The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs


In contrast to microRNAs and Piwi-associated RNAs, short interfering RNAs (siRNAs) are seemingly dispensable for host-directed gene regulation in Drosophila. This notion is based on the fact that mutants lacking the core siRNA-generating enzyme Dicer-2 or the predominant siRNA effector Argonaute 2 are viable, fertile and of relatively normal morphology1,2. Moreover, endogenous Drosophila siRNAs have not yet been identified. Here we report that siRNAs derived from long hairpin RNA genes (hpRNAs) programme Slicer complexes that can repress endogenous target transcripts. The Drosophila hpRNA pathway is a hybrid mechanism that combines canonical RNA interference factors (Dicer-2, Hen1 (known as CG12367) and Argonaute 2) with a canonical microRNA factor (Loquacious) to generate 21-nucleotide siRNAs. These novel regulatory RNAs reveal unexpected complexity in the sorting of small RNAs, and open a window onto the biological usage of endogenous RNA interference in Drosophila.

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Figure 1: Examples of Drosophila hpRNA transcripts.
Figure 2: Distinct biogenesis pathways for miRNAs and hpRNAs.
Figure 3: hpRNAs generate regulatory RNAs that can repress endogenous targets.

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Gene Expression Omnibus

Data deposits

The imaginal disc/brain sample described in paper has been deposited in the NCBI GEO under accession number GSM275691.


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We are grateful to R. Carthew, Q. Liu, H. Siomi and S. Cohen for plasmids and Drosophila strains. K.O. was supported by the Charles H. Revson Foundation. H.G. was supported by A*STAR, Singapore. D.P.B. is an HHMI investigator, and work in his laboratory was supported by a grant from the NIH (GM067031). E.C.L. was supported by grants from the Leukemia and Lymphoma Foundation, the Burroughs Wellcome Foundation, the V Foundation for Cancer Research, the Sidney Kimmel Foundation for Cancer Research, and the NIH (GM083300).

Author Contributions J.G.R. identified hp-CG4068 and hpRNA1. W.-J.C. performed the EINVERTED analysis and identified the additional hpRNA loci and their targets. H.G. performed initial hpRNA northern analysis; all other experiments were designed and carried out by K.O. All authors contributed to the preparation of the manuscript.

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Correspondence to Eric C. Lai.

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Okamura, K., Chung, WJ., Ruby, J. et al. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453, 803–806 (2008).

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