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Surrogate reporters for enrichment of cells with nuclease-induced mutations


Zinc-finger nucleases (ZFNs) and TAL-effector nucleases (TALENs) are powerful tools for creating genetic modifications in eukaryotic cells and organisms. But wild-type and mutant cells that contain genetic modifications induced by these programmable nucleases are often phenotypically indistinguishable, hampering isolation of mutant cells. Here we show that transiently transfected episomal reporters encoding fluorescent proteins can be used as surrogate genes for the efficient enrichment of endogenous gene-modified cells by flow cytometry.

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Figure 1: Principle of the use of surrogate reporters for enrichment of nuclease-modified cells.
Figure 2: A surrogate reporter enriches for TP53-disrupted cells.


  1. Porteus, M.H. & Baltimore, D. Science 300, 763 (2003).

    Article  Google Scholar 

  2. Bibikova, M., Beumer, K., Trautman, J.K. & Carroll, D. Science 300, 764 (2003).

    Article  CAS  Google Scholar 

  3. Urnov, F.D. et al. Nature 435, 646–651 (2005).

    Article  CAS  Google Scholar 

  4. Kim, J.S., Lee, H.J. & Carroll, D. Nat. Methods 7, 91–92 (2010).

    Article  CAS  Google Scholar 

  5. Miller, J.C. et al. Nat. Biotechnol. 29, 143–148 (2011).

    Article  CAS  Google Scholar 

  6. Perez, E.E. et al. Nat. Biotechnol. 26, 808–816 (2008).

    Article  CAS  Google Scholar 

  7. Meyer, M., de Angelis, M.H., Wurst, W. & Kühn, R. Proc. Natl. Acad. Sci. USA 107, 15022–15026 (2010).

    Article  CAS  Google Scholar 

  8. Lee, H.J., Kim, E. & Kim, J.S. Genome Res. 20, 81–89 (2010).

    Article  CAS  Google Scholar 

  9. Lieber, M.R. Annu. Rev. Biochem. 79, 181–211 (2010).

    Article  CAS  Google Scholar 

  10. Santiago, Y. et al. Proc. Natl. Acad. Sci. USA 105, 5809–5814 (2008).

    Article  CAS  Google Scholar 

  11. Kim, H.J., Lee, H.J., Kim, H., Cho, S.W. & Kim, J.S. Genome Res. 19, 1279–1288 (2009).

    Article  CAS  Google Scholar 

  12. Kim, S., Lee, M.J., Kim, H., Kang, M. & Kim, J.S. Nat. Methods 8, 7 (2011).

    Article  CAS  Google Scholar 

  13. Doyon, Y. et al. Nat. Methods 7, 459–460 (2010).

    Article  CAS  Google Scholar 

  14. Doyon, Y. et al. Nat. Methods 8, 74–79 (2011).

    Article  CAS  Google Scholar 

  15. Miller, J.C. et al. Nat. Biotechnol. 25, 778–785 (2007).

    Article  CAS  Google Scholar 

  16. Guo, J., Gaj, T. & Barbas, C.F. III. J. Mol. Biol. 400, 96–107 (2010).

    Article  CAS  Google Scholar 

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J.-S.K. and Hyongbum K. are supported in part by the National Research Foundation of Korea (J.-S.K., 2011-0000402; Hyongbum K., 2011-0013568, 2011-27177, 2011-0019357 and 2011-0028267).

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Hyojin K., E.U., S.-R.C. and C.J. performed the experiments. Hyongbum K. and J.-S.K. wrote the paper.

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Correspondence to Hyongbum Kim or Jin-Soo Kim.

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J.-S.K. filed a patent application (US 61/445,346) based on this work.

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Kim, H., Um, E., Cho, SR. et al. Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat Methods 8, 941–943 (2011).

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