Full Text:   <3986>

CLC number: Q33

On-line Access: 2012-07-05

Received: 2012-02-09

Revision Accepted: 2012-05-30

Crosschecked: 2012-06-18

Cited: 9

Clicked: 7409

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE B 2012 Vol.13 No.7 P.511-524


Conditional gene manipulation: Cre-ating a new biological era

Author(s):  Jian Zhang, Jing Zhao, Wen-jie Jiang, Xi-wei Shan, Xiao-mei Yang, Jian-gang Gao

Affiliation(s):  School of Life Science, Shandong University, Jinan 250100, China

Corresponding email(s):   yxm411@sdu.edu.cn, jggao@sdu.edu.cn

Key Words:  Site-specific recombinase, Gene targeting, Gene trapping, Inducible systems, Φ, C31 system

Share this article to: More |Next Article >>>

Jian Zhang, Jing Zhao, Wen-jie Jiang, Xi-wei Shan, Xiao-mei Yang, Jian-gang Gao. Conditional gene manipulation: Cre-ating a new biological era[J]. Journal of Zhejiang University Science B, 2012, 13(7): 511-524.

@article{title="Conditional gene manipulation: Cre-ating a new biological era",
author="Jian Zhang, Jing Zhao, Wen-jie Jiang, Xi-wei Shan, Xiao-mei Yang, Jian-gang Gao",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Conditional gene manipulation: Cre-ating a new biological era
%A Jian Zhang
%A Jing Zhao
%A Wen-jie Jiang
%A Xi-wei Shan
%A Xiao-mei Yang
%A Jian-gang Gao
%J Journal of Zhejiang University SCIENCE B
%V 13
%N 7
%P 511-524
%@ 1673-1581
%D 2012
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1200042

T1 - Conditional gene manipulation: Cre-ating a new biological era
A1 - Jian Zhang
A1 - Jing Zhao
A1 - Wen-jie Jiang
A1 - Xi-wei Shan
A1 - Xiao-mei Yang
A1 - Jian-gang Gao
J0 - Journal of Zhejiang University Science B
VL - 13
IS - 7
SP - 511
EP - 524
%@ 1673-1581
Y1 - 2012
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1200042

To solve the problem of embryonic lethality in conventional gene knockouts, site-specific recombinase (SSR) systems (Cre-loxP, Flp-FRT, and Φ;C31) have been used for tissue-specific gene knockout. With the combination of an SSR system and inducible gene expression systems (tetracycline and tamoxifen), stage-specific knockout and transgenic expression can be achieved. The application of this “SSR+inducible” conditional tool to genomic manipulation can be extended in various ways. Alternatives to conditional gene targeting, such as conditional gene trapping, multipurpose conditional alleles, and conditional gene silencing, have been developed. SSR systems can also be used to construct precise disease models with point mutations and chromosomal abnormalities. With these exciting achievements, we are moving towards a new era in which the whole genome can be manipulated as we wish.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]Abramowicz, M., 2003. The Human Genome Project in retrospect. Adv. Genet., 50:231-261.

[2]Abuin, A., Hansen, G., Zambrowicz, B., 2007. Gene trap mutagenesis. Handb. Exp. Pharmacol., 178(1):129-147.

[3]Adams, D.J., Biggs, P.J., Cox, T., Davies, R., van der Weyden, L., Jonkers, J., Smith, J., Plumb, B., Taylor, R., Nishijima, I., et al., 2004. Mutagenic insertion and chromosome engineering resource (MICER). Nat. Genet., 36(8):867-871.

[4]Albert, H., Dale, E.C., Lee, E., Ow, D.W., 1995. Site-specific integration of DNA into wild-type and mutant lox sites placed in the plant genome. Plant J., 7(4):649-659.

[5]Austin, C.P., Battey, J.F., Bradley, A., Bucan, M., Capecchi, M., Collins, F.S., Dove, W.F., Duyk, G., Dymecki, S., Eppig, J.T., et al., 2004. The knockout mouse project. Nat. Genet., 36(9):921-924.

[6]Braselmann, S., Graninger, P., Busslinger, M., 1993. A selective transcriptional induction system for mammalian cells based on Gal4-estrogen receptor fusion proteins. PNAS, 90(5):1657-1661.

[7]Calos, M.P., 2006. The ΦC31 integrase system for gene therapy. Curr. Gene. Ther., 6(6):633-645.

[8]Casanova, E., Fehsenfeld, S., Lemberger, T., Shimshek, D.R., Sprengel, R., Mantamadiotis, T., 2002. ER-based double iCre fusion protein allows partial recombination in forebrain. Genesis, 34(3):208-214.

[9]Check, E., 2002. Draft mouse genome makes public debut. Nature, 417(6885):106.

[10]Chow, L.M.L., Tian, Y., Weber, T., Corbett, M., Zuo, J., Baker, S.J., 2006. Inducible Cre recombinase activity in mouse cerebellar granule cell precursors and inner ear hair cells. Dev. Dyn., 235(11):2991-2998.

[11]Cohen-Tannoudji, M., Babinet, C., 1998. Beyond ‘knock-out’ mice: new perspectives for the programmed modification of the mammalian genome. Mol. Hum. Reprod., 4(10):929-938.

[12]Doetschman, T., Gregg, R.G., Maeda, N., Hooper, M.L., Melton, D.W., Thompson, S., Smithies, O., 1987. Targetted correction of a mutant HPRT gene in mouse embryonic stem cells. Nature, 330(6148):576-578.

[13]Dragatsis, I., Zeitlin, S., 2001. A method for the generation of conditional gene repair mutations in mice. Nucleic Acids Res., 29(3):E10.

[14]Feil, R., Brocard, J., Mascrez, B., LeMeur, M., Metzger, D., Chambon, P., 1996. Ligand-activated site-specific recombination in mice. PNAS, 93(20):10887-10890.

[15]Feil, R., Wagner, J., Metzger, D., Chambon, P., 1997. Regulation of Cre recombinase activity by mutated estrogen receptor ligand-binding domains. Biochem. Biophys. Res. Commun., 237(3):752-757.

[16]Friedel, R.H., Seisenberger, C., Kaloff, C., Wurst, W., 2007. EUCOMM—the European conditional mouse mutagenesis program. Brief Funct. Genomic. Proteomic., 6(3):180-185.

[17]Gao, J., Wu, X., Zuo, J., 2004. Targeting hearing genes in mice. Mol. Brain Res., 132(2):192-207.

[18]Gossen, M., Bujard, H., 1992. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. PNAS, 89(12):5547-5551.

[19]Gossen, M., Freundlieb, S., Bender, G., Muller, G., Hillen, W., Bujard, H., 1995. Transcriptional activation by tetracyclines in mammalian cells. Science, 268(5218):1766-1769.

[20]Gossler, A., Joyner, A.L., Rossant, J., Skarnes, W.C., 1989. Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science, 244(4903):463-465.

[21]Groth, A.C., Olivares, E.C., Thyagarajan, B., Calos, M.P., 2000. A phage integrase directs efficient site-specific integration in human cells. PNAS, 97(11):5995-6000.

[22]Guan, C., Ye, C., Yang, X., Gao, J., 2010. A review of current large-scale mouse knockout efforts. Genesis, 48(2):73-85.

[23]Hoess, R.H., Ziese, M., Sternberg, N., 1982. P1 site-specific recombination: nucleotide sequence of the recombining sites. PNAS, 79(11):3398-3402.

[24]Hoess, R., Abremski, K., Sternberg, N., 1984. The nature of the interaction of the P1 recombinase Cre with the recombining site loxP. Cold Spring Harb. Symp. Quant. Biol., 49:761-768.

[25]Huang, L.C., Wood, E.A., Cox, M.M., 1991. A bacterial model system for chromosomal targeting. Nucleic Acids Res., 19(3):443-448.

[26]Indra, A.K., Warot, X., Brocard, J., Bornert, J.M., Xiao, J.H., Chambon, P., Metzger, D., 1999. Temporally-controlled site-specific mutagenesis in the basal layer of the epidermis: comparison of the recombinase activity of the tamoxifen-inducible Cre-ERT and Cre-ERT2 recombinases. Nucleic Acids Res., 27(22):4324-4327.

[27]Ishida, Y., Leder, P., 1999. RET: a poly A-trap retrovirus vector for reversible disruption and expression monitoring of genes in living cells. Nucleic Acids Res., 27(24):e35-e42.

[28]Kappel, S., Matthess, Y., Zimmer, B., Kaufmann, M., Strebhardt, K., 2006. Tumor inhibition by genomically integrated inducible RNAi-cassettes. Nucleic Acids Res., 34(16):4527-4536.

[29]Kistner, A., Gossen, M., Zimmermann, F., Jerecic, J., Ullmer, C., Lübbert, H., Bujard, H., 1996. Doxycycline-mediated quantitative and tissue-specific control of gene expression in transgenic mice. PNAS, 93(20):10933-10938.

[30]Klysik, J., 2002. Mice and humans: chromosome engineering and its application to functional genomics. Acta Biochim. Pol., 49(3):553-569.

[31]Kothary, R., Clapoff, S., Brown, A., Campbell, R., Peterson, A., Rossant, J., 1988. A transgene containing lacZ inserted into the dystonia locus is expressed in neural tube. Nature, 335(6189):435-437.

[32]Lee, S.K., Kumar, P., 2009. Conditional RNAi: towards a silent gene therapy. Adv. Drug Deliv. Rev., 61(7-8):650-664.

[33]Lister, J.A., 2010. Transgene excision in zebrafish using the phiC31 integrase. Genesis, 48(2):137-143.

[34]Logie, C., Stewart, A.F., 1995. Ligand-regulated site-specific recombination. PNAS, 92(13):5940-5944.

[35]Lu, J., Maddison, L.A., Chen, W., 2011. PhiC31 integrase induces efficient site-specific excision in zebrafish. Transgenic Res., 20(1):183-189.

[36]Ma, Q.W., Sheng, H.Q., Yan, J.B., Cheng, S., Huang, Y., Chen-Tsai, Y., Ren, Z.R., Huang, S.Z., Zeng, Y.T., 2006. Identification of pseudo attP sites for phage ΦC31 integrase in bovine genome. Biochem. Biophys. Res. Commun., 345(3):984-988.

[37]Marshall, E., 2002. Genome sequencing. Public group completes draft of the mouse. Science, 296(5570):1005.

[38]Matsuda, T., Cepko, C.L., 2007. Controlled expression of transgenes introduced by in vivo electroporation. PNAS, 104(3):1027-1032.

[39]McLeod, M., Craft, S., Broach, J.R., 1986. Identification of the crossover site during FLP-mediated recombination in the Saccharomyces cerevisiae plasmid 2 microns circle. Mol. Cell Biol., 6(10):3357-3367.

[40]Metzger, D., Clifford, J., Chiba, H., Chambon, P., 1995. Conditional site-specific recombination in mammalian cells using a ligand-dependent chimeric Cre recombinase. PNAS, 92(15):6991-6995.

[41]Montgomery, M.K., Xu, S., Fire, A., 1998. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. PNAS, 95(26):15502-15507.

[42]Morris, A.C., Schaub, T.L., James, A.A., 1991. FLP-mediated recombination in the vector mosquito, Aedes aegypti. Nucleic Acids Res., 19(21):5895-5900.

[43]Nagy, A., 2000. Cre recombinase: the universal reagent for genome tailoring. Genesis, 26(2):99-109.

[44]Nagy, A., Mar, L., Watts, G., 2009. Creation and use of a Cre recombinase transgenic database. Methods Mol. Biol., 530:365-378.

[45]No, D., Yao, T.P., Evans, R.M., 1996. Ecdysone-inducible gene expression in mammalian cells and transgenic mice. PNAS, 93(8):3346-3351.

[46]Orban, P.C., Chui, D., Marth, J.D., 1992. Tissue- and site-specific DNA recombination in transgenic mice. PNAS, 89(15):6861-6865.

[47]Picard, D., 1994. Regulation of protein function through expression of chimaeric proteins. Curr. Opin. Biotechnol., 5(5):511-515.

[48]Ramirez-Solis, R., Liu, P., Bradley, A., 1995. Chromosome engineering in mice. Nature, 378(6558):720-724.

[49]Schnütgen, F., 2006. Generation of multipurpose alleles for the functional analysis of the mouse genome. Brief Funct. Genomic. Proteomic., 5(1):15-18.

[50]Senecoff, J.F., Rossmeissl, P.J., Cox, M.M., 1988. DNA recognition by the FLP recombinase of the yeast 2 mu plasmid: a mutational analysis of the FLP binding site. J. Mol. Biol., 201(2):405-421.

[51]Shaffer, L.G., Lupski, J.R., 2000. Molecular mechanisms for constitutional chromosomal rearrangements in humans. Annu. Rev. Genet., 34:297-329.

[52]Sharma, N., Moldt, B., Dalsgaard, T., Jensen, T.G., Mikkelsen, J.G., 2008. Regulated gene insertion by steroid-induced ΦC31 integrase. Nucleic Acids Res., 36(11):e67.

[53]Shigeoka, T., Kawaichi, M., Ishida, Y., 2005. Suppression of nonsense-mediated mRNA decay permits unbiased gene trapping in mouse embryonic stem cells. Nucleic Acids Res., 33(2):e20.

[54]Skarnes, W.C., Rosen, B., West, A.P., Koutsourakis, M., Bushell, W., Iyer, V., Mujica, A.O., Thomas, M., Harrow, J., Cox, T., et al., 2011. A conditional knockout resource for the genome-wide study of mouse gene function. Nature, 474(7351):337-342.

[55]Smith, M.C., Thorpe, H.M., 2002. Diversity in the serine recombinases. Mol. Microbiol., 44(2):299-307.

[56]Stark, W.M., Boocock, M.R., Sherratt, D.J., 1992. Catalysis by site-specific recombinases. Trends Genet., 8(12):432-439.

[57]Sternberg, N., Hamilton, D., Austin, S., Yarmolinsky, M., Hoess, R., 1981. Site-specific recombination and its role in the life cycle of bacteriophage P1. Cold Spring Harb. Symp. Quant. Biol., 45:297-309.

[58]Thomas, K.R., Capecchi, M.R., 1987. Site-directed mutagenesis by gene targeting in mouse embryo-derived stem cells. Cell, 51(3):503-512.

[59]Thorpe, H.M., Smith, M.C., 1998. In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family. PNAS, 95(10):5505-5510.

[60]Thorpe, H.M., Wilson, S.E., Smith, M.C., 2000. Control of directionality in the site-specific recombination system of the Streptomyces phage ΦC31. Mol. Microbiol., 38(2):232-241.

[61]Thyagarajan, B., Olivares, E.C., Hollis, R.P., Ginsburg, D.S., Calos, M.P., 2001. Site-specific genomic integration in mammalian cells mediated by phage ΦC31 integrase. Mol. Cell. Biol., 21(12):3926-3934.

[62]Tian, Y., James, S., Zuo, J., Fritzsch, B., Beisel, K.W., 2006. Conditional and inducible gene recombineering in the mouse inner ear. Brain Res., 1091(1):243-254.

[63]Uemura, M., Niwa, Y., Kakazu, N., Adachi, N., Kinoshita, K., 2010. Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors. PLoS One, 5(3):e9846.

[64]van Deursen, J., Fornerod, M., van Rees, B., Grosveld, G., 1995. Cre-mediated site-specific translocation between nonhomologous mouse chromosomes. PNAS, 92(16):7376-7380.

[65]Wang, Y., Tsai, S.Y., O′Malley, B.W., 1999. Antiprogestin regulable gene switch for induction of gene expression in vivo. Methods Enzymol., 306:281-294.

[66]Watson, J.D., Cook-Deegan, R.M., 1991. Origins of the Human Genome Project. FASEB J., 5(1):8-11.

[67]Yao, T.P., Forman, B.M., Jiang, Z., Cherbas, L., Chen, J.D., McKeown, M., Cherbas, P., Evans, R.M., 1993. Functional ecdysone receptor is the product of EcR and Ultraspiracle genes. Nature, 366(6454):476-479.

[68]Yu, Y., Bradley, A., 2001. Engineering chromosomal rearrangements in mice. Nat. Rev. Genet., 2(10):780-790.

[69]Zhang, Y., Riesterer, C., Ayrall, A.M., Sablitzky, F., Littlewood, T.D., Reth, M., 1996. Inducible site-directed recombination in mouse embryonic stem cells. Nucleic Acids Res., 24(4):543-548.

Open peer comments: Debate/Discuss/Question/Opinion


Please provide your name, email address and a comment

Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - 2024 Journal of Zhejiang University-SCIENCE