An enhanced gene targeting toolkit for Drosophila: Golic+

Genetics

Volumn 199, Issue 3, 2015, Pages 683-694

  Chen, Hui Min ^a,b   Huang, Yaling ^a,c   Pfeiffer, Barret D ^a   Yao, Xiaohao ^a   Lee, Tzumin ^a,b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

CRISPR; Drosophila; Gene targeting; Homologous recombination; Repressor miRNA based lethality selection

Indexed keywords

CRISPR ASSOCIATED PROTEIN; DNA FRAGMENT; GUIDE RNA; DNA;

ADULT; ARTICLE; CHROMOSOME MAP; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; DROSOPHILA; FEMALE; GENE LOCUS; GENE MAPPING; GENE TARGETING; GENETIC CROSS; GENETIC ENGINEERING; GENETIC SELECTION; GERMLINE STEM CELL; HOMOLOGOUS RECOMBINATION; LOXP SITE; MOLECULAR CLONING; NEUROECTODERM; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REPRESSOR GENE; RNA EDITING; X CHROMOSOME; ANIMAL; GENETICS; OOCYTE DEVELOPMENT; OVUM; PROCEDURES; TRANSGENE;

ANIMALS; DNA; DROSOPHILA; FEMALE; GENE TARGETING; HOMOLOGOUS RECOMBINATION; OOGENESIS; OVUM; TRANSGENES;

EID: 84925004001     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.173716     Document Type: Article

References (58)

1. Awasaki, T., C. F. Kao, Y. J. Lee, C. P. Yang, Y. Huang et al., 2014 Making Drosophila lineage-restricted drivers via patterned recombination in neuroblasts. Nat. Neurosci. 17: 631–637.
2. Baena-Lopez, L. A., C. Alexandre, A. Mitchell, L. Pasakarnis, and J. P. Vincent, 2013 Accelerated homologous recombination and subsequent genome modification in Drosophila. Development 140: 4818–4825.
3. Bassett, A. R., and J. L. Liu, 2014 CRISPR/Cas9 and genome editing in Drosophila. J. Genet. Genomics 41: 7–19.
4. Bassett, A. R., C. Tibbit, C. P. Ponting, and J. L. Liu, 2013 Highly efficient targeted mutagenesis of Drosophila with the CRISPR/ Cas9 system. Cell Rep. 4: 220–228.
5. Beumer, K. J., J. K. Trautman, A. Bozas, J. L. Liu, J. Rutter et al., 2008 Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc. Natl. Acad. Sci. USA 105: 19821–19826.
6. Beumer, K. J., J. K. Trautman, K. Mukherjee, and D. Carroll, 2013 Donor DNA utilization during gene targeting with zincfinger nucleases. G3 3: 657–664.
7. Bibikova, M., M. Golic, K. Golic, and D. Carroll, 2002 Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161: 1169–1175.
8. Bibikova, M., K. Beumer, and J. K. Trautman, and D. Carroll, 2003 Enhancing gene targeting with designed zinc finger nucleases. Science 300: 764.
9. Brand, A. H., and N. Perrimon, 1993 Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118: 401–415.
10. Byrne, S. M., L. Ortiz, P. Mali, J. Aach, and G. M. Church, 2014 Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. pii: gku1246.
11. Capecchi, M. R., 2005 Gene targeting in mice: functional analysis of the mammalian genome for the twenty-first century. Nat. Rev. Genet. 6: 507–512.
12. Chen, C. H., H. Huang, C. M. Ward, J. T. Su, L. V. Schaeffer et al., 2007 A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila. Science 316: 597–600.
13. Chen, D., and D. M. Mckearin, 2003 A discrete transcriptional silencer in the bam gene determines asymmetric division of the Drosophila germline stem cell. Development 130: 1159–1170.
14. Cong, L., F. A. Ran, D. Cox, S. Lin, R. Barretto et al., 2013 Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819–823.
15. Diao, F., and B. H. White, 2012 A novel approach for directing transgene expression in Drosophila: T2A-Gal4 in-frame fusion. Genetics 190: 1139–1144.
16. Ellis, M. C., E. M. O’Neill, and G. M. Rubin, 1993 Expression of Drosophila glass protein and evidence for negative regulation of its activity in non-neuronal cells by another DNA-binding protein. Development 119: 855–865.
17. Gong, W. J., and K. G. Golic, 2003 Ends-out, or replacement, gene targeting in Drosophila. Proc. Natl. Acad. Sci. USA 100: 2556–2561.
18. Gratz, S. J., A. M. Cummings, J. N. Nguyen, D. C. Hamm, L. K. Donohue et al., 2013 Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194: 1029–1035.
19. Gratz, S. J., F. P. Ukken, C. D. Rubinstein, G. Thiede, L. K. Donohue et al., 2014 Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics 196: 961–971.
20. Harrison, M. M., B. V. Jenkins, K. M. O’Connor-Giles, and J. Wildonger, 2014 A CRISPR view of development. Genes Dev. 28: 1859–1872.
21. Hay, B. A., T. Wolff, and G. M. Rubin, 1994 Expression of baculovirus P35 prevents cell death in Drosophila. Development 120: 2121–2129.
22. Hernandez, G., F. Valafar, and W. E. Stumph, 2007 Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity. Nucleic Acids Res. 35: 21–34.
23. Horn, C., B. Jaunich, and E. A. Wimmer, 2000 Highly sensitive, fluorescent transformation marker for Drosophila transgenesis. Dev. Genes Evol. 210: 623–629.
24. Hsu, P. D., E. S. Lander, and F. Zhang, 2014 Development and applications of CRISPR-Cas9 for genome engineering. Cell 157: 1262–1278.
25. Huang, J., W. Zhou, A. M. Watson, Y.-N. Jan, and Y. Hong, 2008 Efficient ends-out gene targeting in Drosophila. Genetics 180: 703–707.
26. Huang, J., P. Ghosh, G. F. Hatfull, and Y. Hong, 2011 Successive and targeted DNA integrations in the Drosophila genome by Bxb1 and fC31 integrases. Genetics 189: 391–395.
27. Hwang, W. Y., Y. Fu, D. Reyon, M. L. Maeder, S. Q. Tsai et al., 2013 Efficient genome editing in zebrafish using a CRISPRCas system. Nat. Biotechnol. 31: 227–229.
28. Isshiki, T., M. Takeichi, and A. Nose, 1997 The role of the msh homeobox gene during Drosophila neurogenesis: implication for the dorsoventral specification of the neuroectoderm. Development 124: 3099–3109.
29. Jasin, M., 1996 Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet. 12: 224–228.
30. Jinek, M., K. Chylinski, I. Fonfara, M. Hauer, J. A. Doudna et al., 2012 A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816–821.
31. Kania, M. A., A. S. Bonner, J. B. Duffy, and J. P. Gergen, 1990 The Drosophila segmentation gene runt encodes a novel nuclear regulatory protein that is also expressed in the developing nervous system. Genes Dev. 4: 1701–1713.
32. Kim, H., and J.-S. Kim, 2014 A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 15: 321–334.
33. Kim, J. H., S.-R. Lee, L.-H. Li, H.-J. Park, J.-H. Park et al., 2011 High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS ONE 6: e18556.
34. Kondo, S., and R. Ueda, 2013 Highly improved gene targeting by germline-specific cas9 expression in Drosophila. Genetics 195: 715–721.
35. Lai, S.-L., and T. Lee, 2006 Genetic mosaic with dual binary transcriptional systems in Drosophila. Nat. Neurosci. 9: 703–709.
36. Lee, T., and L. Luo, 1999 Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22: 451–461.
37. Leismann, O., and C. F. Lehner, 2003 Drosophila securin destruction involves a D-box and a KEN-box and promotes anaphase in parallel with Cyclin A degradation. J. Cell Sci. 116: 2453–2460.
38. Luo, L., Y. J. Liao, L. Y. Jan, and Y. N. Jan, 1994 Distinct morphogenetic functions of similar small GTPases: Drosophila Drac1 is involved in axonal outgrowth and myoblast fusion. Genes Dev. 8: 1787–1802.
39. Mali, P., L. Yang, K. M. Esvelt, J. Aach, M. Guell et al., 2013 RNAguided human genome engineering via Cas9. Science 339: 823–826.
40. Pfeiffer, B. D., T.-T. B. Ngo, K. L. Hibbard, C. Murphy, A. Jenett et al., 2010 Refinement of tools for targeted gene expression in Drosophila. Genetics 186: 735–755.
41. Pfeiffer, B. D., J. W. Truman, and G. M. Rubin, 2012 Using translational enhancers to increase transgene expression in Drosophila. Proc. Natl. Acad. Sci. USA 109: 6626–6631.
42. Port, F., H. M. Chen, T. Lee, and S. L. Bullock, 2014 Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc. Natl. Acad. Sci. USA 111: E2967–E2976.
43. Ren, X., J. Sun, B. E. Housden, Y. Hu, C. Roesel et al., 2013 Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc. Natl. Acad. Sci. USA 110: 19012–19017.
44. Rong, Y. S., and K. G. Golic, 2000 Gene targeting by homologous recombination in Drosophila. Science 288: 2013–2018.
45. Rørth, P., 1998 Gal4 in the Drosophila female germline. Mech. Dev. 78: 113–118.
46. Sander, J. D., and J. K. Joung, 2014 CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32: 347–355.
47. Sauer, B., 1993 Manipulation of transgenes by site-specific recombination: use of cre recombinase. Methods Enzymol. 225: 890–900.
48. Schlake, T., and J. Bode, 1994 Use of mutated FLP recognition target (FRT) sites for the exchange of expression cassettes at defined chromosomal loci. Biochemistry 33: 12746–12751.
49. Sebo, Z. L., H. B. Lee, Y. Peng, and Y. Guo, 2013 A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering. Fly 8: 52–57.
50. Spradling, A. C., 1993 Developmental genetics of oogenesis, pp. 1–70 in The Development of Drosophila melanogaster, Vol. 1 edited by Michael Bate and Alfonso Martinez Arias, Cold Spring Harbor Laboratory Press, Long Island, New York.
51. Szymczak, A. L., C. J. Workman, Y. Wang, K. M. Vignali, S. Dilioglou et al., 2004 Correction of multi-gene deficiency in vivo using a single ‘self-cleaving’ 2A peptide–based retroviral vector. Nat. Biotechnol. 22: 589–594.
52. Thomas, K. R., and M. R. Capecchi, 1987 Site-directed mutagenesis by gene targeting in mouse embryo-derived stem cells. Cell 51: 503–512.
53. Wakiyama, M., T. Matsumoto, and S. Yokoyama, 2005 Drosophila U6 promoter-driven short hairpin RNAs effectively induce RNA interference in Schneider 2 cells. Biochem. Biophys. Res. Commun. 331: 1163–1170.
54. Xue, Z., M. Ren, M. Wu, J. Dai, Y. S. Rong et al., 2014 Efficient gene knock-out and knock-in with transgenic Cas9 in Drosophila. G3 4: 925–929.
55. Yu, H.-H., C. H. Chen, L. Shi, Y. Huang, and T. Lee, 2009 Twinspot MARCM to reveal the developmental origin and identity of neurons. Nat. Neurosci. 12: 947–953.
56. Yu, Z., M. Ren, Z. Wang, B. Zhang, Y. S. Rong et al., 2013 Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics 195: 289–291.
57. Yu, Z., H. Chen, J. Liu, H. Zhang, Y. Yan et al., 2014 Various applications of TALEN-and CRISPR/Cas9-mediated homologous recombination to modify the Drosophila genome. Biol. Open 3: 271–280.
58. Zinyk, D. L., E. H. Mercer, E. Harris, D. J. Anderson, and A. L. Joyner, 1998 Fate mapping of the mouse midbrain–hindbrain constriction using a site-specific recombination system. Curr. Biol. 8: 665–672.