Reply to “Genome editing with modularly assembled zinc-finger nucleases” (original) (raw)

Nature Methods volume 7, pages 91–92 (2010)Cite this article

Subjects

Joung et al. reply:

The publications cited by Kim et al.1 describing successful construction of zinc-finger nucleases (ZFNs) by modular assembly only further support our original conclusion that this method has a high failure rate for engineering functional zinc-finger arrays2. Two3,4 of the three reports cited in their Correspondence1 provide data that enable calculation of failure rates for modular assembly. Although it is true that modular assembly yielded ZFNs for ∼25% of the DNA sites targeted, failure rates measured instead by the number of zinc-finger proteins tested are consistent with those reported in our original Correspondence2. For example, at the human CCR5 gene, Kim et al. screened 315 pairs of ZFNs for activity4; this large-scale effort yielded only a small number of functional ZFN pairs (93.3% failure rate for ZFN pairs tested). Similarly, for the tobacco SuRB gene3, we tested 32 zinc-finger arrays in vitro but identified only three with functional activity (91.6% failure rate for zinc-finger arrays tested). These data are consistent with our original predicted failure rates of ∼94% and ∼76% for modularly assembled ZFN pairs and zinc-finger arrays, respectively2. We believe that failure rates measured by numbers of zinc-finger arrays or ZFN pairs tested rather than by numbers of DNA sites targeted are more relevant statistics for potential ZFN users because these influence how many proteins must be modularly assembled and tested for each potential site.

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

Relevant articles

Open Access articles citing this article.

Access options

Subscribe to this journal

Receive 12 print issues and online access

$259.00 per year

only $21.58 per issue

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Additional access options:

References

  1. Kim, J.-S., Lee, H.J. & Carroll, D. Nat. Methods 7, 91 (2010).
    Article CAS Google Scholar
  2. Ramirez, C.L. et al. Nat. Methods 5, 374–375 (2008).
    Article CAS Google Scholar
  3. Townsend, J.A. et al. Nature 459, 442–445 (2009).
    Article CAS Google Scholar
  4. Kim, H.J., Lee, H.J., Kim, H., Cho, S.W. & Kim, J.S. Genome Res. 19, 1279–1288 (2009).
    Article CAS Google Scholar
  5. Maeder, M.L. et al. Mol. Cell 31, 294–301 (2008).
    Article CAS Google Scholar
  6. Foley, J.E. et al. PLoS ONE 4, e4348 (2009).
    Article Google Scholar
  7. Zou, J. et al. Cell Stem Cell 5, 97–110 (2009).
    Article CAS Google Scholar

Download references

Acknowledgements

We thank the members of our laboratories for helpful discussions. J.K.J. is supported by US National Institutes of Health (R01GM069906, R01GM088040, RC2HL101553, R24GM078369 and R21HL091808), the Cystic Fibrosis Foundation and the Massachusetts General Hospital Pathology Service. D.F.V. is supported by the US National Science Foundation (DBI 0501678 and MCB 0209818). T.C. is supported by the German Research Foundation (SPP1230–CA311/2), the German Ministry of Education and Research (01GU0618) and the European Commission's 6th and 7th Framework Programmes (ZNIP–037783 and PERSIST–222878).

Author information

Authors and Affiliations

  1. Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    J Keith Joung
  2. Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
    J Keith Joung
  3. Department of Genetics, Cell Biology and Development, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
    Daniel F Voytas
  4. Department of Experimental Hematology, Hannover Medical School, Hannover, Germany
    Toni Cathomen

Authors

  1. J Keith Joung
    You can also search for this author inPubMed Google Scholar
  2. Daniel F Voytas
    You can also search for this author inPubMed Google Scholar
  3. Toni Cathomen
    You can also search for this author inPubMed Google Scholar

Corresponding authors

Correspondence toJ Keith Joung, Daniel F Voytas or Toni Cathomen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

About this article

Cite this article

Joung, J., Voytas, D. & Cathomen, T. Reply to “Genome editing with modularly assembled zinc-finger nucleases”.Nat Methods 7, 91–92 (2010). https://doi.org/10.1038/nmeth0210-91b

Download citation

This article is cited by

Associated content