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:

qiRNA is a new type of small interfering RNA induced by DNA damage

Nature volume 459, pages 274–277 (2009)Cite this article

Abstract

RNA interference pathways use small RNAs to mediate gene silencing in eukaryotes. In addition to small interfering RNAs (siRNAs) and microRNAs, several types of endogenously produced small RNAs have important roles in gene regulation, germ cell maintenance and transposon silencing1,2,3,4. The production of some of these RNAs requires the synthesis of aberrant RNAs (aRNAs) or pre-siRNAs, which are specifically recognized by RNA-dependent RNA polymerases to make double-stranded RNA. The mechanism for aRNA synthesis and recognition is largely unknown. Here we show that DNA damage induces the expression of the Argonaute protein QDE-2 and a new class of small RNAs in the filamentous fungus Neurospora crassa. This class of small RNAs, known as qiRNAs because of their interaction with QDE-2, are about 20–21 nucleotides long (several nucleotides shorter than Neurospora siRNAs), with a strong preference for uridine at the 5′ end, and originate mostly from the ribosomal DNA locus. The production of qiRNAs requires the RNA-dependent RNA polymerase QDE-1, the Werner and Bloom RecQ DNA helicase homologue QDE-3 and dicers. qiRNA biogenesis also requires DNA-damage-induced aRNAs as precursors, a process that is dependent on both QDE-1 and QDE-3. Notably, our results suggest that QDE-1 is the DNA-dependent RNA polymerase that produces aRNAs. Furthermore, the Neurospora RNA interference mutants show increased sensitivity to DNA damage, suggesting a role for qiRNAs in the DNA-damage response by inhibiting protein translation.

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: DNA damage induces QDE-2 expression.
Figure 2: DNA damage results in the production of qiRNAs and aRNAs.
Figure 3: QDE-1 is required for the synthesis of DNA-damage-induced rDNA-specific aRNA and exhibits DdRP activity using an ssDNA template.
Figure 4: The role of qiRNA in the DNA-damage response.

Similar content being viewed by others

Accession codes

Data deposits

The Neurospora rDNA sequence has been deposited in GenBank under accession FJ360521.

References

  1. Ghildiyal, M. & Zamore, P. D. Small silencing RNAs: an expanding universe. Nature Rev. Genet. 10, 94–108 (2009)

    Article  CAS  Google Scholar 

  2. Tomari, Y. & Zamore, P. D. Perspective: machines for RNAi. Genes Dev. 19, 517–529 (2005)

    Article  CAS  Google Scholar 

  3. Hannon, G. J. RNA interference. Nature 418, 244–251 (2002)

    Article  ADS  CAS  Google Scholar 

  4. Buhler, M. & Moazed, D. Transcription and RNAi in heterochromatic gene silencing. Nature Struct. Mol. Biol. 14, 1041–1048 (2007)

    Article  Google Scholar 

  5. Catalanotto, C., Nolan, T. & Cogoni, C. Homology effects in Neurospora crassa . FEMS Microbiol. Lett. 254, 182–189 (2006)

    Article  CAS  Google Scholar 

  6. Cogoni, C. & Macino, G. Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. Science 286, 2342–2344 (1999)

    Article  CAS  Google Scholar 

  7. Cogoni, C. & Macino, G. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399, 166–169 (1999)

    Article  ADS  CAS  Google Scholar 

  8. Catalanotto, C. et al. Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa . Mol. Cell. Biol. 24, 2536–2545 (2004)

    Article  CAS  Google Scholar 

  9. Catalanotto, C., Azzalin, G., Macino, G. & Cogoni, C. Involvement of small RNAs and role of the qde genes in the gene silencing pathway in Neurospora . Genes Dev. 16, 790–795 (2002)

    Article  CAS  Google Scholar 

  10. Catalanotto, C., Azzalin, G., Macino, G. & Cogoni, C. Gene silencing in worms and fungi. Nature 404, 245 (2000)

    Article  ADS  CAS  Google Scholar 

  11. Maiti, M., Lee, H. C. & Liu, Y. QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands. Genes Dev. 21, 590–600 (2007)

    Article  CAS  Google Scholar 

  12. Choudhary, S. et al. A double-stranded-RNA response program important for RNA interference efficiency. Mol. Cell. Biol. 27, 3995–4005 (2007)

    Article  CAS  Google Scholar 

  13. Howard, C. A. & Baker, T. I. Relationship of histidine sensitivity to DNA damage and stress induced responses in mutagen sensitive mutants of Neurospora crassa . Curr. Genet. 13, 391–399 (1988)

    Article  CAS  Google Scholar 

  14. Srivastava, V. K., Pall, M. L. & Schroeder, A. L. Deoxyribonucleoside triphosphate pools in Neurospora crassa: effects of histidine and hydroxyurea. Mutat. Res. 200, 45–53 (1988)

    Article  CAS  Google Scholar 

  15. Lin, H. piRNAs in the germ line. Science 316, 397 (2007)

    Article  ADS  CAS  Google Scholar 

  16. Salgado, P. S. et al. The structure of an RNAi polymerase links RNA silencing and transcription. PLoS Biol. 4, e434 (2006)

    Article  Google Scholar 

  17. Sancar, A., Lindsey-Boltz, L. A., Unsal-Kacmaz, K. & Linn, S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 73, 39–85 (2004)

    Article  CAS  Google Scholar 

  18. Calabrese, J. M. & Sharp, P. A. Characterization of the short RNAs bound by the P19 suppressor of RNA silencing in mouse embryonic stem cells. RNA 12, 2092–2102 (2006)

    Article  CAS  Google Scholar 

  19. Pontes, O. et al. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126, 79–92 (2006)

    Article  CAS  Google Scholar 

  20. Peng, J. C. & Karpen, G. H. H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nature Cell Biol. 9, 25–35 (2007)

    Article  CAS  Google Scholar 

  21. Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363–367 (2006)

    Article  ADS  CAS  Google Scholar 

  22. Kato, H. et al. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309, 467–469 (2005)

    Article  ADS  CAS  Google Scholar 

  23. Djupedal, I. et al. RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev. 19, 2301–2306 (2005)

    Article  CAS  Google Scholar 

  24. Herr, A. J., Jensen, M. B., Dalmay, T. & Baulcombe, D. C. RNA polymerase IV directs silencing of endogenous DNA. Science 308, 118–120 (2005)

    Article  ADS  CAS  Google Scholar 

  25. Onodera, Y. et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613–622 (2005)

    Article  CAS  Google Scholar 

  26. Nolan, T. et al. The RNA-dependent RNA polymerase essential for post-transcriptional gene silencing in Neurospora crassa interacts with replication protein A. Nucleic Acids Res. 36, 532–538 (2008)

    Article  ADS  CAS  Google Scholar 

  27. Curaba, J. & Chen, X. Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6. J. Biol. Chem. 283, 3059–3066 (2008)

    Article  CAS  Google Scholar 

  28. 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 

  29. Chary, P., Dillon, D., Schroeder, A. L. & Natvig, D. O. Superoxide dismutase (sod-1) null mutants of Neurospora crassa: oxidative stress sensitivity, spontaneous mutation rate and response to mutagens. Genetics 137, 723–730 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Makeyev, E. V. & Bamford, D. H. Replicase activity of purified recombinant protein P2 of double-stranded RNA bacteriophage φ6. EMBO J. 19, 124–133 (2000)

    Article  CAS  Google Scholar 

  31. Makeyev, E. V. & Bamford, D. H. Cellular RNA-dependent RNA polymerase involved in posttranscriptional gene silencing has two distinct activity modes. Mol. Cell 10, 1417–1427 (2002)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank L. Wang and H. Yuan for technical assistance, and C. Tang for critical comments on the manuscript. We thank Q. Liu and X. Liu for assistance in small RNA cloning, and E. Selker for providing an rDNA plasmid. The work was supported by funds from the Welch Foundation and the National Institutes of Health (NIH) to Y.L. and the Academy of Finland Finnish Centre of Excellence Programme 2006-2011 (1213467, 1213992) to D.H.B. A.P.A. is a fellow of the Helsinki Graduate School in Biotechnology and Molecular Biology.

Author Contributions H.-C.L. conceived the research and conducted experiments with S.-S.C., S.C., A.P.A. and M.M. Y.L. conceived and oversaw the project, and wrote the paper. D.H.B. helped analyse data and contributed ideas. All authors discussed the results and edited the manuscript.

Author information

Author notes

  1. Mekhala Maiti

    Present address: Present address: Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.,

Authors and Affiliations

  1. Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA,

    Heng-Chi Lee, Shwu-Shin Chang, Swati Choudhary, Mekhala Maiti & Yi Liu

  2. Institute of Biotechnology and Department of Biological and Environmental Sciences, Biocenter 2, PO Box 56, FIN-00014 University of Helsinki, Helsinki, Finland

    Antti P. Aalto & Dennis H. Bamford

Authors
  1. Heng-Chi Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shwu-Shin Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Swati Choudhary
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Antti P. Aalto
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mekhala Maiti
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dennis H. Bamford
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yi Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yi Liu.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S6 with Legends and Supplementary Table 1. (PDF 896 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lee, HC., Chang, SS., Choudhary, S. et al. qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459, 274–277 (2009). https://doi.org/10.1038/nature08041

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08041

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