Skip to main content

Thank you for visiting 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.

Two classes of silencing RNAs move between Caenorhabditis elegans tissues


Organism-wide RNA interference (RNAi) is due to the transport of mobile silencing RNA throughout the organism, but the identities of these mobile RNA species in animals are unknown. Here, we present genetic evidence that both the initial double-stranded RNA (dsRNA), which triggers RNAi, and at least one dsRNA intermediate produced during RNAi can act as or generate mobile silencing RNA in C. elegans. This dsRNA intermediate requires the long dsRNA-binding protein RDE-4, the endonuclease DCR-1, which cleaves long dsRNA into double-stranded short-interfering RNA (ds-siRNA), and the putative nucleotidyltransferase MUT-2 (RDE-3). However, single-stranded siRNA and downstream secondary siRNA produced upon amplification by the RNA-dependent RNA polymerase RRF-1 do not generate mobile silencing RNA. Restricting intertissue transport to long dsRNA and directly processed siRNA intermediates rather than amplified siRNA may serve to modulate the extent of systemic silencing in proportion to available dsRNA.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: RNAi-independent biogenesis of mobile RNA from expressed dsRNA.
Figure 2: Restricted expression of RDE-4 and MUT-2 but not RDE-1 enables non–cell-autonomous RNA silencing.
Figure 3: RDE-4- and MUT-2- but not RDE-1–processed ingested dsRNA is mobile.
Figure 4: Biogenesis of mobile RNA in C. elegans.


  1. Jose, A.M. & Hunter, C.P. Transport of sequence-specific RNA interference information between cells. Annu. Rev. Genet. 41, 305–330 (2007).

    CAS  Article  Google Scholar 

  2. Molnar, A. et al. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328, 872–875 (2010).

    CAS  Article  Google Scholar 

  3. Dunoyer, P. et al. Small RNA duplexes function as mobile silencing signals between plant cells. Science 328, 912–916 (2010).

    CAS  Article  Google Scholar 

  4. Dunoyer, P. et al. An endogenous, systemic RNAi pathway in plants. EMBO J. 29, 1699–1712 (2010).

    CAS  Article  Google Scholar 

  5. Winston, W.M., Molodowitch, C. & Hunter, C.P. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science 295, 2456–2459 (2002).

    CAS  Article  Google Scholar 

  6. Feinberg, E.H. & Hunter, C.P. Transport of dsRNA into cells by the transmembrane protein SID-1. Science 301, 1545–1547 (2003).

    CAS  Article  Google Scholar 

  7. Wolfrum, C. et al. Mechanisms and optimization of in vivo delivery of lipophlic siRNAs. Nat. Biotechnol. 25, 1149–1157 (2007).

    CAS  Article  Google Scholar 

  8. Jose, A.M., Smith, J.J. & Hunter, C.P. Export of RNA silencing from C. elegans tissues does not require the RNA channel SID-1. Proc. Natl. Acad. Sci. USA 106, 2283–2288 (2009).

    CAS  Article  Google Scholar 

  9. Faghihi, M.A. & Wahlestedt, C. Regulatory roles of natural antisense transcripts. Nat. Rev. Mol. Cell Biol. 10, 637–643 (2009).

    CAS  Article  Google Scholar 

  10. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).

    CAS  Article  Google Scholar 

  11. Grishok, A. RNAi mechanisms in Caenorhabditis elegans. FEBS Lett. 579, 5932–5939 (2005).

    CAS  Article  Google Scholar 

  12. Aoki, K., Moriguchi, H., Yoshioka, T., Okawa, K. & Tabara, H. In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J. 26, 5007–5019 (2007).

    CAS  Article  Google Scholar 

  13. Steiner, F.A., Okihara, K.L., Hoogstrate, S.W., Sijen, T. & Ketting, R.F. RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans. Nat. Struct. Mol. Biol. 16, 207–211 (2009).

    CAS  Article  Google Scholar 

  14. Chen, C.C. et al. A member of the polymerase beta nucleotidyltransferase superfamily is required for RNA interference in C. elegans. Curr. Biol. 15, 378–383 (2005).

    CAS  Article  Google Scholar 

  15. Moazed, D. et al. Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harb. Symp. Quant. Biol. 71, 461–471 (2006).

    CAS  Article  Google Scholar 

  16. van Wolfswinkel, J.C. et al. CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. Cell 139, 135–148 (2009).

    CAS  Article  Google Scholar 

  17. Tabara, H. et al. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132 (1999).

    CAS  Article  Google Scholar 

  18. Grishok, A., Tabara, H. & Mello, C.C. Genetic requirements for inheritance of RNAi in C. elegans. Science 287, 2494–2497 (2000).

    CAS  Article  Google Scholar 

  19. Parker, G.S., Eckert, D.M. & Bass, B.L. RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA. RNA 12, 807–818 (2006).

    CAS  Article  Google Scholar 

  20. Habig, J.W., Aruscavage, P.J. & Bass, B.L. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4. PLoS ONE 3, e4052 (2008).

    Article  Google Scholar 

  21. Timmons, L. & Fire, A. Specific interference by ingested dsRNA. Nature 395, 854 (1998).

    CAS  Article  Google Scholar 

  22. Qadota, H. et al. Establishment of a tissue-specific RNAi system in C. elegans. Gene 400, 166–173 (2007).

    CAS  Article  Google Scholar 

  23. Kwak, J.E. & Wickens, M. A family of poly(U) polymerases. RNA 13, 860–867 (2007).

    CAS  Article  Google Scholar 

  24. Ren, H. & Zhang, H. Wnt signaling controls temporal identities of seam cells in Caenorhabditis elegans. Dev. Biol. 345, 144–155 (2010).

    CAS  Article  Google Scholar 

  25. Kennedy, S., Wang, D. & Ruvkun, G. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427, 645–649 (2004).

    CAS  Article  Google Scholar 

  26. Hyun, T.K., Uddin, M.N., Rim, Y. & Kim, J.Y. Cell-to-cell trafficking of RNA and RNA silencing through plasmodesmata. Protoplasma 248, 101–116 (2011).

    CAS  Article  Google Scholar 

  27. Shih, J.D. & Hunter, C.P. SID-1 is a ds-RNA selective ds-RNA gated channel. RNA 17, 1057–1065 (2011).

    CAS  Article  Google Scholar 

  28. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001).

    CAS  Article  Google Scholar 

  29. Kok, K.H., Ng, M.-H.J., Ching, Y.-P. & Jin, D.-Y. Human TRBP and PACT directly interact with each other and associate with Dicer to facilitate the production of small interfering RNA. J. Biol. Chem. 282, 17649–17657 (2007).

    CAS  Article  Google Scholar 

  30. Timmons, L., Tabara, H., Mello, C.C. & Fire, A.Z. Inducible systemic RNA silencing in Caenorhabditis elegans. Mol. Biol. Cell 14, 2972–2983 (2003).

    CAS  Article  Google Scholar 

  31. Tournier, B., Tabler, M. & Kalantidis, K. Phloem flow strongly influences the systemic spread of silencing in GFP Nicotiana benthamiana plants. Plant J. 47, 383–394 (2006).

    CAS  Article  Google Scholar 

  32. Calixto, A., Chelur, D., Topalidou, I., Chen, X. & Chalfie, M. Enhanced neuronal RNAi in C. elegans using SID-1. Nat. Methods 7, 554–559 (2010).

    CAS  Article  Google Scholar 

  33. Hobert, O. PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans. Biotechniques 32, 728–730 (2002).

    CAS  Article  Google Scholar 

  34. Mello, C.C., Kramer, J.M., Stinchcomb, D. & Ambros, V. Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J. 10, 3959–3970 (1991).

    CAS  Article  Google Scholar 

  35. Newcombe, R.G. Two-sided confidence intervals for the single proportion: comparison of seven methods. Stat. Med. 17, 857–872 (1998).

    CAS  Article  Google Scholar 

Download references


We thank K. Ragkousi, S. Mango and members of the Hunter lab, particularly K. Pang, J. Brooks and D. Schott for comments on the manuscript; the C. elegans Genetics Center for some strains; H. Zhang, National Institute of Biological Sciences, for HZ202; S. Ekman (Harvard University) for two constructs; and the US National Institutes of Health (grant K99-GM085200 to A.M.J. and GM089795 to C.P.H.) and the National Science Foundation (MCB-0744029 to C.P.H.) for funding.

Author information

Authors and Affiliations



A.M.J. conducted the experiments and G.A.G. generated most of the DNA constructs; A.M.J. and C.P.H. designed the study, analyzed the data and wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Craig P Hunter.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1 and 2, and Supplementary Methods (PDF 5014 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Jose, A., Garcia, G. & Hunter, C. Two classes of silencing RNAs move between Caenorhabditis elegans tissues. Nat Struct Mol Biol 18, 1184–1188 (2011).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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