The Transgeneticist's Toolbox: Novel Methods for the Targeted Modification of Eukaryotic Genomes

Biological Chemistry

Volumn 381, Issue 9-10, 2000, Pages 801-813

  Bode, Jürgen ^a   Schlake, Thomas ^b   Iber, Michaela ^c   Schübeler, Dirk ^d   Seibler, Jost ^e   Snezhkov, Evgeney ^f   Nikolaev, Lev ^f  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b MAX PLANCK INSTITUTE OF IMMUNOBIOLOGY AND EPIGENETICS   (Germany)

^c Basic Science ^*

^d Fred Hutchinson Cancer Research Center   (United States)

^e Artemis Pharmaceuticals GmbH   (Germany)

^f SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

Author keywords

Cosuppresion; Gene transfer; Genomic site; Recombinase mediated cassette exchange (RMCE); Scaffold matrix attached region (S MAR); Site specific recombination

Indexed keywords

RECOMBINASE;

BACTERIOPHAGE; CLONING VECTOR; CONTROLLED STUDY; DNA MODIFICATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; EUKARYOTE; GENE CASSETTE; GENE CONTROL; GENE EXPRESSION; GENE INSERTION; GENE TARGETING; GENE TECHNOLOGY; GENE TRANSFER; GENETIC ANALYSIS; GENETIC RECOMBINATION; GENETIC SCREENING; GENETIC STABILITY; MAMMAL CELL; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; REVIEW; YEAST;

ANIMAL; EUKARYOTIC CELLS; GENE TARGETING; HUMAN; RECOMBINATION, GENETIC; SUPPORT, NON-U.S. GOV'T; TRANSFECTION; TRANSGENES;

EID: 0033790710     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2000.103     Document Type: Article

References (60)

1. Araki, K., Araki, M., and Yamamura, K. I. (1997). Targeted integration of DNA using mutant lox sites in embryonic stem cells. Nucleic Acids Res. 25, 868-872.
2. Artelt, P., Grannemann, R., Stocking, C., Friel, J., Bartsch, J., and Hauser, H. (1991). The prokaryotic neomycin-resistance-encoding gene acts as a transcriptional silencer in eukaryotic cells. Gene 99, 249-254.
3. Askew, G. R., Doetschman, T., and Lingrel, J. B. (1993). Site-directed point mutations in embryonic stem cells: a gene targeting tag-and-exchange strategy. Mol. Cell Biol. 13, 4115-4124.
4. Barinaga, M. (1994). Knockout mice: Round two. Science 265, 26-28.
5. Benham, C., Kohwi-Shigematsu, T., and Bode, J. (1997). Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions. J. Mol. Biol. 274, 181-196.
6. Bethke, B., and Sauer, B. (1997). Segmental genomic replacement by Cre-mediated recombination: Genotoxic stress activation of the p53 promoter in single-copy transformants. Nucleic Acids Res. 25, 2828-2834.
7. Bingham, P. M. (1997). Cosuppression comes to the animals. Cell 90, 385-387.
8. Bode, J., Schlake, T., Rios-Ramirez, M., Mielke, C., Stengert, M., Kay, V., and Klehr-Wirth, D. (1995). Scaffold/Matrix-Attached Regions (S/MARs): Structural Properties Creating Transcriptionally Active Loci. Structural and Functional Organization of the Nuclear Matrix-International Review of Cytology Vol. 162A, K. W. Jeon, and R. Berezney, eds. (Orlando, USA: Academic Press), pp. 389-453.
9. Bode, J., Stengert-Iber, M., Schlake, T., Kay, V., and Dietz-Pfeil-stetter, A. (1996). Scaffold/matrix-attached regions: topological switches with multiple regulatory functions. Crit. Rev. Eukaryot. Gene Expr. 6, 115-138.
10. Bode, J., Bartsch, J., Boulikas, T., Iber, M., Mielke, C., Schubeler, D., Seibler, J., and Benham, C. (1998). Transcription-promoting genomic sites in mammalia: their elucidation and architectural principles. Gene Ther. Mol. Biol. 1, 551-580.
11. Bode, J., Benham, C., Knopp, A., and Mielke, C. (2000). Transcriptional augmentation: modulation of gene expression by scaffold/matrix attached regions (S/MAR elements). Crit. Rev. Eukaryot. Gene Expr. 10, 73-90.
12. Buchholz, F., Ringrose, L., Angrand, P. O., Rossi, F., and Stewart, A. F. (1996). Different thermostabilities of FLP and Cre recombinases: implications for applied site-specific recombination. Nucleic Acids Res. 24, 4256-4262.
13. Capecchi, M. R. (1989). The new mouse genetics: altering the genome by gene targeting. Trends Genet. 5, 70-74.
14. Capecchi, M. R. (1990). Gene targeting: How efficient can you get? Nature 348, 109.
15. Craig, N. L. (1988). The mechanism of conservative site-specific recombination. Annu. Rev. Genet. 22, 77-105.
16. Dang, Q., Auten, J., and Plavec, I. (2000). Human beta interferon scaffold attachment region inhibits de novo methylation and confers long-term, copy number-dependent expression to a retroviral vector. J. Virol. 74, 2671-2678.
17. Feng, Y. Q., Seibler, J., Alami, R., Eisen, A., Westerman, K. A., Leboulch, P., Fiering, S., and Bouhassira, E. E. (1999). Site-specific chromosomal integration in mammalian cells: highly efficient CRE recombinase-mediated cassette exchange. J. Mol. Biol. 292, 779-785.
18. Fiering, S., Kim, C. G., Epner, E. M., and Groudine, M. (1993). An ‘in-out’ strategy using gene targeting and FLP recombinase for the functional dissection of complex DNA regulatory elements: analysis of the 0-globin locus control region. Proc. Natl. Acad. Sci. USA 90, 8469-8473.
19. Fiering, S., Epner, E., Robinson, K., Zhuang, Y., Telling, A., Hu, M., Martin, D. I. K., Enver, T., Ley, T. T., and Groudine, M. (1995). Targeted deletion of 5'HS2 of the murine Beta-globin LCR reveals that it is not essential for proper regulation of the Beta-globin locus. Genes Dev. 9, 2203-2213.
20. Garrick, D., Fiering, S., Martin, D. I. K., and Whitelaw, E. (1998). Repeat-induced gene silencing in mammals. Nature Genet. 18, 56-59.
21. Hortnagel, K., Mautner, J., Strobl, L. J., Wolf, D. A., Christoph, B., Geltinger, C., and Polack, A. (1995). The role of immunoglobulin kappa elements in c-myc activation. Oncogene 10, 1393-1401.
22. Hug, B. A., Wesselschmidt, R. L., Fiering, S., Bender, M. A., Epner, E., Groudine, M., and Ley, T. J. (1996). Analysis of mice containing a targeted deletion of beta-globin locus control region 5' hypersensitive site 3. Mol. Cell. Biol. 16, 2906-2912.
23. Iber, M. (1997). Sequenzspezifische Rekombinationssysteme zur Charakterisierung von SAR-Elementen innerhalb genomischer Referenzintegrationsstellen. Ph.D. thesis, University of Braunschweig, Germany.
24. Iber, M., Schubeler, D., Seibler, J., Hoxter, M., and Bode, J. (1999). Efficient FACS selection procedure for cells undergoing Flp-mediated site-specific conversions. Technical Tips Online, TO1668 (http://tto.trends.com).
25. Kellendonk, C., Tronche, F., Monaghan, A. P., Angrand, P. O., Stewart, F., and Schutz, G. (1996). Regulation of cre recombinase activity by the synthetic steroid RU 48. Nucleic Acids Res. 24, 1404-1411.
26. Kilby, N. J., Snaith, M. R., and Murray, J. A. H. (1993). Site-specific recombinases: tools for genome engineering. Trends Genet. 9, 413-421.
27. Kim, C. G., Epner, E. M., Forrester, W. C., and Groudine, M. (1992). Inactivation of the human beta-globin gene by targeted insertion into the beta-globin locus control region. Genes Dev. 6, 928-938.
28. Klehr, D., and Bode, J. (1988). Comparative evaluation of bovine papilloma virus (BPV) vectors for the study of gene expression in mammalian cells. Mol. Gen. (Life Sci. Adv.) 7, 47-52.
29. Kramer, J. A., Singh, G. B., and Krawetz, S. A. (1996). Computer-assisted search for sites of nuclear matrix attachment. Genomics 33, 305-308.
30. Lakso, M., Pichel, J. G., Gorman, J. R., Sauer, B., Okamoto, Y., Lee, E., Alt, F. W., and Westphal, H. (1996). Efficient in vivo manipulation of mouse genomic sequences at the zygote stage. Proc. Natl. Acad. Sci. USA 93, 5860-5865.
31. Le, Y. Z., Gagneten, S., Tombaccini, D., Bethke, B., and Sauer, B. (1999). Nuclear targeting determinants of the phage P1 Cre DNA recombinase. Nucleic Acids Res. 27, 4703-4709.
32. Lee, G., and Saito, I. (1998). Role of nucleotide sequences of loxP spacer region in Cre-mediated recombination. Gene 216, 55-65.
33. Lyznik, L. A., Mitchell, J. C., Hirayama, L., and Hodges, T. K. (1993). Activity of yeast FLP recombinase in maize and rice protoplasts. Nucleic Acids Res. 21, 969-975.
34. Marshall, E. (1997). The mouse that prompted a roar. Science 277, 24-25.
35. McDevitt, A. M., Shivdasani, A. R., Fujiwara, Y., Yang, D. H., and Orkin, S. (1997). A “knockdown” mutation created by cis-element gene targeting reveals the dependence of erythroid cell maturation on the level of transcription factor GATA-1. Proc. Natl. Acad. Sci. USA 94, 6781-6785.
36. McLeod, M., Craft, S., and Broach, J. R. (1986). Identification of the crossover site during FLP-mediated recombination in the Saccharomyces cerevisiae plasmid 2p, circle. Mol. Cell Biol. 6, 3357-3367.
37. Mielke, C., Maass, K., Tummler, M., and Bode, J. (1996). Anatomy of highly expressing chromosomal sites targeted by retroviral vectors. Biochemistry 35, 2239-2252.
38. O'Gorman, S., Fox, D. T., and Wahl, G. M. (1991). Recombinase-mediated gene activation and site-specific integration in mammalian cells. Science 251, 1351-1355.
39. Oancea, A. E., Berru, M., and Shulman, M. J. (1997). Expression of the (recombinant) endogenous immunoglobulin heavy-chain locus requires the intronic matrix attachment regions. Mol. Cell Biol. 17, 2658-2668.
40. Pham, C. T. N., Maclvor, D. M., Hug, B. A., Heusel, J. W., and Ley, T. J. (1996). Long-range disruption of gene expression by a selectable marker cassette. Proc. Natl. Acad. Sci. USA 93, 13090-13095.
41. Piechaczek, C., Fetzer, C., Baiker, A., Bode, J., and Lipps, H. J. (1999). A vector based on the SV40 origin of replication and chromosomal S/MARs replicates episomally in CHO cells. Nucl. Acids Res. 27, 426-428.
42. Ringrose, L., Angrand, P. O., and Stewart, A. F. (1997). The Kw recombinase, an integrase from Kluyveromyces waltii. Eur. J. Biochem. 248, 903-912.
43. Rodriguez, C. I., Buchholz, F., Galloway, J., Sequerra, R., Kasper, J., Ayala, R., Stewart, A. F., and Dymecki, S. M. (2000). High-efficiency deleter mice show that FLP is an alternative to Cre-loxP Nature Genet. 25, 139-140.
44. Schlake, T., and Bode, J. (1994). Use of mutated FLP-recognition-target-(FRT) sites for the exchange of expression cassettes at defined chromosomal loci. Biochemistry 33, 12746-12751.
45. Schubeler, D., and Bode, J. (1998). Retargeting of retroviral integration sites for the predictable expression of transgenes and the analysis of cis-acting sequences. Biochemistry 37, 11907-11914.
46. Seibler, J., and Bode, J. (1997). Double-reciprocal crossover mediated by FLP-recombinase: a concept and an assay. Biochemistry 36, 1740-1747.
47. Seibler, J., Schubeler, D., Fiering, S., Groudine, M., and Bode, J. (1998a). DNA cassette exchange mediated by FLP recombinase: an efficient strategy for the repeated modification of tagged loci by marker-free constructs. Biochemistry 37, 6229-6234.
48. Seibler, J., Schubeler, D., and Bode, J. (1998b). DNA cassette exchange in regenerative vertebrate cells. European patent application no. 98 103 490.3.
49. Seibler, J. (1999). Sequenzspezifische Rekombination zur geziel-ten Manipulation des Mammaliagenoms. Ph.D. thesis, University of Braunschweig, Germany.
50. Senecoff, J. F., and Cox, M. M. (1986). Directionality in FLP protein-promoted site-specific recombination is mediated by DNA-DNA pairing. J. Biol. Chem. 261, 7380-7386.
51. Senecoff, J. F., Rossmeissl, P. J., and Cox, M. M. (1988). DNA recognition by the FLP recombinase of the yeast 2p, plasmid: a mutational analysis of the FLP binding site. J. Mol. Biol. 201, 405-421.
52. Singh, G. B., Kramer, J. A., and Krawetz, S. A. (1997). Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Res. 25, 1419-1425.
53. Taniguchi, M., Sanbo, M., Watanabe, S., Naruse, I., Mishina, M., and Yagi, T. (1998). 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. 26, 679-680.
54. Umlauf, S. W., and Cox, M. M. (1988). The functional significance of DNA sequence structure in a site-specific genetic recombination reaction. EMBO J. 7, 1845-1852.
55. Verhoeyen, E., Hauser, H., and Wirth, D. (1998). Efficient targeting of retrovirally FRT-tagged chromosomal loci. Technical Tips Online, TO1515 (http://tto.trends.com).
56. Verhoeyen, E. (2000). Efficient targeting of retroviral FRT tagged chromosomal loci and the production of pigs transgenic for human complement regulatory proteins as donors for xenotransplantation. Ph.D. thesis, University of Braunschweig, Germany.
57. Wallace, H., Ansell, R., Clark, J., and McWhir, J. (2000). Pre-selection of integration sites imparts repeatable transgene expression. Nucleic Acids Res. 28, 1455-1464.
58. Waterhouse, P, Griffiths, A. D., Johnson, K. S., and Winter, G. (1993). Combinatorial infection and in vivo recombination: a strategy for making large phage antibody repertoires. Nucleic Acids Res. 21, 2265-2266.
59. Wirth, M., Bode, J., ZettlmeiBl, G., and Hauser, H. (1988). Isolation of overproducing recombinant mammalian cell lines by a fast and simple selection procedure. Gene 73, 419-426.
60. Wu, H., Liu, X., and Jaenisch, R. (1994). Double replacement: strategy for efficient introduction of subtle mutations into the murine Colla-1 gene by homologous recombination in embryonic stem cells. Proc. Natl. Acad. Sci. USA 91, 2819-2823.