Captured segment exchange: A strategy for custom engineering large genomic regions in Drosophila melanogaster

Genetics

Volumn 193, Issue 2, 2013, Pages 421-430

  Bateman, Jack R ^a   Palopoli, Michael F ^a   Dale, Sarah T ^a   Stauffer, Jennifer E ^a   Shah, Anita L ^a   Johnson, Justine E ^a   Walsh, Conor W ^a   Flaten, Hanna ^a   Parsons, Christine M ^a  

^a BOWDOIN COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; RECOMBINASE; SITE SPECIFIC RECOMBINASE; UNCLASSIFIED DRUG;

ARTICLE; CAPTURED SEGMENT EXCHANGE; DROSOPHILA MELANOGASTER; ENZYME ACTIVITY; GENE CASSETTE; GENE FUNCTION; GENE INSERTION; GENE LOCUS; GENE SEQUENCE; GENETIC ENGINEERING; GENETIC MANIPULATION; GENETIC RECOMBINATION; GENOME SIZE; INSECT GENOME; NONHUMAN; PRIORITY JOURNAL; RECOMBINASE MEDIATED CASSETTE EXCHANGE;

ANIMALS; DNA NUCLEOTIDYLTRANSFERASES; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENE TARGETING; GENOME, INSECT; INTEGRASES; MUTAGENESIS, INSERTIONAL; MUTAGENESIS, SITE-DIRECTED; REPRESSOR PROTEINS;

BACTERIA (MICROORGANISMS); DROSOPHILA MELANOGASTER;

EID: 84876348522     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.145748     Document Type: Article

References (39)

1. Anderson, R. P., E. Voziyanova, and Y. Voziyanov, 2012 Flp and Cre expressed from Flp-2A-Cre and Flp-IRES-Cre transcription units mediate the highest level of dual recombinase-mediated cassette exchange. Nucleic Acids Res. 40: e62.
2. Baer, A., and J. Bode, 2001 Coping with kinetic and thermodynamic barriers: RMCE, an efficient strategy for the targeted integration of transgenes. Curr. Opin. Biotechnol. 12: 473-480.
3. Bateman, J. R., and C. T. Wu, 2008 A simple polymerase chain reaction-based method for the construction of recombinase-mediated cassette exchange donor vectors. Genetics 180: 1763-1766.
4. Bateman, J. R., A. M. Lee, and C. T. Wu, 2006 Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange. Genetics 173: 769-777.
5. Bateman, J. R., J. E. Johnson, and M. N. Locke, 2012 Comparing enhancer action in cis and in trans. Genetics 191: 1143-1155.
6. Bellen, H. J., R.W. Levis, G. Liao, Y. He, J. W. Carlson et al., 2004 The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics 167: 761-781.
7. Bischof, J., R. K. Maeda, M. Hediger, F. Karch, and K. Basler, 2007 An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc. Natl. Acad. Sci. USA 104: 3312-3317.
8. Branda, C. S., and S. M. Dymecki, 2004 Talking about a revolution: the impact of site-specific recombinases on genetic analyses in mice. Dev. Cell 6: 7-28.
9. Choi, C. M., S. Vilain, M. Langen, S. Van Kelst, N. De Geest et al., 2009 Conditional mutagenesis in Drosophila. Science 324: 54.
10. Court, D. L., S. Swaminathan, D. Yu, H. Wilson, T. Baker et al., 2003 Mini-lambda: a tractable system for chromosome and BAC engineering. Gene 315: 63-69.
11. Crosby, M. A., J. L. Goodman, V. B. Strelets, P. Zhang, W. M. Gelbart et al., 2007 FlyBase: genomes by the dozen. Nucleic Acids Res. 35: D486-D491.
12. Gao, G., C. McMahon, J. Chen, and Y. S. Rong, 2008 A powerful method combining homologous recombination and site-specific recombination for targeted mutagenesis in Drosophila. Proc. Natl. Acad. Sci. USA 105: 13999-14004.
13. Gloor, G. B., N. A. Nassif, D. M. Johnson-Schlitz, C. R. Preston, and W. R. Engels, 1991 Targeted gene replacement in Drosophila via P element-induced gap repair. Science 253: 1110-1117.
14. Golic, K. G., and M. M. Golic, 1996 Engineering the Drosophila genome: chromosome rearrangements by design. Genetics 144: 1693-1711.
15. Gong, W. J., and K. G. Golic, 2003 Ends-out, or replacement, gene targeting in Drosophila. Proc. Natl. Acad. Sci. USA 100: 2556-2561.
16. Groth, A. C., M. Fish, R. Nusse, and M. P. Calos, 2004 Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics 166: 1775-1782.
17. Horton, R. M., Z. L. Cai, S. N. Ho, and L. R. Pease, 1990 Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques 8: 528-535.
18. Huang, J., W. Zhou, W. Dong, A. M. Watson, and Y. Hong, 2009 From the cover: directed, efficient, and versatile modifications of the Drosophila genome by genomic engineering. Proc. Natl. Acad. Sci. USA 106: 8284-8289.
19. Lauth, M., F. Spreafico, K. Dethleffsen, and M. Meyer, 2002 Stable and efficient cassette exchange under non-selectable conditions by combined use of two site-specific recombinases. Nucleic Acids Res. 30: e115.
20. Lee, E. C., D. Yu, J. Martinez de Velasco, L. Tessarollo, D. A. Swing et al., 2001 A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73: 56-65.
21. Markstein, M., C. Pitsouli, C. Villalta, S. E. Celniker, and N. Perrimon, 2008 Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat. Genet. 40: 476-483.
22. Morris, J. R., J. L. Chen, P. K. Geyer, and C. T. Wu, 1998 Two modes of transvection: enhancer action in trans and bypass of a chromatin insulator in cis. Proc. Natl. Acad. Sci. USA 95: 10740-10745.
23. Moses, K., and G. M. Rubin, 1991 Glass encodes a site-specific DNA-binding protein that is regulated in response to positional signals in the developing Drosophila eye. Genes Dev. 5: 583-593.
24. Negre, N., C. D. Brown, L. Ma, C. A. Bristow, S. W. Miller et al., 2011 A cis-regulatory map of the Drosophila genome. Nature 471: 527-531.
25. Nern, A., B. D. Pfeiffer, K. Svoboda, and G. M. Rubin, 2011 Multiple new site-specific recombinases for use in manipulating animal genomes. Proc. Natl. Acad. Sci. USA 108: 14198-14203.
26. Osterwalder, M., A. Galli, B. Rosen, W. C. Skarnes, R. Zeller et al., 2010 Dual RMCE for efficient re-engineering of mouse mutant alleles. Nat. Methods 7: 893-895.
27. Parks, A. L., K. R. Cook, M. Belvin, N. A. Dompe, R. Fawcett et al., 2004 Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome. Nat. Genet. 36: 288-292.
28. Rong, Y. S., and K. G. Golic, 2000 Gene targeting by homologous recombination in Drosophila. Science 288: 2013-2018.
29. Roy, S., J. Ernst, P. V. Kharchenko, P. Kheradpour, N. Negre et al., 2010 Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
30. Ryder, E., F. Blows, M. Ashburner, R. Bautista-Llacer, D. Coulson et al., 2004 The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. Genetics 167: 797-813.
31. Sharan, S. K., L. C. Thomason, S. G. Kuznetsov, and D. L. Court, 2009 Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 4: 206-223.
32. Smith, M. C., W. R. Brown, A. R. McEwan, and P. A. Rowley, 2010 Site-specific recombination by phiC31 integrase and other large serine recombinases. Biochem. Soc. Trans. 38: 388-394.
33. Thibault, S. T., M. A. Singer, W. Y. Miyazaki, B. Milash, N. A. Dompe et al., 2004 A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat. Genet. 36: 283-287.
34. Venken, K. J., and H. J. Bellen, 2005 Emerging technologies for gene manipulation in Drosophila melanogaster. Nat. Rev. Genet. 6: 167-178.
35. Venken, K. J., and H. J. Bellen, 2007 Transgenesis upgrades for Drosophila melanogaster. Development 134: 3571-3584.
36. Venken, K. J., Y. He, R. A. Hoskins, and H. J. Bellen, 2006 P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster. Science 314: 1747-1751.
37. Venken, K. J. T., K. L. Schulze, N. A. Haelterman, H. Pan, Y. He et al., 2011 MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes. Nat. Methods 8: 737-743.
38. Warming, S., N. Costantino, D. L. Court, N. A. Jenkins, and N. G. Copeland, 2005 Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res. 33: e36.
39. Weng, R., Y. W. Chen, N. Bushati, A. Cliffe, and S. M. Cohen, 2009 Recombinase-mediated cassette exchange provides a versatile platform for gene targeting: knockout of miR-31b. Genetics 183: 399-402.