Slicer and the Argonautes (original) (raw)

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

Download references