Gene Knockout Protocols pp 49-77

Part of the Methods in Molecular Biology book series (MIMB, volume 530) | Cite as

Chromosome Engineering in ES Cells

  • Louise van der Weyden
  • Charles Shaw-Smith
  • Allan Bradley
Protocol

Abstract

Chromosomal rearrangements, such as deletions, duplications, inversions and translocations, occur frequently in humans and can be disease-associated or phenotypically neutral. To understand the genetic consequences of such genomic changes, these mutations need to be modelled in experimentally tractable systems. The mouse is an excellent organism for this analysis because of its biological and genetic similarity to humans, the ease with which its genome can be manipulated and the similarity of observed affects. Through chromosome engineering, defined rearrangements can be introduced into the mouse genome. The resulting mouse models are leading to a better understanding of the molecular and cellular basis of dosage alterations in human disease phenotypes, in turn opening new diagnostic and therapeutic opportunities.

Key words

Chromosomal rearrangements Cre recombinase loxP mouse genome embryonic stem cell 

References

  1. 1.
    Davisson MT, Schmidt C, Reeves RH et al. Segmental trisomy as a mouse model for Down syndrome. Prog Clin Biol Res 1993;384:117–33.PubMedGoogle Scholar
  2. 2.
    Reeves RH, Irving NG, Moran TH et al. A mouse model for Down syndrome exhibits learning and behaviour deficits. Nat Genet 1995;11:177–84.PubMedCrossRefGoogle Scholar
  3. 3.
    Zheng B, Mills AA, Bradley A. A system for rapid generation of coat color-tagged knockouts and defined chromosomal rearrangements in mice. Nucleic Acids Res 1999;27:2354–60.PubMedCrossRefGoogle Scholar
  4. 4.
    van der Weyden L, Bradley A. Mouse: chromosome engineering for modeling human disease. Annu Rev Genomics Hum Genet 2006;7:247–76.PubMedCrossRefGoogle Scholar
  5. 5.
    Ramirez-Solis R, Liu P, Bradley A. Chromosome engineering in mice. Nature 1995;378:720–4.PubMedCrossRefGoogle Scholar
  6. 6.
    Smith AJ, De Sousa MA, Kwabi-Addo B, Heppell-Parton A, Impey H, Rabbitts P. A site-directed chromosomal translocation induced in embryonic stem cells by Cre-loxP recombination. Nat Genet 1995;9:376–85.PubMedCrossRefGoogle Scholar
  7. 7.
    Li ZW, Stark G, Gotz J et al. Generation of mice with a 200-kb amyloid precursor protein gene deletion by Cre recombinase-mediated site-specific recombination in embryonic stem cells. Proc Natl Acad Sci USA 1996;93:6158–62.PubMedCrossRefGoogle Scholar
  8. 8.
    Van Deursen J, Fornerod M, Van Rees B, Grosveld G. Cre-mediated site-specific translocation between nonhomologous mouse chromosomes. Proc Natl Acad Sci USA 1995;92:7376–80.PubMedCrossRefGoogle Scholar
  9. 9.
    Mills AA, Zheng B, Wang XJ, Vogel H, Roop DR, Bradley A. p63 is a p53 homologue required for limb and epidermal morphogenesis. Nature 1999;398:708–13.PubMedCrossRefGoogle Scholar
  10. 10.
    Lindsay EA, Botta A, Jurecic V et al. Congenital heart disease in mice deficient for the DiGeorge syndrome region. Nature 1999;401:379–83.PubMedGoogle Scholar
  11. 11.
    Walz K, Caratini-Rivera S, Bi W, Fonseca P et al. Modeling del(17)(p11.2p11.2) and dup(17)(p11.2p11.2) contiguous gene syndromes by chromosome engineering in mice: phenotypic consequences of gene dosage imbalance. Mol Cell Biol 2003;23:3646–55.PubMedCrossRefGoogle Scholar
  12. 12.
    Medina-Martinez O, Bradley A, Ramirez-Solis R. A large targeted deletion of Hoxb1-Hoxb9 produces a series of single-segment anterior homeotic transformations. Dev Biol 2000;222:71–83.PubMedCrossRefGoogle Scholar
  13. 13.
    Zheng B, Sage M, Sheppeard EA, Jurecic V, Bradley A. Engineering mouse chromosomes with Cre-loxP: range, efficiency, and somatic applications. Mol Cell Biol 2000;20:648–55.PubMedCrossRefGoogle Scholar
  14. 14.
    Nishijima I, Mills A, Qi Y, Mills M, Bradley A. Two new balancer chromosomes on mouse chromosome 4 to facilitate functional annotation of human chromosome 1p. Genesis 2003;36:142–8.PubMedCrossRefGoogle Scholar
  15. 15.
    O’Gorman S, Dagenais NA, Qian M, Marchuk Y. Protamine-Cre recombinase transgenes efficiently recombine target sequences in the male germ line of mice, but not in embryonic stem cells. Proc Natl Acad Sci USA 1997;94:14602–7.PubMedCrossRefGoogle Scholar
  16. 16.
    Taniguchi M, Sanbo M, Watanabe S, Naruse I, Mishina M, Yagi T. Efficient production of Cre-mediated site-directed recombinants through the utilization of the puromycin resistance gene, pac: a transient gene-integration marker for ES cells. Nucleic Acids Res 1998;26:679–80.PubMedCrossRefGoogle Scholar
  17. 17.
    Sauer B, Henderson N. Targeted insertion of exogenous DNA into the eukaryotic genome by the Cre recombinase. New Biol 1990;2:441–9.PubMedGoogle Scholar
  18. 18.
    Liu Q, Li MZ, Leibham D, Cortez D, Elledge SJ. The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes. Curr Biol 1998;8:1300–9.PubMedCrossRefGoogle Scholar
  19. 19.
    Adams DJ, Biggs PJ, Cox T et al. Mutagenic insertion and chromosome engineering resource (MICER). Nat Genet 2004;36:867–71.PubMedCrossRefGoogle Scholar
  20. 20.
    van der Weyden L, Adams DJ, Bradley A. Tools for targeted manipulation of the mouse genome. Physiol Genomics 2002;11:133–64.PubMedGoogle Scholar
  21. 21.
    Hubbard TJ, Aken BL, Beal K et al. Ensembl. Nucleic Acids Res 2007;35:D610–7.PubMedCrossRefGoogle Scholar
  22. 22.
    Liu P, Jenkins NA, Copeland NG. A highly efficient recombineering-based method for generating conditional knockout mutations. Genome Res 13: 476–484.Google Scholar
  23. 23.
    Adams DJ, Quail MA, Cox T et al. A genome-wide, end-sequenced 129 Sv BAC library resource for targeting vector construction. Genomics 2005;86:753–8.PubMedCrossRefGoogle Scholar
  24. 24.
    Ohtsuka M, Ishii K, Kikuti YY et al. Construction of mouse 129/Ola BAC library for targeting experiments using E14 embryonic stem cells. Genes Genet Syst 2006;81:143–6.PubMedCrossRefGoogle Scholar
  25. 25.
    Yokoyama T, Silversides DW, Waymire KG, Kwon BS, Takeuchi T, Overbeek PA. Conserved cysteine to serine mutation in tyrosinase is responsible for the classical albino mutation in laboratory mice. Nucleic Acids Res 1990;18:7293–8.PubMedCrossRefGoogle Scholar
  26. 26.
    Overbeek PA, Aguilar-Cordova E, Hanten G et al. Coinjection strategy for visual identification of transgenic mice. Transgenic Res 1991;1:31–7.PubMedCrossRefGoogle Scholar
  27. 27.
    Kucera GT, Bortner DM, Rosenberg MP. Overexpression of an Agouti cDNA in the skin of transgenic mice recapitulates dominant coat color phenotypes of spontaneous mutants. Dev Biol 1996;173:162–73.PubMedCrossRefGoogle Scholar
  28. 28.
    Bagchi A, Papazoglu C, Wu Y et al. CHD5 is a tumor suppressor at human 1p36. Cell 2007;128:459–75.PubMedCrossRefGoogle Scholar
  29. 29.
    You Y, Bergstrom R, Klemm M et al. Chromosomal deletion complexes in mice by radiation of embryonic stem cells. Nat Genet 1997;15:285–8.PubMedCrossRefGoogle Scholar
  30. 30.
    Schimenti JC, Libby BJ, Bergstrom RA et al. Interdigitated deletion complexes on mouse chromosome 5 induced by irradiation of embryonic stem cells. Genome Res 2000;10:1043–50.PubMedCrossRefGoogle Scholar
  31. 31.
    Chick WS, Mentzer SE, Carpenter DA, Rinchik EM, Johnson D, You Y. X-ray-induced deletion complexes in embryonic stem cells on mouse chromosome 15. Mamm Genome 2005;16:661–71.PubMedCrossRefGoogle Scholar
  32. 32.
    You Y, Browning VL, Schimenti JC. Generation of radiation-induced deletion complexes in the mouse genome using embryonic stem cells. Methods 1997;13:409–21.PubMedCrossRefGoogle Scholar
  33. 33.
    Thomas JW, LaMantia C, Magnuson T. X-ray-induced mutations in mouse embryonic stem cells. Proc Natl Acad Sci USA 1998;95:1114–9.PubMedCrossRefGoogle Scholar
  34. 34.
    Goodwin NC, Ishida Y, Hartford S, Wnek C, Bergstrom RA, Leder P, Schimenti JC. DelBank: a mouse ES-cell resource for generating deletions. Nat Genet 2001;28:310–1.PubMedCrossRefGoogle Scholar
  35. 35.
    Herault Y, Rassoulzadegan M, Cuzin F, Duboule D. Engineering chromosomes in mice through targeted meiotic recombination (TAMERE). Nat Genet 1998;20:381–4.PubMedCrossRefGoogle Scholar
  36. 36.
    Tarchini B, Huynh TH, Cox GA, Duboule D. HoxD cluster scanning deletions identify multiple defects leading to paralysis in the mouse mutant Ironside. Genes Dev 2005;19:2862–76.PubMedCrossRefGoogle Scholar
  37. 37.
    Tang SH, Silva FJ, Tsark WM, Mann JR. A Cre/loxP-deleter transgenic line in mouse strain 129S1/SvImJ. Genesis 2002;32:199–202.PubMedCrossRefGoogle Scholar
  38. 38.
    Wu S, Ying G, Wu Q, Capecchi MR. Toward simpler and faster genome-wide mutagenesis in mice. Nat Genet 2007;39:922–30.PubMedCrossRefGoogle Scholar
  39. 39.
    Olson LE, Tien J, South S, Reeves RH. Long-range chromosomal engineering is more efficient in vitro than in vivo. Transgenic Res 2005;4:25–32.Google Scholar
  40. 40.
    Spitz F, Herkenne C, Morris MA, Duboule D. Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat Genet 2005;37:889–93.PubMedCrossRefGoogle Scholar
  41. 41.
    Lindsay EA, Vitelli F, Su H et al. Tbx1 haploinsufficiency in the DiGeorge syndrome region causes aortic arch defects in mice. Nature 2001;410:97–101.PubMedCrossRefGoogle Scholar
  42. 42.
    Yu Y, Bradley A. Mouse genomic technologies: engineering chromosomal rearrangements in mice. Nat Rev Genet 2001;2:780–90.PubMedCrossRefGoogle Scholar
  43. 43.
    Su H, Wang X, Bradley A. Nested chromosomal deletions induced with retroviral vectors in mice. Nat Genet 2000;24:92–5.PubMedCrossRefGoogle Scholar
  44. 44.
    Yan J, Keener VW, Bi W et al. Reduced penetrance of craniofacial anomalies as a function of deletion size and genetic background in a chromosome engineered partial mouse model for Smith–Magenis syndrome. Hum Mol Genet 2004;13:2613–24.PubMedCrossRefGoogle Scholar
  45. 45.
    LePage DF, Church DM, Millie E, Hassold TJ, Conlon RA. Rapid generation of nested chromosomal deletions on mouse chromosome 2. Proc Natl Acad Sci USA 2000;97:10471–76.PubMedCrossRefGoogle Scholar
  46. 46.
    Kushi A, Edamura K, Noguchi M, Akiyama K, Nishi Y, Sasai H. Generation of mutant mice with large chromosomal deletion by use of irradiated ES cells: analysis of large deletion around hprt locus of ES cell. Mamm Genome 1998;9:269–73.PubMedCrossRefGoogle Scholar
  47. 47.
    Bergstrom DE, Bergstrom RA, Munroe RJ et al. Overlapping deletions spanning the proximal two-thirds of the mouse t complex. Mamm Genome 2003;14:817–29.PubMedCrossRefGoogle Scholar
  48. 48.
    Liu P, Zhang H, McLellan A, Vogel H, Bradley A. Embryonic lethality and tumorigenesis caused by segmental aneuploidy on mouse chromosome 11. Genetics 1998;150:1155–68.PubMedGoogle Scholar
  49. 49.
    Yu YE, Morishima M, Pao A et al. A deficiency in the region homologous to human 17q21.33–q23.2 causes heart defects in mice. Genetics 2006;173:297–307.PubMedCrossRefGoogle Scholar
  50. 50.
    Schwenk F, Baron U, Rajewsky K. A cre-transgenic mouse strain for the ubiquitous deletion of loxP-flanked gene segments including deletion in germ cells. Nucleic Acids Res 1995;23:5080–1.PubMedCrossRefGoogle Scholar
  51. 51.
    Su H, Mills AA, Wang X, Bradley A. A targeted X-linked CMV-Cre line. Genesis 2002;32:187–8.PubMedCrossRefGoogle Scholar
  52. 52.
    Davisson MT, Schmidt C, Akeson EC. Segmental trisomy of murine chromosome 16: a new model system for studying Down syndrome. Prog Clin Biol Res 1990;360:263–80.PubMedGoogle Scholar
  53. 53.
    Davisson MT, Schmidt C, Reeves RH et al. Segmental trisomy as a mouse model for Down syndrome. Prog Clin Biol Res 1993;384:117–33.PubMedGoogle Scholar
  54. 54.
    Richtsmeier JT, Baxter LL, Reeves RH. Parallels of craniofacial maldevelopment in Down syndrome and Ts65Dn mice. Dev Dyn 2000;217:137–45.PubMedCrossRefGoogle Scholar
  55. 55.
    Olson LE, Richtsmeier JT, Leszl J, Reeves RH. A chromosome 21 critical region does not cause specific Down syndrome phenotypes. Science 2004;306:687–90.PubMedCrossRefGoogle Scholar
  56. 56.
    Li Z, Yu T, Morishima M et al. Duplication of the entire 22.9 Mb human chromosome 21 syntenic region on mouse chromosome 16 causes cardiovascular and gastrointestinal abnormalities. Hum Mol Genet 2007;16:1359–66.PubMedCrossRefGoogle Scholar
  57. 57.
    Hentges KE, Justice MJ. Checks and balancers: balancer chromosomes to facilitate genome annotation. Trends Genet 2004;20:252–59.PubMedCrossRefGoogle Scholar
  58. 58.
    Roderick TH, Hawes NL. Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci USA 1970;67:961–7.PubMedCrossRefGoogle Scholar
  59. 59.
    Roderick TH, Hawes NL. Nineteen paracentric chromosomal inversions in mice. Genetics 1974;76:109–17.PubMedGoogle Scholar
  60. 60.
    Zheng B, Sage M, Cai WW et al. Engineering a mouse balancer chromosome. Nat Genet 1999;22:375–8.PubMedCrossRefGoogle Scholar
  61. 61.
    Chick WS, Mentzer SE, Carpenter DA, Rinchik EM, You Y. Modification of an existing chromosomal inversion to engineer a balancer for mouse chromosome 15. Genetics 2004;167:889–95.PubMedCrossRefGoogle Scholar
  62. 62.
    Klysik J, Dinh C, Bradley A. Two new mouse chromosome 11 balancers. Genomics 2004;83:303–10.PubMedCrossRefGoogle Scholar
  63. 63.
    Rabbitts TH. Chromosomal translocations in human cancer. Nature 1994;372:143–9.PubMedCrossRefGoogle Scholar
  64. 64.
    Mitelman F, Mertens F, Johansson B. A breakpoint map of recurrent chromosomal rearrangements in human neoplasia. Nat Genet 1997;15:417–74.PubMedCrossRefGoogle Scholar
  65. 65.
    Look AT. Oncogenic transcription factors in the human acute leukemias. Science 1997;278:1059–64.PubMedCrossRefGoogle Scholar
  66. 66.
    Corral J, Lavenir I, Impey H et al. An Mll-AF9 fusion gene made by homologous recombination causes acute leukemia in chimeric mice: a method to create fusion oncogenes. Cell 1996;85:853–61.PubMedCrossRefGoogle Scholar
  67. 67.
    Okuda T, Cai Z, Yang S et al. Expression of a knocked-in AML1-ETO leukemia gene inhibits the establishment of normal definitive hematopoiesis and directly generates dysplastic hematopoietic progenitors. Blood 1998;91:3134–43.PubMedGoogle Scholar
  68. 68.
    Yergeau DA, Hetherington CJ, Wang Q et al. Embryonic lethality and impairment of haematopoiesis in mice heterozygous for an AML1-ETO fusion gene. Nat Genet 1997;15:303–6.PubMedCrossRefGoogle Scholar
  69. 69.
    Pollock JL, Westervelt P, Kurichety AK, Pelicci PG, Grisolano JL, Ley TJ. A bcr-3 isoform of RARα-PML potentiates the development of PML-RARα-driven acute promyelocytic leukemia. Proc Natl Acad Sci USA 1999;96:15103–8.PubMedCrossRefGoogle Scholar
  70. 70.
    Higuchi M, O’Brien D, Kumaravelu P, Lenny N, Yeoh EJ, Downing JR. Expression of a conditional AML1-ETO oncogene bypasses embryonic lethality and establishes a murine model of human t(8;21) acute myeloid leukemia. Cancer Cell 2002;163–74.Google Scholar
  71. 71.
    Collins EC, Pannell R, Simpson EM, Forster A, Rabbitts TH. Inter-chromosomal recombination of Mll and Af9 genes mediated by cre-loxP in mouse development. EMBO Rep 2000;1:127–32.PubMedCrossRefGoogle Scholar
  72. 72.
    Forster A, Pannell R, Drynan LF et al. Engineering de novo reciprocal chromosomal translocations associated with Mll to replicate primary events of human cancer. Cancer Cell 2003;3:449–58.PubMedCrossRefGoogle Scholar
  73. 73.
    Drynan LF, Pannell R, Forster A et al. Mll fusions generated by Cre-loxP-mediated de novo translocations can induce lineage reassignment in tumorigenesis. EMBO J 2005;24:3136–46.PubMedCrossRefGoogle Scholar
  74. 74.
    Lyon MF, Meredith R. Autosomal translocations causing male sterility and viable aneuploidy in the mouse. Cytogenetics 1966;5:335–54.PubMedCrossRefGoogle Scholar
  75. 75.
    Zheng B, Mills AA, Bradley A. Introducing defined chromosomal rearrangements into the mouse genome. Methods 2001;24:81–94.PubMedCrossRefGoogle Scholar
  76. 76.
    Chung YJ, Jonkers J, Kitson H et al. A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization. Genome Res 2004;14:188–96.PubMedCrossRefGoogle Scholar
  77. 77.
    Agah R, Frenkel PA, French BA, Michael LH, Overbeek PA, Schneider MD. Gene recombination in postmitotic cells. Targeted expression of Cre recombinase provokes cardiac-restricted, site-specific rearrangement in adult ventricular muscle in vivo. J Clin Invest 1997;100:169–79.PubMedCrossRefGoogle Scholar
  78. 78.
    Johnson L, Mercer K, Greenbaum D et al. Somatic activation of the K-ras oncogene causes early onset lung cancer in mice. Nature 2001;410:1111–6.PubMedCrossRefGoogle Scholar
  79. 79.
    Garcia-Otin AL, Guillou F. Mammalian genome targeting using site-specific recombinases. Front Biosci 2006;11:1108–36.PubMedCrossRefGoogle Scholar
  80. 80.
    Saam JR, Gordon JI. Inducible gene knockouts in the small intestine and colonic epithelium. J Biol Chem 1999;274:38071–82.PubMedCrossRefGoogle Scholar
  81. 81.
    Schönig K, Schwenk F, Rajewsky K, Bujard H. Stringent doxycycline dependent control of Cre recombinase in vivo. Nucleic Acids Res 2002;30 e134.PubMedCrossRefGoogle Scholar
  82. 82.
    Perl AK, Wert SE, Nagy A, Lobe CG, Whittsett JA. Early restriction of peripheral and proximal cell lineages during formation of the lung. Proc Natl Acad Sci USA 2002;99:10482–7.PubMedCrossRefGoogle Scholar
  83. 83.
    Schuler M, Dierich A, Chambon P, Metzger D. Efficient temporally controlled targeted somatic mutagenesis in hepatocytes of the mouse. Genesis 2004;39:167–72.PubMedCrossRefGoogle Scholar
  84. 84.
    El Marjou F, Janssen KP, Chang BHJ et al. Tissue-specific and inducible Cre-mediated recombination in the gut epithelium. Genesis 2004;39:186–93.PubMedCrossRefGoogle Scholar
  85. 85.
    Kemp R, Ireland H, Clayton E, Houghton C, Howard L, Winton DJ. Elimination of background recombination: somatic induction of Cre by combined transcriptional regulation and hormone binding affinity. Nucleic Acids Res 2004;32:e92.PubMedCrossRefGoogle Scholar
  86. 86.
    Weber P, Schuler M, Gerard C, Mark M, Metzger D, Chambon P. Temporally controlled site-specific mutagenesis in the germ cell lineage of the mouse testis. Biol Reprod 2003;68:553–9.PubMedCrossRefGoogle Scholar
  87. 87.
    Yajima I, Belloir E, Bourgeois Y, Kumasaka M, Delmas V, Larue L. Spatiotemporal gene control by the Cre-ERT2 system in melanocytes. Genesis 2006;44:34–43.PubMedCrossRefGoogle Scholar
  88. 88.
    Hirrlinger PG, Scheller A, Braun C, Hirrlinger J, Kirchhoff F. Temporal control of gene recombination in astrocytes by transgenic expression of the tamoxifen-inducible DNA recombinase variant CreERT2. Glia 2006;54:11–20.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Louise van der Weyden
    • 1
  • Charles Shaw-Smith
    • 1
  • Allan Bradley
    • 1
  1. 1.Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusHinxtonUK

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