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Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans


We established a transcription-based binary gene expression system in Caenorhabditis elegans using the recently developed Q system. This system, derived from genes in Neurospora crassa, uses the transcriptional activator QF to induce the expression of target genes. Activation can be efficiently suppressed by the transcriptional repressor QS, and suppression can be relieved by the nontoxic small molecule quinic acid. We used QF, QS and quinic acid to achieve temporal and spatial control of transgene expression in various tissues in C. elegans. We also developed a split Q system, in which we separated QF into two parts encoding its DNA-binding and transcription-activation domains. Each domain showed negligible transcriptional activity when expressed alone, but expression of both reconstituted QF activity, providing additional combinatorial power to control gene expression.

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Figure 1: The repressible Q binary system functions effectively in C. elegans.
Figure 2: Refining expression patterns in VA motor neurons with a 'not' gate.
Figure 3: The split Q system.
Figure 4: The Q system functions effectively with single-copy transgene.


  1. Gossen, M. & Bujard, H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. USA 89, 5547–5551 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Brand, A.H. & Perrimon, N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401–415 (1993).

    CAS  PubMed  Google Scholar 

  3. Lee, T. & Luo, L.Q. Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22, 451–461 (1999).

    Article  CAS  PubMed  Google Scholar 

  4. Macosko, E.Z. et al. A hub-and-spoke circuit drives pheromone attraction and social behaviour in C. elegans. Nature 458, 1171–1175 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Davis, M.W., Morton, J.J., Carroll, D. & Jorgensen, E.M. Gene activation using FLP recombinase in C. elegans. PLoS Genet. 4, e1000028 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Bacaj, T. & Shaham, S. Temporal control of cell-specific transgene expression in Caenorhabditis elegans. Genetics 176, 2651–2655 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Potter, C.J., Tasic, B., Russler, E.V., Liang, L. & Luo, L.Q. The Q system: a repressible binary system for transgene expression, lineage tracing, and mosaic analysis. Cell 141, 536–548 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. White, J.G., Southgate, E., Thomson, J.N. & Brenner, S. The structure of the nervous-system of the nematode Caenorhabditis elegans. Philos. Trans. Royal Soc., B 314, 1–340 (1986).

    Article  CAS  Google Scholar 

  9. Miller, D.M. & Niemeyer, C.J. Expression of the Unc-4 homeoprotein in Caenorhabditis elegans motor-neurons specifies presynaptic input. Development 121, 2877–2886 (1995).

    CAS  PubMed  Google Scholar 

  10. Spieth, J., Brooke, G., Kuersten, S., Lea, K. & Blumenthal, T. Operons in C. elegans polycistronic messenger RNA precursors are processed by transsplicing of Sl2 to downstream coding regions. Cell 73, 521–532 (1993).

    Article  CAS  PubMed  Google Scholar 

  11. Seydoux, G. & Fire, A. Soma-germline asymmetry in the distributions of embryonic RNAs in Caenorhabditis elegans. Development 120, 2823–2834 (1994).

    CAS  PubMed  Google Scholar 

  12. Mello, C. & Fire, A. DNA transformation. Methods Cell Biol. 48, 451–482 (1995).

    Article  CAS  PubMed  Google Scholar 

  13. Nollet, L.M.L. Food Analysis by HPLC. Vol. 100 (CRC, 2000).

  14. Clark, D.V., Suleman, D.S., Beckenbach, K.A., Gilchrist, E.J. & Baillie, D.L. Molecular cloning and characterization of the dpy-20 gene of Caenorhabditis elegans. Mol. Gen. Genet. 247, 367–378 (1995).

    Article  CAS  PubMed  Google Scholar 

  15. Zhang, S., Ma, C. & Chalfie, M. Combinatorial marking of cells and organelles with reconstituted fluorescent proteins. Cell 119, 137–144 (2004).

    Article  CAS  PubMed  Google Scholar 

  16. Luan, H., Peabody, N.C., Vinson, C.R. & White, B.H. Refined spatial manipulation of neuronal function by combinatorial restriction of transgene expression. Neuron 52, 425–436 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Giles, N.H., Geever, R.F., Asch, D.K., Avalos, J. & Case, M.E. The Wilhelmine E. Key 1989 invitational lecture. Organization and regulation of the qa (quinic acid) genes in Neurospora crassa and other fungi. J. Hered. 82, 1–7 (1991).

    Article  CAS  PubMed  Google Scholar 

  18. Ghosh, I., Hamilton, A.D. & Regan, L. Antiparallel leucine zipper-directed protein reassembly: application to the green fluorescent protein. J. Am. Chem. Soc. 122, 5658–5659 (2000).

    Article  CAS  Google Scholar 

  19. Sym, M., Robinson, N. & Kenyon, C. MIG-13 positions migrating cells along the anteroposterior body axis of C. elegans. Cell 98, 25–36 (1999).

    Article  CAS  PubMed  Google Scholar 

  20. Hsieh, J. & Fire, A. Recognition and silencing of repeated DNA. Annu. Rev. Genet. 34, 187–204 (2000).

    Article  CAS  PubMed  Google Scholar 

  21. Frokjaer-Jensen, C. et al. Single-copy insertion of transgenes in Caenorhabditis elegans. Nat. Genet. 40, 1375–1383 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Luo, L., Callaway, E.M. & Svoboda, K. Genetic dissection of neural circuits. Neuron 57, 634–660 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Tursun, B., Cochella, L., Carrera, I. & Hobert, O. A toolkit and robust pipeline for the generation of fosmid-based reporter genes in C. elegans. PLoS ONE 4, e4625 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  24. Gilleard, J.S., Barry, J.D. & Johnstone, I.L. cis-regulatory requirements for hypodermal cell-specific expression of the Caenorhabditis elegans cuticle collagen gene dpy-7. Mol. Cell. Biol. 17, 2301–2311 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Chelur, D.S. & Chalfie, M. Targeted cell killing by reconstituted caspases. Proc. Natl. Acad. Sci. USA 104, 2283–2288 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77, 71–94 (1974).

    CAS  PubMed  PubMed Central  Google Scholar 

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This work was funded by the Howard Hughes Medical Institute. We thank M. Vanhoven (San José State University) for the unc-4c promoter and the wyEx1817 transgene, members of the E. Jorgensen laboratory for the MosSCI protocol, M. Nonet for the long-fragment PCR protocol, members of the Caenorhabditis Genetics Center for providing strains, C. Gao, T. Boshika and Y. Fu for technical assistance, and members of the Shen lab for comments on the manuscript.

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Authors and Affiliations



X.W. and K.S. designed the experiments and wrote the paper. X.W. performed all experiments and data analysis. L.L. and C.J.P. provided unpublished information on the Q system and guided experimental design.

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Correspondence to Kang Shen.

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The authors declare no competing financial interests.

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Supplementary Figures 1–5, Supplementary Table 1, Supplementary Notes 1–3 (PDF 718 kb)

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Wei, X., Potter, C., Luo, L. et al. Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans. Nat Methods 9, 391–395 (2012).

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