Mechanisms of gene silencing by double-stranded RNA (original) (raw)

References

1. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).
   Article ADS CAS PubMed Google Scholar
2. Tijsterman, M., Ketting, R. F. & Plasterk, R. H. The genetics of RNA silencing. Annu. Rev. Genet. 36, 489–519 (2002).
   CAS PubMed Google Scholar
3. Ullu, E., Tschudi, C. & Chakraborty, T. RNA interference in protozoan parasites. Cell Microbiol. 6, 509–519 (2004).
   CAS PubMed Google Scholar
4. Waterhouse, P. M., Wang, M. B. & Lough, T. Gene silencing as an adaptive defence against viruses. Nature 411, 834–842 (2001).
   ADS CAS PubMed Google Scholar
5. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004).
   CAS PubMed Google Scholar
6. Lee, Y., Jeon, K., Lee, J. T., Kim, S. & Kim, V. N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663–4670 (2002).
   CAS PubMed PubMed Central Google Scholar
7. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).
   ADS CAS PubMed Google Scholar
8. Basyuk, E., Suavet, F., Doglio, A., Bordonne, R. & Bertrand, E. Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res. 31, 6593–6597 (2003).
   CAS PubMed PubMed Central Google Scholar
9. Bohnsack, M. T., Czaplinski, K. & Görlich, D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10, 185–191 (2004).
   CAS PubMed PubMed Central Google Scholar
10. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004).
    ADS CAS PubMed Google Scholar
11. 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).
    CAS PubMed PubMed Central Google Scholar
12. Hutvágner, G., McLachlan, J., Bálint, É., Tuschl, T. & Zamore, P. D. A cellular function for the RNA interference enzyme Dicer in small temporal RNA maturation. Science 93, 834–838 (2001).
    Google Scholar
13. 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).
    CAS PubMed Google Scholar
14. Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81 (2004).
    CAS PubMed Google Scholar
15. Xie, Z. et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104 (2004).
    PubMed PubMed Central Google Scholar
16. 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 ADS CAS PubMed Google Scholar
17. Elbashir, S. M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21 and 22 nt RNAs. Genes Dev. 15, 188–200 (2001).
    CAS PubMed PubMed Central Google Scholar
18. Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921–1925 (2003).
    ADS CAS PubMed Google Scholar
19. Pham, J. W., Pellino, J. L., Lee, Y. S., Carthew, R. W. & Sontheimer, E. J. A Dicer-2-dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117, 83–94 (2004).
    CAS PubMed Google Scholar
20. Nykänen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309–321 (2001).
    PubMed Google Scholar
21. Provost, P. et al. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21, 5864–5874 (2002).
    CAS PubMed PubMed Central Google Scholar
22. Zhang, H., Kolb, F. A., Brondani, V., Billy, E. & Filipowicz, W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875–5885 (2002).
    CAS PubMed PubMed Central Google Scholar
23. Boutet, S. et al. Arabidopsis HEN1: A genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol. 13, 843–848 (2003).
    CAS PubMed PubMed Central Google Scholar
24. Vazquez, F., Gasciolli, V., Crete, P. & Vaucheret, H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not post-transcriptional transgene silencing. Curr. Biol. 14, 346–351 (2004).
    CAS PubMed Google Scholar
25. Han, M. H., Goud, S., Song, L. & Fedoroff, N. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl Acad. Sci. USA 101, 1093–1098 (2004).
    ADS CAS PubMed PubMed Central Google Scholar
26. Tabara, H., Yigit, E., Siomi, H. & Mello, C. C. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell 109, 861–871 (2002).
    CAS PubMed Google Scholar
27. 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).
    ADS CAS PubMed Google Scholar
28. Mourelatos, Z. et al. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728 (2002).
    CAS PubMed PubMed Central Google Scholar
29. 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).
    CAS PubMed Google Scholar
30. Martinez, J., Patkaniowska, A., Urlaub, H., Lührmann, R. & Tuschl, T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563–574 (2002).
    CAS PubMed Google Scholar
31. Hutvágner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002).
    ADS PubMed Google Scholar
32. Martinez, J. & Tuschl, T. RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev. 18, 975–980 (2004).
    CAS PubMed PubMed Central Google Scholar
33. Tahbaz, N. et al. Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep. 5, 189–194 (2004).
    CAS PubMed PubMed Central Google Scholar
34. Tomari, Y. et al. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116, 831–841 (2004).
    CAS PubMed Google Scholar
35. Cook, H. A., Koppetsch, B. S., Wu, J. & Theurkauf, W. E. The Drosophila SDE3 homolog armitage is required for oskar mRNA silencing and embryonic axis specification. Cell 116, 817–829 (2004).
    CAS PubMed Google Scholar
36. Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003).
    CAS PubMed Google Scholar
37. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).
    CAS PubMed Google Scholar
38. 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).
    CAS PubMed Google Scholar
39. Song, J. J., Smith, S. K., Hannon, G. J. & Joshua-Tor, L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science; published online 29 July 2004 (doi:10.1126/science.1102514).
40. 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).
    ADS CAS PubMed PubMed Central Google Scholar
41. 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).
    CAS Google Scholar
42. Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877–6888 (2001).
    CAS PubMed PubMed Central Google Scholar
43. Hunter, C., Sun, H. & Poethig, R. S. The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr. Biol. 13, 1734–1739 (2003).
    CAS PubMed Google Scholar
44. Williams, R. W. & Rubin, G. M. ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proc. Natl Acad. Sci. USA 99, 6889–6894 (2002).
    ADS CAS PubMed PubMed Central Google Scholar
45. Sasaki, T., Shiohama, A., Minoshima, S. & Shimizu, N. Identification of eight members of the Argonaute family in the human genome. Genomics 82, 323–330 (2003).
    CAS PubMed Google Scholar
46. 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).
    CAS PubMed PubMed Central Google Scholar
47. Meister, G. et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185–197 (2004).
    CAS PubMed Google Scholar
48. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science published online 29 July 2004 (doi: 10.1126/science.1102513).
49. 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).
    CAS PubMed PubMed Central Google Scholar
50. Caudy, A. A. et al. A micrococcal nuclease homologue in RNAi effector complexes. Nature 425, 411–414 (2003).
    ADS CAS PubMed Google Scholar
51. 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).
    CAS PubMed PubMed Central Google Scholar
52. Jin, P. et al. Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nature Neurosci. 7, 113–117 (2004).
    CAS PubMed Google Scholar
53. Schwarz, D. S., Tomari, Y. & Zamore, P. D. The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr. Biol. 14, 787–791 (2004).
    CAS PubMed Google Scholar
54. 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).
    CAS PubMed Google Scholar
55. Seggerson, K., Tang, L. & Moss, E. G. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev. Biol. 243, 215–225 (2002).
    CAS PubMed Google Scholar
56. Kim, J. et al. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl Acad. Sci. USA 101, 360–365 (2004).
    ADS CAS PubMed Google Scholar
57. Doench, J. G., Petersen, C. P. & Sharp, P. A. siRNAs can function as miRNAs. Genes Dev. 17, 438–442 (2003).
    CAS PubMed PubMed Central Google Scholar
58. Saxena, S., Jonsson, Z. O. & Dutta, A. Small RNAs with imperfect match to endogenous mRNA repress translation: implications for off-target activity of siRNA in mammalian cells. J. Biol. Chem. 278, 44312–44319 (2003).
    CAS PubMed Google Scholar
59. Wassenegger, M. & Pelissier, T. A model for RNA-mediated gene silencing in higher plants. Plant Mol. Biol. 37, 349–362 (1998).
    CAS PubMed Google Scholar
60. Sijen, T. et al. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107, 465–476 (2001).
    CAS PubMed Google Scholar
61. Schwarz, D. S., Hutvágner, G., Haley, B. & Zamore, P. D. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol. Cell 10, 537–548 (2002).
    CAS PubMed Google Scholar
62. Roignant, J. Y. et al. Absence of transitive and systemic pathways allows cell-specific and isoform-specific RNAi in Drosophila. RNA 9, 299–308 (2003).
    CAS PubMed PubMed Central Google Scholar
63. Stein, P., Svoboda, P., Anger, M. & Schultz, R. M. RNAi: mammalian oocytes do it without RNA-dependent RNA polymerase. RNA 9, 187–192 (2003).
    CAS PubMed PubMed Central Google Scholar
64. Waterhouse, P. M., Wang, M. & Finnegan, E. J. Role of short RNAs in gene silencing. Trends Plant Sci. 6, 297–301 (2001).
    CAS PubMed Google Scholar
65. Gitlin, L. & Andino, R. Nucleic acid-based immune system: the antiviral potential of mammalian RNA silencing. J. Virol. 77, 7159–7165 (2003).
    CAS PubMed PubMed Central Google Scholar
66. Li, W. X. & Ding, S. W. Viral suppressors of RNA silencing. Curr. Opin. Biotechnol. 12, 150–154 (2001).
    CAS PubMed Google Scholar
67. Voinnet, O. RNA silencing as a plant immune system against viruses. Trends Genet. 17, 449–459 (2001).
    CAS PubMed Google Scholar
68. Li, H., Li, W. X. & Ding, S. W. Induction and suppression of RNA silencing by an animal virus. Science 296, 1319–1321 (2002).
    ADS CAS PubMed Google Scholar
69. Vargason, J. M., Szittya, G., Burgyan, J. & Hall, T. M. Size selective recognition of siRNA by an RNA silencing suppressor. Cell 115, 799–811 (2003).
    CAS PubMed Google Scholar
70. Ye, K., Malinina, L. & Patel, D. J. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426, 874–878 (2003).
    ADS CAS PubMed PubMed Central Google Scholar
71. Knight, S. W. & Bass, B. L. The role of RNA editing by ADARs in RNAi. Mol. Cell 10, 809–817 (2002).
    CAS PubMed Google Scholar
72. Tonkin, L. A. & Bass, B. L. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants. Science 302, 1725 (2003).
    CAS PubMed PubMed Central Google Scholar
73. Kennedy, S., Wang, D. & Ruvkun, G. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427, 645–649 (2004).
    ADS CAS PubMed Google Scholar
74. Simmer, F. et al. Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Curr. Biol. 12, 1317–1319 (2002).
    CAS PubMed Google Scholar
75. Calin, G. A. et al. Frequent deletions and down-regulation of microRNA genes miR-15 and miR-16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl Acad. Sci. USA 99, 15524–15529 (2002).
    ADS CAS PubMed PubMed Central Google Scholar
76. Michael, M. Z., O' Connor, S. M., van Holst Pellekaan, N. G., Young, G. P. & James, R. J. Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol. Cancer Res. 1, 882–891 (2003).
    CAS PubMed Google Scholar
77. Moroy, T. et al. Structure and expression of hcr, a locus rearranged with c-myc in a woodchuck hepatocellular carcinoma. Oncogene 4, 59–65 (1989).
    CAS PubMed Google Scholar
78. Gauwerky, C. E., Huebner, K., Isobe, M., Nowell, P. C. & Croce, C. M. Activation of MYC in a masked t(8;17) translocation results in an aggressive B-cell leukemia. Proc. Natl Acad. Sci. USA 86, 8867–8871 (1989).
    ADS CAS PubMed PubMed Central Google Scholar
79. Pfeffer, S. et al. Identification of virus-encoded microRNAs. Science 304, 734–736 (2004).
    ADS CAS PubMed Google Scholar
80. Bohmert, K. et al. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J. 17, 170–180 (1998).
    CAS PubMed PubMed Central Google Scholar
81. Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).
    ADS CAS PubMed PubMed Central Google Scholar
82. Zilberman, D., Cao, X. & Jacobsen, S. E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299, 716–719 (2003).
    ADS CAS PubMed Google Scholar
83. Pal-Bhadra, M., Bhadra, U. & Birchler, J. A. RNAi-related mechanism affects both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell 9, 315–327 (2002).
    CAS PubMed Google Scholar
84. Kennerdell, J. R., Yamaguchi, S. & Carthew, R. W. RNAi is activated during Drosophila oocyte maturation in a manner dependent on aubergine and spindle-E. Genes Dev. 16, 1884–1889 (2002).
    CAS PubMed PubMed Central Google Scholar
85. 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).
    CAS PubMed Google Scholar
86. Fagard, M., Boutet, S., Morel, J. B., Bellini, C. & Vaucheret, H. AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc. Natl Acad. Sci. USA 97, 11650–11654 (2000).
    ADS CAS PubMed PubMed Central Google Scholar
87. Dalmay, T., Horsefield, R., Braunstein, T. H. & Baulcombe, D. C. SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO J. 20, 2069–2078 (2001).
    CAS PubMed PubMed Central Google Scholar
88. Tijsterman, M., Ketting, R. F., Okihara, K. L. & Plasterk, R. H. RNA helicase MUT-14-dependent silencing triggered in C. elegans by short antisense RNAs. Science 295, 694–697 (2002).
    ADS CAS PubMed Google Scholar
89. Domeier, M. E. et al. A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans. Science 289, 1928–1931 (2000).
    ADS CAS PubMed Google Scholar
90. Mourrain, P. et al. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101, 533–542 (2000).
    CAS PubMed Google Scholar
91. Chan, S. W. et al. RNA silencing genes control de novo DNA methylation. Science 303, 1336 (2004).
    CAS PubMed Google Scholar
92. Smardon, A. et al. EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Curr. Biol. 10, 169–178 (2000).
    CAS PubMed Google Scholar
93. Cogoni, C. & Macino, G. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399, 166–169 (1999).
    ADS CAS PubMed Google Scholar
94. Glazov, E. et al. A gene encoding an RNase D exonuclease-like protein is required for post-transcriptional silencing in Arabidopsis. Plant J. 35, 342–349 (2003).
    CAS PubMed Google Scholar
95. Ketting, R. F., Haverkamp, T. H., van Luenen, H. G. & Plasterk, R. H. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99, 133–141 (1999).
    CAS PubMed Google Scholar
96. Winston, W. M., Molodowitch, C. & Hunter, C. P. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science 295, 2456–2459 (2002).
    ADS CAS PubMed Google Scholar
97. Cogoni, C. & Macino, G. Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. Science 286, 2342–2344 (1999).
    CAS PubMed Google Scholar
98. Kidner, C. A. & Martienssen, R. A. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428, 81–84 (2004).
    ADS CAS PubMed Google Scholar

Download references