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The nuclear RNase III Drosha initiates microRNA processing

Nature volume 425, pages 415–419 (2003)Cite this article

Abstract

Hundreds of small RNAs of ∼22 nucleotides, collectively named microRNAs (miRNAs), have been discovered recently in animals and plants1,2,3,4,5,6,7,8,9,10. Although their functions are being unravelled1,2,11,12,13, their mechanism of biogenesis remains poorly understood. miRNAs are transcribed as long primary transcripts (pri-miRNAs) whose maturation occurs through sequential processing events: the nuclear processing of the pri-miRNAs into stem-loop precursors of ∼70 nucleotides (pre-miRNAs), and the cytoplasmic processing of pre-miRNAs into mature miRNAs14. Dicer, a member of the RNase III superfamily of bidentate nucleases, mediates the latter step15,16,17,18,19, whereas the processing enzyme for the former step is unknown. Here we identify another RNase III, human Drosha, as the core nuclease that executes the initiation step of miRNA processing in the nucleus. Immunopurified Drosha cleaved pri-miRNA to release pre-miRNA in vitro. Furthermore, RNA interference of Drosha resulted in the strong accumulation of pri-miRNA and the reduction of pre-miRNA and mature miRNA in vivo. Thus, the two RNase III proteins, Drosha and Dicer, may collaborate in the stepwise processing of miRNAs, and have key roles in miRNA-mediated gene regulation in processes such as development and differentiation.

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Figure 1: Cleavage sites and cis-acting requirements for the initiation step of miRNA processing.
Figure 2: In vitro processing of miRNA by Drosha.
Figure 3: In vitro processing activities of Drosha and Dicer.
Figure 4: In vivo function of Drosha.

References

  1. 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  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  3. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853–858 (2001)

    Article  ADS  CAS  Google Scholar 

  4. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001)

    Article  ADS  CAS  Google Scholar 

  5. Lee, R. C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001)

    Article  ADS  CAS  Google Scholar 

  6. Mourelatos, Z. et al. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728 (2002)

    Article  CAS  Google Scholar 

  7. Llave, C., Kasschau, K. D., Rector, M. A. & Carrington, J. C. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605–1619 (2002)

    Article  CAS  Google Scholar 

  8. Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B. & Bartel, D. P. MicroRNAs in plants. Genes Dev. 16, 1616–1626 (2002)

    Article  CAS  Google Scholar 

  9. Lagos-Quintana, M. et al. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12, 735–739 (2002)

    Article  CAS  Google Scholar 

  10. Park, W., Li, J., Song, R., Messing, J. & Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12, 1484–1495 (2002)

    Article  CAS  Google Scholar 

  11. Llave, C., Xie, Z., Kasschau, K. D. & Carrington, J. C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053–2056 (2002)

    Article  ADS  CAS  Google Scholar 

  12. Tang, G., Reinhart, B. J., Bartel, D. P. & Zamore, P. D. A biochemical framework for RNA silencing in plants. Genes Dev. 17, 49–63 (2003)

    Article  CAS  Google Scholar 

  13. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B. & Cohen, S. M. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36 (2003)

    Article  CAS  Google Scholar 

  14. 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)

    Article  CAS  Google Scholar 

  15. 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  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  Google Scholar 

  17. 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  Google Scholar 

  18. 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  Google Scholar 

  19. Knight, S. W. & Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269–2271 (2001)

    Article  ADS  CAS  Google Scholar 

  20. Zeng, Y. & Cullen, B. R. Sequence requirements for micro RNA processing and function in human cells. RNA 9, 112–123 (2003)

    Article  CAS  Google Scholar 

  21. 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  Google Scholar 

  22. Zamore, P. D. Thirty-three years later, a glimpse at the ribonuclease III active site. Mol. Cell 8, 1158–1160 (2001)

    Article  CAS  Google Scholar 

  23. 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  Google Scholar 

  24. Fortin, K. R., Nicholson, R. H. & Nicholson, A. W. Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location. BMC Genomics 3, 26 (2002)

    Article  Google Scholar 

  25. Koc, E. C. et al. The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present. J. Biol. Chem. 276, 43958–43969 (2001)

    Article  CAS  Google Scholar 

  26. Billy, E., Brondani, V., Zhang, H., Muller, U. & Filipowicz, W. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc. Natl Acad. Sci. USA 98, 14428–14433 (2001)

    Article  ADS  CAS  Google Scholar 

  27. Provost, P. et al. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21, 5864–5874 (2002)

    Article  CAS  Google Scholar 

  28. Wu, H., Xu, H., Miraglia, L. J. & Crooke, S. T. Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J. Biol. Chem. 275, 36957–36965 (2000)

    Article  CAS  Google Scholar 

  29. Zeng, Y., Wagner, E. J. & Cullen, B. R. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell 9, 1327–1333 (2002)

    Article  CAS  Google Scholar 

  30. Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to members of our laboratory and to K. Mitrophanous, J. M. Park and H. E. Kim for their critical reading of this manuscript and for discussion. This work was supported by the Korea Research Foundation and the BK21 Research Fellowship from the Ministry of Education and Human Resources Development of Korea.

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Authors and Affiliations

  1. Institute of Molecular Biology and Genetics and School of Biological Sciences, Seoul National University, 151-742, Seoul, Korea

    Yoontae Lee, Chiyoung Ahn, Jinju Han, Hyounjeong Choi, Jaekwang Kim, Jeongbin Yim, Sunyoung Kim & V. Narry Kim

  2. Department of Biology, Yonsei University, 120-749, Seoul, Korea

    Junho Lee

  3. Centre de Recherche en Rhumatologie et Immunologie, Centre de Recherche du CHUL, Ste-Foy, Quebec, G1V 4G2, Canada

    Patrick Provost

  4. Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 77, Stockholm, Sweden

    Olof Rådmark

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Correspondence to V. Narry Kim.

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Lee, Y., Ahn, C., Han, J. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003). https://doi.org/10.1038/nature01957

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