Protocols for Use of Homologous Recombination Gene Targeting to Produce MicroRNA Mutants in Drosophila (original) (raw)

References

  1. Bartel, D. P. (2009) MicroRNAs: target recognition and regulatory functions. Cell 136, 215–33.
    Article PubMed CAS Google Scholar
  2. Flynt, A. S., and Lai, E. C. (2008) Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet 9, 831–42.
    Article PubMed CAS Google Scholar
  3. Bushati, N., and Cohen, S. M. (2007) microRNA functions. Annu Rev Cell Dev Biol 23, 175–205.
    Article PubMed CAS Google Scholar
  4. Lee, R. C., Feinbaum, R. L., and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–54.
    Google Scholar
  5. Wightman, B., Ha, I., and Ruvkun, G. (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855–62.
    Google Scholar
  6. Rorth, P., Szabo, K., Bailey, A., Laverty, T., Rehm, J., Rubin, G. M., Weigmann, K., Milan, M., Benes, V., Ansorge, W., and Cohen, S. M. (1998) Systematic gain-of-function genetics in Drosophila. Development 125, 1049–57.
    PubMed CAS Google Scholar
  7. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B., and Cohen, S. M. (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36.
    Article PubMed CAS Google Scholar
  8. Xu, P., Vernooy, S. Y., Guo, M., and Hay, B. A. (2003) The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 13, 790–5.
    Article PubMed CAS Google Scholar
  9. Li, X., and Carthew, R. W. (2005) A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye. Cell 123, 1267–77.
    Article PubMed CAS Google Scholar
  10. Karres, J. S., Hilgers, V., Carrera, I., Treisman, J., and Cohen, S. M. (2007) The conserved microRNA miR-8 tunes atrophin levels to prevent neurodegeneration in Drosophila. Cell 131, 136–45.
    Article PubMed CAS Google Scholar
  11. Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T., Hannon, G. J., and Plasterk, R. H. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15, 2654–9.
    Google Scholar
  12. Knight, S. W., and Bass, B. L. (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269–71.
    Article PubMed CAS Google Scholar
  13. Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish, S., Ha, I., Baillie, D. L., Fire, A., Ruvkun, G., and Mello, C. C. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34.
    Google Scholar
  14. Hatfield, S. D., Shcherbata, H. R., Fischer, K. A., Nakahara, K., Carthew, R. W., and Ruohola-Baker, H. (2005) Stem cell division is regulated by the microRNA pathway. Nature 435, 974–8.
    Article PubMed CAS Google Scholar
  15. Jin, Z., and Xie, T. (2007) Dcr-1 maintains Drosophila ovarian stem cells. Curr Biol 17, 539–44.
    Article PubMed CAS Google Scholar
  16. Wienholds, E., Koudijs, M. J., van Eeden, F. J., Cuppen, E., and Plasterk, R. H. (2003) The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat Genet 35, 217–8.
    Article PubMed CAS Google Scholar
  17. Murchison, E. P., Partridge, J. F., Tam, O. H., Cheloufi, S., and Hannon, G. J. (2005) Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci USA 102, 12135–40.
    Article PubMed CAS Google Scholar
  18. Kanellopoulou, C., Muljo, S. A., Kung, A. L., Ganesan, S., Drapkin, R., Jenuwein, T., Livingston, D. M., and Rajewsky, K. (2005) Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev 19, 489–501.
    Article PubMed CAS Google Scholar
  19. Cayirlioglu, P., Kadow, I. G., Zhan, X., Okamura, K., Suh, G. S., Gunning, D., Lai, E. C., and Zipursky, S. L. (2008) Hybrid neurons in a microRNA mutant are putative evolutionary intermediates in insect CO2 sensory systems. Science 319, 1256–60.
    Article PubMed CAS Google Scholar
  20. Robertson, H. M., Preston, C. R., Phillis, R. W., Johnson-Schlitz, D. M., Benz, W. K., and Engels, W. R. (1988) A stable genomic source of P element transposase in Drosophila melanogaster. Genetics 118, 461–70.
    PubMed CAS Google Scholar
  21. Preston, C. R., Sved, J. A., and Engels, W. R. (1996) Flanking duplications and deletions associated with P-induced male recombination in Drosophila. Genetics 144, 1623–38.
    PubMed CAS Google Scholar
  22. Rong, Y. S., and Golic, K. G. (2000) Gene targeting by homologous recombination in Drosophila. Science 288, 2013–8.
    Article PubMed CAS Google Scholar
  23. Rong, Y. S., and Golic, K. G. (2001) A targeted gene knockout in Drosophila. Genetics 157, 1307–12.
    PubMed CAS Google Scholar
  24. Rong, Y. S., Titen, S. W., Xie, H. B., Golic, M. M., Bastiani, M., Bandyopadhyay, P., Olivera, B. M., Brodsky, M., Rubin, G. M., and Golic, K. G. (2002) Targeted mutagenesis by homologous recombination in D. melanogaster. Genes Dev 16, 1568–81.
    Google Scholar
  25. Gong, W. J., and Golic, K. G. (2003) Ends-out, or replacement, gene targeting in Drosophila. Proc Natl Acad Sci USA 100, 2556–61.
    Article PubMed CAS Google Scholar
  26. Gong, W. J., and Golic, K. G. (2004) Genomic deletions of the Drosophila melanogaster Hsp70 genes. Genetics 168, 1467–76.
    Article PubMed CAS Google Scholar
  27. Xie, H. B., and Golic, K. G. (2004) Gene deletions by ends-in targeting in Drosophila melanogaster. Genetics 168, 1477–89.
    Article PubMed CAS Google Scholar
  28. Sokol, N. S., and Ambros, V. (2005) Mesodermally expressed Drosophila micro­RNA-1 is regulated by Twist and is required in muscles during larval growth. Genes Dev 19, 2343–54.
    Article PubMed CAS Google Scholar
  29. Teleman, A. A., Maitra, S., and Cohen, S. M. (2006) Drosophila lacking microRNA miR-278 are defective in energy homeostasis. Genes Dev 20, 417–22.
    Article PubMed CAS Google Scholar
  30. Li, Y., Wang, F., Lee, J. A., and Gao, F. B. (2006) MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev 20, 2793–805.
    Article PubMed CAS Google Scholar
  31. Bushati, N., Stark, A., Brennecke, J., and Cohen, S. M. (2008) Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr Biol 18, 501–6.
    Article PubMed CAS Google Scholar
  32. Friggi-Grelin, F., Lavenant-Staccini, L., and Therond, P. (2008) Control of antagonistic components of the hedgehog signaling pathway by microRNAs in Drosophila. Genetics 179, 429–39.
    Article PubMed CAS Google Scholar
  33. Sokol, N. S., Xu, P., Jan, Y. N., and Ambros, V. (2008) Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. Genes Dev 22, 1591–6.
    Article PubMed CAS Google Scholar
  34. Maggert, K. A., Gong, W. J., and Golic, K. G. (2008) Methods for homologous recombination in Drosophila. Methods Mol Biol 420, 155–74.
    Article PubMed CAS Google Scholar
  35. Gao, G., McMahon, C., Chen, J., and Rong, Y. S. (2008) A powerful method combining homologous recombination and site-specific recombination for targeted mutagenesis in Drosophila. Proc Natl Acad Sci USA 105, 13999–4004.
    Article PubMed CAS Google Scholar
  36. Choi, C. M., Vilain, S., Langen, M., Van Kelst, S., De Geest, N., Yan, J., Verstreken, P., and Hassan, B. A. (2009) Conditional mutagenesis in Drosophila. Science 324, 54.
    Article PubMed CAS Google Scholar
  37. Weng, R., Chen, Y. W., Bushati, N., Cliffe, A., and Cohen, S. M. (2009) Recombinase-mediated cassette exchange provides a versatile platform for gene targeting: knockout of miR-31b. Genetics 183, 399–402.
    Article PubMed CAS Google Scholar
  38. Bateman, J. R., Lee, A. M., and Wu, C. T. (2006) Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange. Genetics 173, 769–77.
    Article PubMed CAS Google Scholar
  39. Bischof, J., Maeda, R. K., Hediger, M., Karch, F., and Basler, K. (2007) An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc Natl Acad Sci USA 104, 3312–7.
    Article PubMed CAS Google Scholar
  40. Markstein, M., Pitsouli, C., Villalta, C., Celniker, S. E., and Perrimon, N. (2008) Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat Genet 40, 476–83.
    Article PubMed CAS Google Scholar
  41. Groth, A. C., Fish, M., Nusse, R., and Calos, M. P. (2004) Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics 166, 1775–82.
    Article PubMed CAS Google Scholar
  42. Gloor, G. B., Preston, C. R., Johnson-Schlitz, D. M., Nassif, N. A., Phillis, R. W., Benz, W. K., Robertson, H. M., and Engels, W. R. (1993) Type I repressors of P element mobility. Genetics 135, 81–95.
    PubMed CAS Google Scholar
  43. Siegal, M. L., and Hartl, D. L. (1996) Transgene Coplacement and high efficiency site-specific recombination with the Cre/loxP system in Drosophila. Genetics 144, 715–26.
    PubMed CAS Google Scholar
  44. Venken, K. J., He, Y., Hoskins, R. A., and Bellen, H. J. (2006) P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster. Science 314, 1747–51.
    Google Scholar
  45. Spradling, A. C. (1986) P element-mediated transformation in “Drosophila: a practical approach” (Roberts, D. B., Ed.), pp. 175–97, IRL Press Limited, Oxford, England.
    Google Scholar
  46. Kuhstoss, S., and Rao, R. N. (1991) Analysis of the integration function of the streptomycete bacteriophage phi C31. J Mol Biol 222, 897–908.
    Article PubMed CAS Google Scholar
  47. Rausch, H., and Lehmann, M. (1991) Structural analysis of the actinophage phi C31 attachment site. Nucleic Acids Res 19, 5187–9.
    Article PubMed CAS Google Scholar
  48. Thorpe, H. M., Wilson, S. E., and Smith, M. C. (2000) Control of directionality in the site-specific recombination system of the Streptomyces phage phiC31. Mol Microbiol 38, 232–41.
    Article PubMed CAS Google Scholar
  49. Klemenz, R., Weber, U., and Gehring, W. J. (1987) The white gene as a marker in a new P-element vector for gene transfer in Drosophila. Nucleic Acids Res 15, 3947–59.
    Article PubMed CAS Google Scholar
  50. Ruby, J. G., Jan, C. H., and Bartel, D. P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83–6.
    Article PubMed CAS Google Scholar
  51. Okamura, K., Hagen, J. W., Duan, H., Tyler, D. M., and Lai, E. C. (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130, 89–100.
    Article PubMed CAS Google Scholar
  52. Li, M. Z., and Elledge, S. J. (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4, 251–6.
    Article PubMed CAS Google Scholar

Download references