Role for a bidentate ribonuclease in the initiation step of RNA interference (original) (raw)

Nature volume 409, pages 363–366 (2001)Cite this article

Abstract

RNA interference (RNAi) is the mechanism through which double-stranded RNAs silence cognate genes1,2,3,4,5. In plants, this can occur at both the transcriptional and the post-transcriptional levels1,2,5; however, in animals, only post-transcriptional RNAi has been reported to date. In both plants and animals, RNAi is characterized by the presence of RNAs of about 22 nucleotides in length that are homologous to the gene that is being suppressed6,7,8. These 22-nucleotide sequences serve as guide sequences that instruct a multicomponent nuclease, RISC, to destroy specific messenger RNAs6. Here we identify an enzyme, Dicer, which can produce putative guide RNAs. Dicer is a member of the RNase III family of nucleases that specifically cleave double-stranded RNAs, and is evolutionarily conserved in worms, flies, plants, fungi and mammals. The enzyme has a distinctive structure, which includes a helicase domain and dual RNase III motifs. Dicer also contains a region of homology to the RDE1/QDE2/ARGONAUTE family that has been genetically linked to RNAi9,10.

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References

  1. Baulcombe, D. C. RNA as a target and an initiator of post-transcriptional gene silencing in transgenic plants. Plant Mol. Biol. 32, 79–88 (1996).
    Article CAS PubMed Google Scholar
  2. Wassenegger, M. & Pelissier, T. A model for RNA-mediated gene silencing in higher plants. Plant Mol. Biol. 37, 349–62 ( 1998).
    Article CAS PubMed Google Scholar
  3. Montgomery, M. K. & Fire, A. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet. 14, 255–258 (1998).
    Article CAS PubMed Google Scholar
  4. Sharp, P. A. RNAi and double-strand RNA. Genes Dev. 13, 139–141 (1999).
    Article CAS PubMed Google Scholar
  5. Sijen, T. & Kooter, J. M. Post-transcriptional gene-silencing: RNAs on the attack or on the defense? BioEssays 22, 520–531 (2000).
    Article CAS PubMed Google Scholar
  6. 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 ADS CAS PubMed Google Scholar
  7. Hamilton, A. J. & Baulcombe, D. C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286, 950–952 ( 1999).
    Article CAS PubMed Google Scholar
  8. Zamore, P. D., Tuschl, T., Sharp, P. A. & Bartel, D. P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25–33 (2000).
    Article CAS PubMed Google Scholar
  9. 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
  10. Catalanotto, C., Azzalin, G., Macino, G. & Cogoni, C. Gene silencing in worms and fungi. Nature 404, 245 (2000).
    Article ADS CAS PubMed Google Scholar
  11. Tuschl, T., Zamore, P. D., Lehmann, R., Bartel, D. P. & Sharp, P. A. Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev. 13, 3191 –3197 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  12. Nicholson, A. W. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol. Rev. 23, 371–390 (1999).
    Article CAS PubMed Google Scholar
  13. Filippov, V., Solovyev, V., Filippova, M. & Gill, S. S. A novel type of RNase III family proteins in eukaryotes. Gene 245, 213–221 (2000).
    Article CAS PubMed Google Scholar
  14. Bass, B. L. Double-stranded RNA as a template for gene silencing. Cell 101, 235–238 (2000).
    Article CAS PubMed Google Scholar
  15. Gillespie, D. E. & Berg, C. A. Homeless is required for RNA localization in Drosophila oogenesis and encodes a new member of the DE-H family of RNA-dependent ATPases. Genes Dev. 9, 2495–2508 (1995).
    Article CAS PubMed Google Scholar
  16. 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
  17. Matsuda, S. et al. Molecular cloning and characterization of a novel human gene (HERNA) which encodes a putative RNA-helicase. Biochim. Biophys. Acta 1490, 163–169 ( 2000).
    Article CAS PubMed Google Scholar
  18. Wianny, F. & Zernicka-Goetz, M. Specific interference with gene function by double-stranded RNA in early mouse development. Nature Cell Biol. 2, 70–75 (2000).
    Article CAS PubMed Google Scholar
  19. Sonnhammer, E. L., Eddy, S. R. & Durbin, R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins Struct. Funct. Genet. 28, 405–420 (1997).
    Article CAS PubMed Google Scholar
  20. 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
  21. 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
  22. Yang, D., Lu, H. & Erickson, J. W. Evidence that processed small dsRNAs may mediate sequence-specific mRNA degradation during RNAi in Drosophila embryos. Curr. Biol. 10, 1191–1200 ( 2000).
    Article CAS PubMed Google Scholar
  23. Fagard, M., Bouter, 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).
    Article ADS CAS PubMed PubMed Central Google Scholar

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Acknowledgements

We thank A. Nicholson for his gift of purified RNase III, and P. Fisher, M. McConnel and M. Pang for providing aid and materials for large-scale fly embryo culture. The Homeless clone was a gift from D. E. Gillespie and C. A. Berg. We also thank R. Kobayashi and R. Martiennsen for discussion and critical reading of the manuscript, and K. Velinzon for FACS. A.A.C. is an Anderson Fellow of the Watson School of Biological Sciences and a Predoctoral Fellow of the Howard Hughes Medical Institute. S.M.H. is a visiting scientist from Genetica, (Cambridge, MA). G.J.H. is a Pew Scholar in the biomedical sciences. This work was supported in part by grants from the NIH (G.J.H.).

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Authors and Affiliations

  1. Cold Spring Harbor Laboratory,
    Emily Bernstein, Amy A. Caudy, Scott M. Hammond & Gregory J. Hannon
  2. Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, 11724, New York, USA
    Amy A. Caudy
  3. Graduate Program in Genetics, State University of New York at Stony Brook, Stony Brook, 11794, New York, USA
    Emily Bernstein
  4. Genetica, 1 Kendall Square, Building 600, Cambridge, 01239, Massachusetts, USA
    Scott M. Hammond

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  1. Emily Bernstein
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  2. Amy A. Caudy
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  3. Scott M. Hammond
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  4. Gregory J. Hannon
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Bernstein, E., Caudy, A., Hammond, S. et al. Role for a bidentate ribonuclease in the initiation step of RNA interference .Nature 409, 363–366 (2001). https://doi.org/10.1038/35053110

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