Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Processing of primary microRNAs by the Microprocessor complex

Abstract

Mature microRNAs (miRNAs) are generated via a two-step processing pathway to yield 22-nucleotide small RNAs that regulate gene expression at the post-transcriptional level1. Initial cleavage is catalysed by Drosha, a nuclease of the RNase III family, which acts on primary miRNA transcripts (pri-miRNAs) in the nucleus2. Here we show that Drosha exists in a multiprotein complex, the Microprocessor, and begin the process of deconstructing that complex into its constituent components. Along with Drosha, the Microprocessor also contains Pasha (partner of Drosha), a double-stranded RNA binding protein. Suppression of Pasha expression in Drosophila cells or Caenorhabditis elegans interferes with pri-miRNA processing, leading to an accumulation of pri-miRNAs and a reduction in mature miRNAs. Finally, depletion or mutation of pash-1 in C. elegans causes de-repression of a let-7 reporter and the appearance of phenotypic defects overlapping those observed upon examination of worms with lesions in Dicer (dcr-1) or Drosha (drsh-1). Considered together, these results indicate a role for Pasha in miRNA maturation and miRNA-mediated gene regulation.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Pri-miRNA processing is conserved in Drosophila.
Figure 2: Pasha, a nuclear dsRNA binding domain (dsRBD) protein, associates with Drosha.
Figure 3: Drosha and Pasha co-exist in a Microprocessor complex.
Figure 4: Depletion of Pasha reduces pri-miRNA processing.

Similar content being viewed by others

References

  1. 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 

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

    Article  ADS  CAS  Google Scholar 

  3. Carrington, J. C. & Ambros, V. Role of microRNAs in plant and animal development. Science 301, 336–338 (2003)

    Article  ADS  CAS  Google Scholar 

  4. 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)

    Article  CAS  Google Scholar 

  5. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004)

    Article  ADS  CAS  Google Scholar 

  6. Bohnsack, M. T., Czaplinski, K. & Gorlich, D. Exportin-5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10, 185–191 (2004)

    Article  CAS  Google Scholar 

  7. 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 

  8. 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 

  9. 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 

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

    Article  CAS  Google Scholar 

  11. Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. & Filipowicz, W. Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57–68 (2004)

    Article  CAS  Google Scholar 

  12. Siolas, D. et al. Synthetic shRNAs as highly potent RNAi triggers. Nature Biotechnol. (submitted)

  13. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003)

    Article  CAS  Google Scholar 

  14. 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 

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

    Article  ADS  CAS  Google Scholar 

  16. 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)

    Article  CAS  Google Scholar 

  17. 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 

  18. Doench, J. G., Petersen, C. P. & Sharp, P. A. siRNAs can function as miRNAs. Genes Dev. 17, 438–442 (2003)

    Article  CAS  Google Scholar 

  19. 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 

  20. 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 

  21. Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736 (2003)

    Article  ADS  CAS  Google Scholar 

  22. Shiohama, A., Sasaki, T., Noda, S., Minoshima, S. & Shimizu, N. Molecular cloning and expression analysis of a novel gene DGCR8 located in the DiGeorge syndrome chromosomal region. Biochem. Biophys. Res. Commun. 304, 184–190 (2003)

    Article  CAS  Google Scholar 

  23. 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 

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

    Article  ADS  CAS  Google Scholar 

  25. Gregory, R. I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature doi:10.1038/nature03120 (this issue)

  26. 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)

    Article  ADS  CAS  Google Scholar 

  27. Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921–1925 (2003)

    Article  ADS  CAS  Google Scholar 

  28. 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)

    Article  CAS  Google Scholar 

  29. 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  Google Scholar 

  30. Spector, D. L. & Smith, H. C. Redistribution of U-snRNPs during mitosis. Exp. Cell Res. 163, 87–94 (1986)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank F. Rivas for critical reading of the manuscript. Strain BC3825 was obtained from the C. elegans Genetics Center, and drsh-1(tm0654) was obtained from the NBP in Japan (Mitani laboratory). We thank E. Cuppen and his group for help in target-selected mutagenesis. A.M.D. is a David Koch Fellow of the Watson School of Biological Sciences. G.J.H. is supported by an Innovator Award from the US Army Breast Cancer Research Program. This work was also supported by a grant from the NIH (G.J.H.) and by a VENI fellowship from the Netherlands Organisation for Scientific Research (R.F.K.).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gregory J. Hannon.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Denli, A., Tops, B., Plasterk, R. et al. Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235 (2004). https://doi.org/10.1038/nature03049

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature03049

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing