Skip to main content

Beyond knockouts: cre resources for conditional mutagenesis

An Erratum to this article was published on 05 October 2012

Abstract

With the effort of the International Phenotyping Consortium to produce thousands of strains with conditional potential gathering steam, there is growing recognition that it must be supported by a rich toolbox of cre driver strains. The approaches to build cre strains have evolved in both sophistication and reliability, replacing first-generation strains with tools that can target individual cell populations with incredible precision and specificity. The modest set of cre drivers generated by individual labs over the past 15+ years is now growing rapidly, thanks to a number of large-scale projects to produce new cre strains for the community. The power of this growing resource, however, depends upon the proper deep characterization of strain function, as even the best designed strain can display a variety of undesirable features that must be considered in experimental design. This must be coupled with the parallel development of informatics tools to provide functional data to the user and facilitated access to the strains through public repositories. We discuss the current progress on all of these fronts and the challenges that remain to ensure the scientific community can capitalize on the tremendous number of mouse resources at their disposal.

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

References

  • Anastassiadis K, Fu J, Patsch C, Hu S, Weidlich S, Duerschke K, Buchholz F, Edenhofer F, Stewart AF (2009) Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice. Dis Model Mech 2(9–10):508–515

    PubMed  Article  CAS  Google Scholar 

  • Badea TC, Wang Y, Nathans J (2003) A noninvasive genetic/pharmacologic strategy for visualizing cell morphology and clonal relationships in the mouse. J Neurosci 23(6):2314–2322

    PubMed  CAS  Google Scholar 

  • Balordi F, Fishell G (2007) Mosaic removal of hedgehog signaling in the adult SVZ reveals that the residual wild-type stem cells have a limited capacity for self-renewal. J Neurosci 27(52):14248–14259

    PubMed  Article  CAS  Google Scholar 

  • Belteki G, Gertsenstein M, Ow DW, Nagy A (2003) Site-specific cassette exchange and germline transmission with mouse ES cells expressing phiC31 integrase. Nat Biotechnol 21(3):321–324

    PubMed  Article  CAS  Google Scholar 

  • Belteki G, Haigh J, Kabacs N, Haigh K, Sison K, Costantini F, Whitsett J, Quaggin SE, Nagy A (2005) Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction. Nucleic Acids Res 33(5):e51

    PubMed  Article  Google Scholar 

  • Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT (2011) The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 39(Database issue):D842–D848

    Google Scholar 

  • Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C et al (2012) The mammalian gene function resource: The International Knockout Mouse Consortium. Mamm Genome 23:000. doi:10.1007/s00335-012-9422-2

    Google Scholar 

  • Branda CS, Dymecki SM (2004) Talking about a revolution: the impact of site-specific recombinases on genetic analyses in mice. Dev Cell 6(1):7–28

    PubMed  Article  CAS  Google Scholar 

  • Corbel SY, Rossi FM (2002) Latest developments and in vivo use of the Tet system: ex vivo and in vivo delivery of tetracycline-regulated genes. Curr Opin Biotechnol 13(5):448–452

    PubMed  Article  CAS  Google Scholar 

  • Douin V, Bornes S, Creancier L, Rochaix P, Favre G, Prats AC, Couderc B (2004) Use and comparison of different internal ribosomal entry sites (IRES) in tricistronic retroviral vectors. BMC Biotechnol 4:16

    PubMed  Article  Google Scholar 

  • Dymecki SM (1996) Flp recombinase promotes site-specific DNA recombination in embryonic stem cells and transgenic mice. Proc Natl Acad Sci USA 93(12):6191–6196

    PubMed  Article  CAS  Google Scholar 

  • Dymecki SM, Ray RS, Kim JC (2010) Mapping cell fate and function using recombinase-based intersectional strategies. Methods Enzymol 477:183–213

    PubMed  Article  CAS  Google Scholar 

  • Eagleson KL, Schlueter McFadyen-Ketchum LJ, Ahrens ET, Mills PH, Does MD, Nickols J, Levitt P (2007) Disruption of Foxg1 expression by knock-in of cre recombinase: effects on the development of the mouse telencephalon. Neuroscience 148(2):385–399

    PubMed  Article  CAS  Google Scholar 

  • Eckardt D, Theis M, Doring B, Speidel D, Willecke K, Ott T (2004) Spontaneous ectopic recombination in cell-type-specific Cre mice removes loxP-flanked marker cassettes in vivo. Genesis 38(4):159–165

    PubMed  Article  CAS  Google Scholar 

  • Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE (2012) The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res 40(Database issue):D881–D886

  • 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

    PubMed  Article  CAS  Google Scholar 

  • Fex M, Wierup N, Nitert MD, Ristow M, Mulder H (2007) Rat insulin promoter 2-Cre recombinase mice bred onto a pure C57BL/6J background exhibit unaltered glucose tolerance. J Endocrinol 194(3):551–555

    PubMed  Article  CAS  Google Scholar 

  • Forni PE, Scuoppo C, Imayoshi I, Taulli R, Dastru W, Sala V, Betz UA, Muzzi P, Martinuzzi D, Vercelli AE et al (2006) High levels of Cre expression in neuronal progenitors cause defects in brain development leading to microencephaly and hydrocephaly. J Neurosci 26(37):9593–9602

    PubMed  Article  CAS  Google Scholar 

  • Galichet C, Lovell-Badge R, Rizzoti K (2010) Nestin-Cre mice are affected by hypopituitarism, which is not due to significant activity of the transgene in the pituitary gland. PLoS One 5(7):e11443

    PubMed  Article  Google Scholar 

  • Gallardo T, Shirley L, John GB, Castrillon DH (2007) Generation of a germ cell-specific mouse transgenic Cre line, Vasa-Cre. Genesis 45(6):413–417

    PubMed  Article  CAS  Google Scholar 

  • Gong S, Doughty M, Harbaugh CR, Cummins A, Hatten ME, Heintz N, Gerfen CR (2007) Targeting Cre recombinase to specific neuron populations with bacterial artificial chromosome constructs. J Neurosci 27(37):9817–9823

    PubMed  Article  CAS  Google Scholar 

  • Gong S, Kus L, Heintz N (2010) Rapid bacterial artificial chromosome modification for large-scale mouse transgenesis. Nat Protoc 5(10):1678–1696

    PubMed  Article  CAS  Google Scholar 

  • Hebert JM, McConnell SK (2000) Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222(2):296–306

    PubMed  Article  CAS  Google Scholar 

  • Hennecke M, Kwissa M, Metzger K, Oumard A, Kroger A, Schirmbeck R, Reimann J, Hauser H (2001) Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic Acids Res 29(16):3327–3334

    PubMed  Article  CAS  Google Scholar 

  • Higashi AY, Ikawa T, Muramatsu M, Economides AN, Niwa A, Okuda T, Murphy AJ, Rojas J, Heike T, Nakahata T et al (2009) Direct hematological toxicity and illegitimate chromosomal recombination caused by the systemic activation of CreERT2. J Immunol 182(9):5633–5640

    PubMed  Article  CAS  Google Scholar 

  • Hirrlinger J, Requardt RP, Winkler U, Wilhelm F, Schulze C, Hirrlinger PG (2009a) Split-CreERT2: temporal control of DNA recombination mediated by split-Cre protein fragment complementation. PLoS One 4(12):e8354

    PubMed  Article  Google Scholar 

  • Hirrlinger J, Scheller A, Hirrlinger PG, Kellert B, Tang W, Wehr MC, Goebbels S, Reichenbach A, Sprengel R, Rossner MJ et al (2009b) Split-cre complementation indicates coincident activity of different genes in vivo. PLoS One 4(1):e4286

    PubMed  Article  Google Scholar 

  • Hochheiser H, Aronow BJ, Artinger K, Beaty TH, Brinkley JF, Chai Y, Clouthier D, Cunningham ML, Dixon M, Donahue LR et al (2011) The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev Biol 355(2):175–182

    PubMed  Article  CAS  Google Scholar 

  • Huh WJ, Mysorekar IU, Mills JC (2010) Inducible activation of Cre recombinase in adult mice causes gastric epithelial atrophy, metaplasia, and regenerative changes in the absence of “floxed” alleles. Am J Physiol Gastrointest Liver Physiol 299(2):G368–G380

    PubMed  Article  CAS  Google Scholar 

  • Indra AK, Warot X, Brocard J, Bornert JM, Xiao JH, 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-ER(T) and Cre-ER(T2) recombinases. Nucleic Acids Res 27(22):4324–4327

    PubMed  Article  CAS  Google Scholar 

  • Jimeno D, Feiner L, Lillo C, Teofilo K, Goldstein LS, Pierce EA, Williams DS (2006) Analysis of kinesin-2 function in photoreceptor cells using synchronous Cre-loxP knockout of Kif3a with RHO-Cre. Invest Ophthalmol Vis Sci 47(11):5039–5046

    PubMed  Article  Google Scholar 

  • Jullien N, Sampieri F, Enjalbert A, Herman JP (2003) Regulation of Cre recombinase by ligand-induced complementation of inactive fragments. Nucleic Acids Res 31(21):e131

    PubMed  Article  Google Scholar 

  • Jullien N, Goddard I, Selmi-Ruby S, Fina JL, Cremer H, Herman JP (2007) Conditional transgenesis using Dimerizable Cre (DiCre). PLoS One 2(12):e1355

    PubMed  Article  Google Scholar 

  • Kemp R, Ireland H, Clayton E, Houghton C, Howard L, Winton DJ (2004) Elimination of background recombination: somatic induction of Cre by combined transcriptional regulation and hormone binding affinity. Nucleic Acids Res 32(11):e92

    PubMed  Article  Google Scholar 

  • Kim JH, Lee SR, Li LH, Park HJ, Park JH, Lee KY, Kim MK, Shin BA, Choi SY (2011) High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS One 6(4):e18556

    PubMed  Article  CAS  Google Scholar 

  • Kucherlapati MH, Nguyen AA, Bronson RT, Kucherlapati RS (2006) Inactivation of conditional Rb by Villin-Cre leads to aggressive tumors outside the gastrointestinal tract. Cancer Res 66(7):3576–3583

    PubMed  Article  CAS  Google Scholar 

  • Lan Y, Wang Q, Ovitt CE, Jiang R (2007) A unique mouse strain expressing Cre recombinase for tissue-specific analysis of gene function in palate and kidney development. Genesis 45(10):618–624

    PubMed  Article  CAS  Google Scholar 

  • Lee JY, Ristow M, Lin X, White MF, Magnuson MA, Hennighausen L (2006) RIP-Cre revisited, evidence for impairments of pancreatic beta-cell function. J Biol Chem 281(5):2649–2653

    PubMed  Article  CAS  Google Scholar 

  • Leu NA, Kurosaka S, Kashina A (2009) Conditional Tek promoter-driven deletion of arginyltransferase in the germ line causes defects in gametogenesis and early embryonic lethality in mice. PLoS One 4(11):e7734

    PubMed  Article  Google Scholar 

  • Liu Y, Suckale J, Masjkur J, Magro MG, Steffen A, Anastassiadis K, Solimena M (2010) Tamoxifen-independent recombination in the RIP-CreER mouse. PLoS One 5(10):e13533

    PubMed  Article  CAS  Google Scholar 

  • Lomeli H, Ramos-Mejia V, Gertsenstein M, Lobe CG, Nagy A (2000) Targeted insertion of Cre recombinase into the TNAP gene: excision in primordial germ cells. Genesis 26(2):116–117

    PubMed  Article  CAS  Google Scholar 

  • Lu P, Ewald AJ, Martin GR, Werb Z (2008) Genetic mosaic analysis reveals FGF receptor 2 function in terminal end buds during mammary gland branching morphogenesis. Dev Biol 321(1):77–87

    PubMed  Article  CAS  Google Scholar 

  • Madisen L, Zwingman TA, Sunkin SM, Oh SW, Zariwala HA, Gu H, Ng LL, Palmiter RD, Hawrylycz MJ, Jones AR et al (2010) A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat Neurosci 13(1):133–140

    PubMed  Article  CAS  Google Scholar 

  • Madisen L, Mao T, Koch H, Zhuo JM, Berenyi A, Fujisawa S, Hsu YW, Garcia AJ 3rd, Gu X, Zanella S et al (2012) A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing. Nat Neurosci 15(5):793–802

    PubMed  Article  CAS  Google Scholar 

  • Matthaei KI (2007) Genetically manipulated mice: a powerful tool with unsuspected caveats. J Physiol 582(Pt 2):481–488

    PubMed  Article  CAS  Google Scholar 

  • Means AL, Chytil A, Moses HL, Coffey RJ Jr, Wright CV, Taketo MM, Grady WM (2005) Keratin 19 gene drives Cre recombinase expression throughout the early postimplantation mouse embryo. Genesis 42(1):23–27

    PubMed  Article  CAS  Google Scholar 

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

    PubMed  Article  CAS  Google Scholar 

  • Monetti C, Nishino K, Biechele S, Zhang P, Baba T, Woltjen K, Nagy A (2011) PhiC31 integrase facilitates genetic approaches combining multiple recombinases. Methods 53(4):380–385

    PubMed  Article  CAS  Google Scholar 

  • Murray SA (2011) Mouse resources for craniofacial research. Genesis 49(4):190–199

    PubMed  Article  Google Scholar 

  • Nagy A, Mar L, Watts G (2009) Creation and use of a cre recombinase transgenic database. Methods Mol Biol 530:365–378

    PubMed  Article  CAS  Google Scholar 

  • Naiche LA, Papaioannou VE (2007) Cre activity causes widespread apoptosis and lethal anemia during embryonic development. Genesis 45(12):768–775

    PubMed  Article  CAS  Google Scholar 

  • Pilon N, Raiwet D, Viger RS, Silversides DW (2008) Novel pre- and post-gastrulation expression of Gata4 within cells of the inner cell mass and migratory neural crest cells. Dev Dyn 237(4):1133–1143

    PubMed  Article  CAS  Google Scholar 

  • Portales-Casamar E, Swanson DJ, Liu L, de Leeuw CN, Banks KG, Ho Sui SJ, Fulton DL, Ali J, Amirabbasi M, Arenillas DJ et al (2010) A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc Natl Acad Sci USA 107(38):16589–16594

    PubMed  Article  CAS  Google Scholar 

  • Raymond CS, Soriano P (2007) High-efficiency FLP and PhiC31 site-specific recombination in mammalian cells. PLoS One 2(1):e162

    PubMed  Article  Google Scholar 

  • Schmidt-Supprian M, Rajewsky K (2007) Vagaries of conditional gene targeting. Nat Immunol 8(7):665–668

    PubMed  Article  CAS  Google Scholar 

  • Schonig K, Schwenk F, Rajewsky K, Bujard H (2002) Stringent doxycycline dependent control of CRE recombinase in vivo. Nucleic Acids Res 30(23):e134

    PubMed  Article  Google Scholar 

  • Shen L, Nam HS, Song P, Moore H, Anderson SA (2006) FoxG1 haploinsufficiency results in impaired neurogenesis in the postnatal hippocampus and contextual memory deficits. Hippocampus 16(10):875–890

    PubMed  Article  CAS  Google Scholar 

  • Siegenthaler JA, Tremper-Wells BA, Miller MW (2008) Foxg1 haploinsufficiency reduces the population of cortical intermediate progenitor cells: effect of increased p21 expression. Cereb Cortex 18(8):1865–1875

    PubMed  Article  Google Scholar 

  • Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A (2009) BioMart—biological queries made easy. BMC Genomics 10:22

    PubMed  Article  Google Scholar 

  • Smedley D, Salimova E, Rosenthal N (2011) Cre recombinase resources for conditional mouse mutagenesis. Methods 53(4):411–416

    PubMed  Article  CAS  Google Scholar 

  • Soriano P (1999) Generalized lacZ expression with the ROSA26 Cre reporter strain. Nat Genet 21(1):70–71

    PubMed  Article  CAS  Google Scholar 

  • St-Onge L, Furth PA, Gruss P (1996) Temporal control of the Cre recombinase in transgenic mice by a tetracycline responsive promoter. Nucleic Acids Res 24(19):3875–3877

    PubMed  Article  CAS  Google Scholar 

  • Szymczak AL, Vignali DA (2005) Development of 2A peptide-based strategies in the design of multicistronic vectors. Exp Opin Biol Ther 5(5):627–638

    Article  CAS  Google Scholar 

  • Szymczak AL, Workman CJ, Wang Y, Vignali KM, Dilioglou S, Vanin EF, Vignali DA (2004) Correction of multi-gene deficiency in vivo using a single self-cleaving 2A peptide-based retroviral vector. Nat Biotechnol 22(5):589–594

    PubMed  Article  CAS  Google Scholar 

  • Takebayashi H, Usui N, Ono K, Ikenaka K (2008) Tamoxifen modulates apoptosis in multiple modes of action in CreER mice. Genesis 46(12):775–781

    PubMed  Article  CAS  Google Scholar 

  • Taniguchi H, He M, Wu P, Kim S, Paik R, Sugino K, Kvitsiani D, Fu Y, Lu J, Lin Y et al (2011) A resource of Cre driver lines for genetic targeting of GABAergic neurons in cerebral cortex. Neuron 71(6):995–1013

    PubMed  Article  CAS  Google Scholar 

  • Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen-Tsai Y, Luo L (2011) Site-specific integrase-mediated transgenesis in mice via pronuclear injection. Proc Natl Acad Sci USA 108(19):7902–7907

    PubMed  Article  CAS  Google Scholar 

  • Tchorz JS, Suply T, Ksiazek I, Giachino C, Cloetta D, Danzer CP, Doll T, Isken A, Lemaistre M, Taylor V et al (2012) A modified RMCE-compatible Rosa26 locus for the expression of transgenes from exogenous promoters. PLoS One 7(1):e30011

    PubMed  Article  CAS  Google Scholar 

  • Threadgill DW, Dlugosz AA, Hansen LA, Tennenbaum T, Lichti U, Yee D, LaMantia C, Mourton T, Herrup K, Harris RC et al (1995) Targeted disruption of mouse EGF receptor: effect of genetic background on mutant phenotype. Science 269(5221):230–234

    PubMed  Article  CAS  Google Scholar 

  • Ventura A, Kirsch DG, McLaughlin ME, Tuveson DA, Grimm J, Lintault L, Newman J, Reczek EE, Weissleder R, Jacks T (2007) Restoration of p53 function leads to tumour regression in vivo. Nature 445(7128):661–665

    PubMed  Article  CAS  Google Scholar 

  • Weng DY, Zhang Y, Hayashi Y, Kuan CY, Liu CY, Babcock G, Weng WL, Schwemberger S, Kao WW (2008) Promiscuous recombination of LoxP alleles during gametogenesis in cornea Cre driver mice. Mol Vis 14:562–571

    PubMed  CAS  Google Scholar 

  • Wicksteed B, Brissova M, Yan W, Opland DM, Plank JL, Reinert RB, Dickson LM, Tamarina NA, Philipson LH, Shostak A et al (2010) Conditional gene targeting in mouse pancreatic β-cells: analysis of ectopic Cre transgene expression in the brain. Diabetes 59(12):3090–3098

    PubMed  Article  CAS  Google Scholar 

  • Yang GS, Banks KG, Bonaguro RJ, Wilson G, Dreolini L, de Leeuw CN, Liu L, Swanson DJ, Goldowitz D, Holt RA et al (2009) Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the Hprt1 locus. Genomics 93(3):196–204

    PubMed  Article  CAS  Google Scholar 

  • Zambrowicz BP, Imamoto A, Fiering S, Herzenberg LA, Kerr WG, Soriano P (1997) Disruption of overlapping transcripts in the ROSA beta geo 26 gene trap strain leads to widespread expression of beta-galactosidase in mouse embryos and hematopoietic cells. Proc Natl Acad Sci USA 94(8):3789–3794

    PubMed  Article  CAS  Google Scholar 

  • Zhu J, Nguyen MT, Nakamura E, Yang J, Mackem S (2012) Cre-mediated recombination can induce apoptosis in vivo by activating the p53 DNA damage-induced pathway. Genesis 50(2):102–111

    PubMed  Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Laura Kus, Hongkui Zeng, Marie-Christine Burling, and Lauryl Nutter for information about individual cre driver programs. Special thanks to Caleb Heffner for his help with details and references for the JAX cre characterization program. This work was supported by NIH Grants HG000330 (JTE), HD062499 (JTE), RR032656 (JTE and SAM), DE020052 (SAM), RR026117 (SAM), and EU Grant HEALTH-F4-2009-223487 (JTE, DS, and NR).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stephen A. Murray.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Murray, S.A., Eppig, J.T., Smedley, D. et al. Beyond knockouts: cre resources for conditional mutagenesis. Mamm Genome 23, 587–599 (2012). https://doi.org/10.1007/s00335-012-9430-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00335-012-9430-2

Keywords

  • Embryonic Stem Cell Line
  • Public Repository
  • Mouse Genome Informatics
  • International Mouse Phenotyping Consortium
  • International Knockout Mouse Consortium