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.

Efficient genome editing in zebrafish using a CRISPR-Cas system


In bacteria, foreign nucleic acids are silenced by clustered, regularly interspaced, short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems. Bacterial type II CRISPR systems have been adapted to create guide RNAs that direct site-specific DNA cleavage by the Cas9 endonuclease in cultured cells. Here we show that the CRISPR-Cas system functions in vivo to induce targeted genetic modifications in zebrafish embryos with efficiencies similar to those obtained using zinc finger nucleases and transcription activator–like effector nucleases.

Your institute does not have access to this article

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: Schematic illustrating naturally occurring and engineered CRISPR-Cas systems.


  1. Wiedenheft, B., Sternberg, S.H. & Doudna, J.A. Nature 482, 331–338 (2012).

    CAS  Article  Google Scholar 

  2. Horvath, P. & Barrangou, R. Science 327, 167–170 (2010).

    CAS  Article  Google Scholar 

  3. Terns, M.P. & Terns, R.M. Curr. Opin. Microbiol. 14, 321–327 (2011).

    CAS  Article  Google Scholar 

  4. Barrangou, R. et al. Science 315, 1709–1712 (2007).

    CAS  Article  Google Scholar 

  5. Brouns, S.J. et al. Science 321, 960–964 (2008).

    CAS  Article  Google Scholar 

  6. Jinek, M. et al. Science 337, 816–821 (2012).

    CAS  Article  Google Scholar 

  7. Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Proc. Natl. Acad. Sci. USA 109, E2579–E2586 (2012).

    CAS  Article  Google Scholar 

  8. Mali, P. et al. Science doi:10.1126/science.1232033 (3 January 2013).

  9. Cong, L. et al. Science doi:10.1126/science.1231143 (3 January 2013).

  10. Urnov, F.D., Rebar, E.J., Holmes, M.C., Zhang, H.S. & Gregory, P.D. Nat. Rev. Genet. 11, 636–646 (2010).

    CAS  Article  Google Scholar 

  11. Joung, J.K. & Sander, J.D. Nat. Rev. Mol. Cell Biol. 14, 49–55 (2012).

    Article  Google Scholar 

  12. Holkers, M. et al. Nucleic Acids Res. doi:10.1093/nar/gks1446 (28 December 2012).

    CAS  Article  Google Scholar 

  13. Schneider, T.D. & Stormo, G.D. Nucleic Acids Res. 17, 659–674 (1989).

    CAS  Article  Google Scholar 

  14. Sander, J.D. et al. Nucleic Acids Res. 38, W462–W468 (2010).

    CAS  Article  Google Scholar 

  15. Foley, J.E. et al. PLoS ONE 4, e4348 (2009).

    Article  Google Scholar 

  16. Huang, P. et al. Nat. Biotechnol. 29, 699–700 (2011).

    Article  Google Scholar 

  17. Cade, L. et al. Nucleic Acids Res. 40, 8001–8010 (2012).

    CAS  Article  Google Scholar 

  18. Sander, J.D. et al. Nat. Biotechnol. 29, 697–698 (2011).

    CAS  Article  Google Scholar 

  19. Sander, J.D. et al. Nat. Methods 8, 67–69 (2011).

    CAS  Article  Google Scholar 

  20. Zuker, M. Nucleic Acids Res. 31, 3406–3415 (2003).

    CAS  Article  Google Scholar 

Download references


This work was supported by a US National Institutes of Health (NIH) Director's Pioneer Award DP1 GM105378 (J.K.J.), NIH R01 GM088040 (J.K.J. & R.T.P.), NIH P50 HG005550 (J.K.J.), the Jim and Ann Orr Research Scholar Award (J.K.J.), NIH K01 AG031300 (J.-R.J.Y.) and a Massachusetts General Hospital Claflin award (J.-R.J.Y.). We thank G. Church, J. Aach and P. Mali for sharing unpublished results and helpful discussions.

Author information

Authors and Affiliations



W.Y.H., Y.F., M.L.M., D.R., S.Q.T., J.D.S., R.T.P., J.-R.J.Y. and J.K.J. designed experiments. W.Y.H., Y.F., M.L.M., D.R., S.Q.T. and J.D.S. performed experiments. W.Y.H., Y.F., M.L.M., D.R., S.Q.T., J.D.S., R.T.P., J.-R.J.Y. and J.K.J. wrote the paper.

Corresponding authors

Correspondence to J-R Joanna Yeh or J Keith Joung.

Ethics declarations

Competing interests

J.K.J. has a financial interest in Transposagen Biopharmaceuticals.

Supplementary information

Supplementary Text and Figures

Supplementary Discussion, Supplementary Methods, Supplementary Figures 1–5 and Supplementary Tables 1–5 (PDF 487 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Hwang, W., Fu, Y., Reyon, D. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31, 227–229 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


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