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:

An endogenous small interfering RNA pathway in Drosophila

Nature volume 453, pages 798–802 (2008)Cite this article

Abstract

Drosophila endogenous small RNAs are categorized according to their mechanisms of biogenesis and the Argonaute protein to which they bind. MicroRNAs are a class of ubiquitously expressed RNAs of ∼22 nucleotides in length, which arise from structured precursors through the action of Drosha–Pasha and Dicer-1–Loquacious complexes1,2,3,4,5,6,7. These join Argonaute-1 to regulate gene expression8,9. A second endogenous small RNA class, the Piwi-interacting RNAs, bind Piwi proteins and suppress transposons10,11. Piwi-interacting RNAs are restricted to the gonad, and at least a subset of these arises by Piwi-catalysed cleavage of single-stranded RNAs12,13. Here we show that Drosophila generates a third small RNA class, endogenous small interfering RNAs, in both gonadal and somatic tissues. Production of these RNAs requires Dicer-2, but a subset depends preferentially on Loquacious1,4,5 rather than the canonical Dicer-2 partner, R2D2 (ref. 14). Endogenous small interfering RNAs arise both from convergent transcription units and from structured genomic loci in a tissue-specific fashion. They predominantly join Argonaute-2 and have the capacity, as a class, to target both protein-coding genes and mobile elements. These observations expand the repertoire of small RNAs in Drosophila, adding a class that blurs distinctions based on known biogenesis mechanisms and functional roles.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: AGO2 binds endogenous small RNAs.
Figure 2: A subset of endo-siRNAs originates from transposons.
Figure 3: Two types of genic endo-siRNA loci in Drosophila.
Figure 4: Genetic requirements for siRNA biogenesis.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

Small RNA sequences were deposited in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE11086.

References

  1. Forstemann, K. et al. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3, e236 (2005)

    Article  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. 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  ADS  CAS  Google Scholar 

  4. Saito, K., Ishizuka, A., Siomi, H. & Siomi, M. C. Processing of pre-microRNAs by the Dicer-1–Loquacious complex in Drosophila cells. PLoS Biol. 3, e235 (2005)

    Article  Google Scholar 

  5. Jiang, F. et al. Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila . Genes Dev. 19, 1674–1679 (2005)

    Article  CAS  Google Scholar 

  6. 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)

    Article  CAS  Google Scholar 

  7. 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)

    ADS  CAS  Google Scholar 

  8. Eulalio, A., Huntzinger, E. & Izaurralde, E. Getting to the root of miRNA-mediated gene silencing. Cell 132, 9–14 (2008)

    Article  CAS  Google Scholar 

  9. Bushati, N. & Cohen, S. M. microRNA functions. Annu. Rev. Cell Dev. Biol. 23, 175–205 (2007)

    Article  CAS  Google Scholar 

  10. Aravin, A. A., Hannon, G. J. & Brennecke, J. The Piwi–piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761–764 (2007)

    Article  ADS  CAS  Google Scholar 

  11. Klattenhoff, C. & Theurkauf, W. Biogenesis and germline functions of piRNAs. Development 135, 3–9 (2008)

    Article  CAS  Google Scholar 

  12. Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila . Cell 128, 1089–1103 (2007)

    Article  CAS  Google Scholar 

  13. Gunawardane, L. S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila . Science 315, 1587–1590 (2007)

    Article  ADS  CAS  Google Scholar 

  14. 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 

  15. Ruby, J. G. et al. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17, 1850–1864 (2007)

    Article  CAS  Google Scholar 

  16. Galiana-Arnoux, D., Dostert, C., Schneemann, A., Hoffmann, J. A. & Imler, J. L. Essential function in vivo for Dicer-2 in host defense against RNA viruses in Drosophila . Nature Immunol. 7, 590–597 (2006)

    Article  CAS  Google Scholar 

  17. Wang, X. H. et al. RNA interference directs innate immunity against viruses in adult Drosophila . Science 312, 452–454 (2006)

    Article  ADS  CAS  Google Scholar 

  18. 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  Google Scholar 

  19. Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006)

    Article  ADS  CAS  Google Scholar 

  20. Rehwinkel, J. et al. Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster . Mol. Cell. Biol. 26, 2965–2975 (2006)

    Article  CAS  Google Scholar 

  21. Allen, E., Xie, Z., Gustafson, A. M. & Carrington, J. C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207–221 (2005)

    Article  CAS  Google Scholar 

  22. Tomari, Y., Du, T. & Zamore, P. D. Sorting of Drosophila small silencing RNAs. Cell 130, 299–308 (2007)

    Article  CAS  Google Scholar 

  23. Forstemann, K., Horwich, M. D., Wee, L., Tomari, Y. & Zamore, P. D. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by Dicer-1. Cell 130, 287–297 (2007)

    Article  Google Scholar 

  24. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans . Cell 127, 1193–1207 (2006)

    Article  CAS  Google Scholar 

  25. Sijen, T., Steiner, F. A., Thijssen, K. L. & Plasterk, R. H. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315, 244–247 (2007)

    Article  ADS  CAS  Google Scholar 

  26. Pak, J. & Fire, A. Distinct populations of primary and secondary effectors during RNAi in C. elegans . Science 315, 241–244 (2007)

    Article  ADS  CAS  Google Scholar 

  27. Yigit, E. et al. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 127, 747–757 (2006)

    Article  CAS  Google Scholar 

  28. Tam, O. H. et al. Pseudogene-derived siRNAs regulate gene expression in mouse oocytes. Nature advance online publication, 10.1038/nature06904 (10 April 2008)

  29. Watanabe, T. et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature advance online publication, 10.1038/nature06908 (10 April 2008)

  30. 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)

    Article  CAS  Google Scholar 

  31. Stark, A. et al. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17, 1865–1879 (2007)

    Article  CAS  Google Scholar 

  32. Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank R. Carthew, H. Siomi, P. Zamore and D. Smith for reagents. We are grateful to M. Rooks, E. Hodges and D. McCombie for help with deep sequencing. B.C. was supported by the German Academic Exchange Service. C.D.M. is a Beckman fellow of the Watson School of Biological Sciences and is supported by an NSF Graduate Research Fellowship. R.Z. is a Special Fellow of the Leukemia and Lymphoma Society. M.D. is an Engelhorn fellow of the Watson School of Biological Sciences. J.B. is supported by the Ernst Schering foundation. A.S. is supported by an HFSP fellowship. This work was supported in part from grants from the NIH to G.J.H. and N.P. and a gift from K. W. Davis (G.J.H.).

Author information

Author notes

  1. Benjamin Czech and Colin D. Malone: These authors contributed equally to this work.

Authors and Affiliations

  1. Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA ,

    Benjamin Czech, Colin D. Malone, Catherine Schlingeheyde, Monica Dus, Ravi Sachidanandam, Gregory J. Hannon & Julius Brennecke

  2. Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA,

    Rui Zhou & Norbert Perrimon

  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA ,

    Alexander Stark & Manolis Kellis

  4. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA ,

    Alexander Stark

  5. Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA,

    James A. Wohlschlegel

Authors
  1. Benjamin Czech
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Colin D. Malone
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rui Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alexander Stark
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Catherine Schlingeheyde
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Monica Dus
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Norbert Perrimon
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Manolis Kellis
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. James A. Wohlschlegel
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Ravi Sachidanandam
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Gregory J. Hannon
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Julius Brennecke
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Gregory J. Hannon or Julius Brennecke.

Supplementary information

Supplementary Information

The file contains Supplementary Methods, Supplementary Tables S1-S2, Supplementary Figures S1-S13 and additional references. (PDF 1479 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Czech, B., Malone, C., Zhou, R. et al. An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798–802 (2008). https://doi.org/10.1038/nature07007

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07007

This article is cited by

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

Advanced 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