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RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway

Nature Structural & Molecular Biology volume 24, pages 258269 (2017) | Download Citation

Abstract

Expression of rRNA affects cell growth and proliferation, but mechanisms that modulate rRNA levels are poorly understood. We conducted a genetic screen for factors that negatively regulate generation of endogenous short interfering RNA (endo-siRNA) in Caenorhabditis elegans and identified a suppressor of siRNA (susi-1) and antisense ribosomal siRNAs (risiRNAs). risiRNAs show sequence complementary to 18S and 26S rRNAs and require RNA-dependent RNA polymerases (RdRPs) for their production. They act through the nuclear RNA interference (RNAi) pathway to downregulate pre-rRNA. Stress stimuli, including low temperature and UV irradiation, induced the accumulation of risiRNAs. SUSI-1 is a homolog of the human DIS3L2 exonuclease involved in 3′–5′ degradation of oligouridylated RNAs. In susi-1 mutant and in low temperature-treated animals, 3′-tail oligouridylated 26S rRNA accumulated. The injection of oligouridylated rRNA elicited nuclear accumulation of NRDE-3. Our findings identify a new subset of 22G-RNAs that regulate pre-rRNA expression and a mechanism to maintain rRNA homeostasis.

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Acknowledgements

We are grateful to S. Kenney, X. Fu, B. Buckley, X. Liu, B. Dong, C. Liu and members of S.G.'s lab for their comments. We are grateful to the Caenorhabditis Genetics Center (CGC), the International C. elegans Gene Knockout Consortium and the National Bioresource Project for providing the strains. A. Fire (Stanford University) provided HT115 bacteria expressing the empty vector L4440. This work was supported by grants from the National Natural Science Foundation of China (31371323, 31671346, 91640110 and 81501329), the Fundamental Research Funds for Central Universities (WK2060190018 and WK2070000034) and KJZD-EW-L01-2 to S.G.

Author information

Author notes

    • Xufei Zhou
    •  & Xuezhu Feng

    These authors contributed equally to this work.

Affiliations

  1. School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Hefei, China.

    • Xufei Zhou
    • , Xuezhu Feng
    • , Hui Mao
    • , Mu Li
    • , Fei Xu
    • , Kai Hu
    •  & Shouhong Guang

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Contributions

X.Z. constructed the transgenes and generated Figures 3,4,5,6,7, Supplementary Figures 3, 4 and 6 and Supplementary Tables 1 and 3. X.F. conducted the genetic screening, identified risiRNA, mapped susi-1 and contributed to Figures 1, 2 and 8, Supplementary Figures 2, 5, 7 and 8 and Supplementary Table 2. H.M. contributed to Figure 8 and Supplementary Figure 8. M.L., F.X. and K.H. contributed to Figure 3b,e. X.Z., X.F. and S.G. designed the project and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Shouhong Guang.

Integrated supplementary information

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8 and Supplementary Tables 1–5

  2. 2.

    Supplementary Data Set 1

    NRDE-3 reassociates with siRNAs in susi-1 mutant.

  3. 3.

    Supplementary Data Set 2

    NRDE-3 reassociates with siRNAs after 50 mJ/cm2 UV irradiation.

  4. 4.

    Supplementary Data Set 3

    Biochemical analysis of risiRNA.

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DOI

https://doi.org/10.1038/nsmb.3376