister, A.J., Kouzarides, T. & Allshire, R.C. cis-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site. Curr. Biol. 12, 1652–1660 (2002).

    Article  CAS  PubMed  Google Scholar 

  76. Horn, P.J., Bastie, J.N. & Peterson, C.L.A. Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev. 19, 1705–1714 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Jia, S., Kobayashi, R. & Grewal, S.I. Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat. Cell Biol. 7, 1007–1013 (2005).

    Article  CAS  PubMed  Google Scholar 

  78. Li, F. et al. Two novel proteins, dos1 and dos2, interact with rik1 to regulate heterochromatic RNA interference and histone modification. Curr. Biol. 15, 1448–1457 (2005).

    Article  CAS  PubMed  Google Scholar 

  79. Thon, G. et al. The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate heterochromatin formation in the fission yeast Schizosaccharomyces pombe. Genetics 171, 1583–1595 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Motamedi, M.R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004).

    Article  CAS  PubMed  Google Scholar 

  81. 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).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  83. Denli, A.M., Tops, B.B., Plasterk, R.H., Ketting, R.F. & Hannon, G.J. Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235 (2004).

    Article  CAS  PubMed  Google Scholar 

  84. 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).

    Article  CAS  PubMed  Google Scholar 

  85. 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).

    Article  CAS  PubMed  Google Scholar 

  86. 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 

  87. Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H.L. & Poethig, R.S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 18, 2368–2379 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Ambros, V., Lee, R.C., Lavanway, A., Williams, P.T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807–818 (2003).

    Article  CAS  PubMed  Google Scholar 

  89. Lee, R.C., Hammell, C.M. & Ambros, V. Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. RNA 12, 589–597 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Liu, Y., Mochizuki, K. & Gorovsky, M.A. Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena. Proc. Natl. Acad. Sci. USA 101, 1679–1684 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. 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 

  92. Taverna, S.D., Coyne, R.S. & Allis, C.D. Methylation of histone h3 at lysine 9 targets programmed DNA elimination in Tetrahymena. Cell 110, 701–711 (2002).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

RNAi is a flourishing field with a great deal of wonderful studies, some of which we were not able to cite in this short survey, and for that we apologize. This work was supported by a grant from the US National Institutes of Health to L.J. (R01-GM072659).

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Tolia, N., Joshua-Tor, L. Slicer and the Argonautes. Nat Chem Biol 3, 36–43 (2007). https://doi.org/10.1038/nchembio848

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