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

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.

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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.

Accession codes

Data deposits

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

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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.

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Correspondence to Yi Liu.

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Lee, H., Chang, S., 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

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