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.

  • Technical Report
  • Published:

A directional strategy for monitoring Cre-mediated recombination at the cellular level in the mouse


Functional redundancies, compensatory mechanisms, and lethal phenotypes often prevent the full analysis of gene functions through generation of germline null mutations in the mouse1. The use of site-specific recombinases, such as Cre, which catalyzes recombination between loxP sites2, has allowed the engineering of mice harboring targeted somatic mutations, which are both temporally controlled and cell-type restricted1,3. Many Cre-expressing mouse lines exist, but only a few transgenic lines are available that harbor a reporter gene whose expression is dependent on a Cre-mediated event3. Moreover, their use to monitor gene ablation at the level of individual cells is often limited, as in some tissues the reporter gene may be silenced1, be affected by position-effect variegation4, or reside in a chromatin configuration inaccessible for recombination5. Thus, one cannot validly extrapolate from the expression of a reporter transgene to an identical ablation pattern for the conditional allele of a given gene. By combining the ability of Cre recombinase to invert or excise a DNA fragment, depending on the orientation of the flanking loxP sites6, and the availability of both wild-type (WT) and mutant loxP sites7, we designed a Cre-dependent genetic switch (FLEx switch) through which the expression of a given gene is turned off, while the expression of another one is concomitantly turned on. We demonstrate the efficiency and reliability of this switch to readily detect, in the mouse, at the single cell level, Cre-mediated gene ablation. We discuss how this strategy can be used to generate genetic modifications in a conditional manner.

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

Access options

Buy this article

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

Figure 1: The FLEx switch.
Figure 2: The Rarg FLEx allele in the mouse.
Figure 3: The FLEx switch, which is reliable and efficient in the mouse, makes possible novel applications.

Similar content being viewed by others


  1. Metzger, D. & Chambon, P. Site- and time-specific gene targeting in the mouse. Methods 24, 71–80 (2001).

    Article  CAS  Google Scholar 

  2. Sauer, B. & Henderson, N. Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1. Proc. Natl. Acad. Sci. USA 85, 5166–5170 (1988).

    Article  CAS  Google Scholar 

  3. Nagy, A. Cre recombinase: the universal reagent for genome tailoring. Genesis 26, 99–109 (2000).

    Article  CAS  Google Scholar 

  4. Montoliu, L., Chavez, S. & Vidal, M. Variegation associated with lacZ in transgenic animals: a warning note. Transgenic Res. 9, 237–239 (2000).

    Article  CAS  Google Scholar 

  5. Vooijs, M., Jonkers, J. & Berns, A. A highly efficient ligand-regulated Cre recombinase mouse line shows that LoxP recombination is position dependent. EMBO Rep. 2, 292–297 (2001).

    Article  CAS  Google Scholar 

  6. Abremski, K., Hoess, R. & Sternberg, N. Studies on the properties of P1 site-specific recombination: evidence for topologically unlinked products following recombination. Cell 32, 1301–1311 (1983).

    Article  CAS  Google Scholar 

  7. Siegel, R.W., Jain, R. & Bradbury, A. Using an in vivo phagemid system to identify non-compatible loxP sequences. FEBS Lett. 499, 147–153 (2001).

    Article  CAS  Google Scholar 

  8. Hoess, R.H., Wierzbicki, A. & Abremski, K. Formation of small circular DNA molecules via an in vitro site-specific recombination system. Gene 40, 325–329 (1985).

    Article  CAS  Google Scholar 

  9. Ringrose, L. et al. Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination. J. Mol. Biol. 284, 363–384 (1998).

    Article  CAS  Google Scholar 

  10. Chapellier, B. et al. A conditional floxed (loxP-flanked) allele for the retinoic acid receptor gamma (RARγ) gene. Genesis 32, 95–98 (2002).

    Article  CAS  Google Scholar 

  11. Lohnes, D. et al. Function of retinoic acid receptor gamma in the mouse. Cell 73, 643–658 (1993).

    Article  CAS  Google Scholar 

  12. O' Gorman, S., Fox, D.T. & Wahl, G.M. Recombinase mediated gene activation and site-specific integration in mammalian cells. Science 251, 1351–1355 (1991).

    Article  CAS  Google Scholar 

  13. Bonnerot, C., Rocancourt, D., Briand, P., Grimber, G. & Nicolas, J.F. A β-galactosidase hybrid protein targeted to nuclei as a marker for developmental studies. Proc. Natl. Acad. Sci. USA 84, 6795–6799 (1987).

    Article  CAS  Google Scholar 

  14. Li, M. et al. RXR-α ablation in skin keratinocytes results in alopecia and epidermal alterations. Development 128, 675–688 (2000).

    Google Scholar 

  15. Lee, G. & Saito, I. Role of nucleotide sequences of loxP spacer region in Cre-mediated recombination. Gene 216, 55–65 (1998).

    Article  CAS  Google Scholar 

  16. Kolb, A.F. Selection-marker-free modification of the murine β-casein gene using a lox2272 [correction of lox2722] site. Anal. Biochem. 290, 260–271 (2001).

    Article  CAS  Google Scholar 

  17. Aranda, M. et al. Altered directionality in the Cre-LoxP site-specific recombination pathway. J. Mol. Biol. 311, 453–459 (2001).

    Article  CAS  Google Scholar 

  18. Theis, M. et al. Endothelium-specific replacement of the connexin 43 coding region by a lacZ reporter gene. Genesis 29, 1–13 (2001).

    Article  CAS  Google Scholar 

  19. Feng, Y.Q. et al. Site-specific chromosomal integration in mammalian cells: highly efficient Cre recombinase-mediated cassette exchange. J. Mol. Biol. 292, 779–785 (1999).

    Article  CAS  Google Scholar 

  20. Buchholz, F., Angrand, P.O. & Stewart, F. A simple assay to determine the functionality of Cre or FLP recombination targets in genomic manipulation constructs. Nucleic Acids Res. 24, 3118–3119 (1996).

    Article  CAS  Google Scholar 

Download references


We thank B. Féret, G. Kimmich, and E. Blondelle for technical assistance, J.M. Garnier, A. Dierich, and M. Mark for their active contribution to this work, and G. Richards for critical reading of the manuscript. We also thank M. Li for K14-Cre mice and J.F. Nicolas for the lacZ gene. This work was supported by funds from the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé et de la Recherche Médicale (INSERM), the Université Louis Pasteur (ULP), the Hôpital Universitaire de Strasbourg, the Collège de France, and the Association pour la Recherche sur le Cancer (ARC). F.S. was supported by a Marie Curie Fellowship from the European Community and C.C. by the Institut National de la Recherche Agronomique (INRA).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Norbert B. Ghyselinck.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schnütgen, F., Doerflinger, N., Calléja, C. et al. A directional strategy for monitoring Cre-mediated recombination at the cellular level in the mouse. Nat Biotechnol 21, 562–565 (2003).

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