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Volume 41 Issue 1
Jan.  2014
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Article Contents

CRISPR/Cas9 and Genome Editing in Drosophila

doi: 10.1016/j.jgg.2013.12.004
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  • Corresponding author: E-mail address: andrew.bassett@dpag.ox.ac.uk (Andrew R. Bassett); E-mail address: jilong.liu@dpag.ox.ac.uk (Ji-Long Liu)
  • Received Date: 2013-11-25
  • Accepted Date: 2013-12-11
  • Rev Recd Date: 2013-12-10
  • Available Online: 2013-12-18
  • Publish Date: 2014-01-20
  • Recent advances in our ability to design DNA binding factors with specificity for desired sequences have resulted in a revolution in genetic engineering, enabling directed changes to the genome to be made relatively easily. Traditional techniques for generating genetic mutations in most organisms have relied on selection from large pools of randomly induced mutations for those of particular interest, or time-consuming gene targeting by homologous recombination. Drosophila melanogaster has always been at the forefront of genetic analysis, and application of these new genome editing techniques to this organism will revolutionise our approach to performing analysis of gene function in the future. We discuss the recent techniques that apply the CRISPR/Cas9 system to Drosophila, highlight potential uses for this technology and speculate upon the future of genome engineering in this model organism.
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  • [1]
    Barrangou, R., Fremaux, C., Deveau, H. et al. CRISPR provides acquired resistance against viruses in prokaryotes Science, 315 (2007),pp. 1709-1712
    [2]
    Baena-Lopez, L.A., Alexandre, C., Mitchell, A. et al. Development, 140 (2013),pp. 4818-4825
    [3]
    Bassett, A.R., Tibbit, C., Ponting, C.P. et al. Cell Rep., 4 (2013),pp. 220-228
    [4]
    Bassett, A.R., Tibbit, C., Ponting, C.P. et al. Biol. Open, 3 (2014),pp. 42-49
    [5]
    Bellen, H.J., Levis, R.W., He, Y. et al. Genetics, 188 (2011),pp. 731-743
    [6]
    Bellen, H.J., Levis, R.W., Liao, G. et al. Genetics, 167 (2004),pp. 761-781
    [7]
    Bernstein, B.E., Birney, E., Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome Nature, 489 (2012),pp. 57-74
    [8]
    Beumer, K., Bhattacharyya, G., Bibikova, M. et al. Genetics, 172 (2006),pp. 2391-2403
    [9]
    Beumer, K.J., Trautman, J.K., Bozas, A. et al. Proc. Natl. Acad. Sci. USA, 105 (2008),pp. 19821-19826
    [10]
    Beumer, K.J., Trautman, J.K., Mukherjee, K. et al. Donor DNA utilization during gene targeting with zinc-finger nucleases G3 (Bethesda), 3 (2013),pp. 657-664
    [11]
    Bibikova, M., Beumer, K., Trautman, J.K. et al. Enhancing gene targeting with designed zinc finger nucleases Science, 300 (2003),p. 764
    [12]
    Bibikova, M., Golic, M., Golic, K.G. et al. Genetics, 161 (2002),pp. 1169-1175
    [13]
    Biswas, A., Gagnon, J.N., Brouns, S.J. et al. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets RNA Biol., 10 (2013),pp. 817-827
    [14]
    Boch, J., Scholze, H., Schornack, S. et al. Breaking the code of DNA binding specificity of TAL-type III effectors Science, 326 (2009),pp. 1509-1512
    [15]
    Bonas, U., Stall, R.E., Staskawicz, B. Mol. Gen. Genet., 218 (1989),pp. 127-136
    [16]
    Brockdorff, N. Noncoding RNA and polycomb recruitment RNA, 19 (2013),pp. 429-442
    [17]
    Brouns, S.J., Jore, M.M., Lundgren, M. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes Science, 321 (2008),pp. 960-964
    [18]
    Bulyk, M.L., Johnson, P.L., Church, G.M. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors Nucleic Acids Res., 30 (2002),pp. 1255-1261
    [19]
    Cermak, T., Doyle, E.L., Christian, M. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting Nucleic Acids Res., 39 (2011),p. e82
    [20]
    Cheng, A.W., Wang, H., Yang, H. et al. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system Cell Res., 23 (2013),pp. 1163-1171
    [21]
    Choo, Y., Klug, A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions Proc. Natl. Acad. Sci. USA, 91 (1994),pp. 11168-11172
    [22]
    Choo, Y., Klug, A. Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage Proc. Natl. Acad. Sci. USA, 91 (1994),pp. 11163-11167
    [23]
    Choulika, A., Perrin, A., Dujon, B. et al. Mol. Cell. Biol., 15 (1995),pp. 1968-1973
    [24]
    Cong, L., Ran, F.A., Cox, D. et al. Multiplex genome engineering using CRISPR/Cas systems Science, 339 (2013),pp. 819-823
    [25]
    Dahlem, T.J., Hoshijima, K., Jurynec, M.J. et al. Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome PLoS Genet., 8 (2012),p. e1002861
    [26]
    Davidovich, C., Zheng, L., Goodrich, K.J. et al. Promiscuous RNA binding by polycomb repressive complex 2 Nat. Struct. Mol. Biol., 20 (2013),pp. 1250-1257
    [27]
    Del Rio, S., Menezes, S.R., Setzer, D.R. The function of individual zinc fingers in sequence-specific DNA recognition by transcription factor IIIA J. Mol. Biol., 233 (1993),pp. 567-579
    [28]
    DiCarlo, J.E., Norville, J.E., Mali, P. et al. Nucleic Acids Res., 41 (2013),pp. 4336-4343
    [29]
    Dickinson, D.J., Ward, J.D., Reiner, D.J. et al. Nat. Methods, 10 (2013),pp. 1028-1034
    [30]
    Esvelt, K.M., Mali, P., Braff, J.L. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing Nat. Methods, 10 (2013),pp. 1116-1121
    [31]
    Farzadfard, F., Perli, S.D., Lu, T.K. Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas ACS Synth. Biol., 2 (2013),pp. 604-613
    [32]
    Flockhart, I., Booker, M., Kiger, A. et al. Nucleic Acids Res., 34 (2006),pp. D489-D494
    [33]
    Flockhart, I.T., Booker, M., Hu, Y. et al. Nucleic Acids Res., 40 (2012),pp. D715-D719
    [34]
    Fu, Y., Foden, J.A., Khayter, C. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells Nat. Biotechnol., 31 (2013),pp. 822-826
    [35]
    Garneau, J.E., Dupuis, M.E., Villion, M. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA Nature, 468 (2010),pp. 67-71
    [36]
    Gasiunas, G., Barrangou, R., Horvath, P. et al. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria Proc. Natl. Acad. Sci. USA, 109 (2012),pp. E2579-E2586
    [37]
    Gilbert, L.A., Larson, M.H., Morsut, L. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes Cell, 154 (2013),pp. 442-451
    [38]
    Gloor, G.B., Nassif, N.A., Johnson-Schlitz, D.M. et al. Science, 253 (1991),pp. 1110-1117
    [39]
    Golic, K.G., Lindquist, S. Cell, 59 (1989),pp. 499-509
    [40]
    Gratz, S.J., Cummings, A.M., Nguyen, J.N. et al. Genetics, 194 (2013),pp. 1029-1035
    [41]
    Grissa, I., Vergnaud, G., Pourcel, C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats BMC Bioinformatics, 8 (2007),p. 172
    [42]
    Grissa, I., Vergnaud, G., Pourcel, C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats Nucleic Acids Res., 35 (2007),pp. W52-W57
    [43]
    Grissa, I., Vergnaud, G., Pourcel, C. CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats Nucleic Acids Res., 36 (2008),pp. W145-W148
    [44]
    Groth, A.C., Fish, M., Nusse, R. et al. Genetics, 166 (2004),pp. 1775-1782
    [45]
    Gupta, A., Hall, V.L., Kok, F.O. et al. Targeted chromosomal deletions and inversions in zebrafish Genome Res., 23 (2013),pp. 1008-1017
    [46]
    Hsu, P.D., Scott, D.A., Weinstein, J.A. et al. DNA targeting specificity of RNA-guided Cas9 nucleases Nat. Biotechnol, 31 (2013),pp. 827-832
    [47]
    Huang, J., Zhou, W., Watson, A.M. et al. Genetics, 180 (2008),pp. 703-707
    [48]
    Hwang, W.Y., Fu, Y., Reyon, D. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system Nat. Biotechnol., 31 (2013),pp. 227-229
    [49]
    Ishino, Y., Shinagawa, H., Makino, K. et al. J. Bacteriol., 169 (1987),pp. 5429-5433
    [50]
    Jansen, R., Embden, J.D., Gaastra, W. et al. Identification of genes that are associated with DNA repeats in prokaryotes Mol. Microbiol., 43 (2002),pp. 1565-1575
    [51]
    Jinek, M., Chylinski, K., Fonfara, I. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Science, 337 (2012),pp. 816-821
    [52]
    Jinek, M., East, A., Cheng, A. et al. RNA-programmed genome editing in human cells Elife, 2 (2013),p. e00471
    [53]
    Khalil, A.M., Guttman, M., Huarte, M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression Proc. Natl. Acad. Sci. USA, 106 (2009),pp. 11667-11672
    [54]
    Kondo, S., Ueda, R. Genetics, 195 (2013),pp. 715-721
    [55]
    Lange, S.J., Alkhnbashi, O.S., Rose, D. et al. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems Nucleic Acids Res., 41 (2013),pp. 8034-8044
    [56]
    Lee, H.Y., Haurwitz, R.E., Apffel, A. et al. RNA-protein analysis using a conditional CRISPR nuclease Proc. Natl. Acad. Sci. USA, 110 (2013),pp. 5416-5421
    [57]
    Li, T., Huang, S., Zhao, X. et al. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes Nucleic Acids Res., 39 (2011),pp. 6315-6325
    [58]
    Lin, M.F., Carlson, J.W., Crosby, M.A. et al. Genome Res., 17 (2007),pp. 1823-1836
    [59]
    Liu, J., Li, C., Yu, Z. et al. J. Genet. Genomics, 39 (2012),pp. 209-215
    [60]
    Mali, P., Aach, J., Stranges, P.B. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering Nat. Biotechnol., 31 (2013),pp. 833-838
    [61]
    Mali, P., Yang, L., Esvelt, K.M. et al. Science, 339 (2013),pp. 823-826
    [62]
    McCarthy, M.I., Abecasis, G.R., Cardon, L.R. et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges Nat. Rev. Genet., 9 (2008),pp. 356-369
    [63]
    Meader, S., Ponting, C.P., Lunter, G. Massive turnover of functional sequence in human and other mammalian genomes Genome Res., 20 (2010),pp. 1335-1343
    [64]
    Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J. et al. Short motif sequences determine the targets of the prokaryotic CRISPR defence system Microbiology, 155 (2009),pp. 733-740
    [65]
    Moscou, M.J., Bogdanove, A.J. A simple cipher governs DNA recognition by TAL effectors Science, 326 (2009),p. 1501
    [66]
    Park, P.J. ChIP-seq: advantages and challenges of a maturing technology Nat. Rev. Genet., 10 (2009),pp. 669-680
    [67]
    Perez-Pinera, P., Kocak, D.D., Vockley, C.M. et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors Nat. Methods, 10 (2013),pp. 973-976
    [68]
    Qi, L.S., Larson, M.H., Gilbert, L.A. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression Cell, 152 (2013),pp. 1173-1183
    [69]
    Ran, F.A., Hsu, P.D., Lin, C.Y. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity Cell, 154 (2013),pp. 1380-1389
    [70]
    Ren, X., Sun, J., Housden, B.E. et al. Proc. Natl. Acad. Sci. USA, 110 (2013),pp. 19012-19017
    [71]
    Reyon, D., Tsai, S.Q., Khayter, C. et al. FLASH assembly of TALENs for high-throughput genome editing Nat. Biotechnol., 30 (2012),pp. 460-465
    [72]
    Rong, Y.S., Golic, K.G. Science, 288 (2000),pp. 2013-2018
    [73]
    Rousseau, C., Gonnet, M., Le Romancer, M. et al. CRISPI: a CRISPR interactive database Bioinformatics, 25 (2009),pp. 3317-3318
    [74]
    Roy, S., Ernst, J., Kharchenko, P.V. et al. Science, 330 (2010),pp. 1787-1797
    [75]
    Sander, J.D., Maeder, M.L., Reyon, D. et al. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool Nucleic Acids Res., 38 (2010),pp. W462-W468
    [76]
    Sander, J.D., Zaback, P., Joung, J.K. et al. Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool Nucleic Acids Res., 35 (2007),pp. W599-W605
    [77]
    Sanjana, N.E., Cong, L., Zhou, Y. et al. A transcription activator-like effector toolbox for genome engineering Nat. Protoc., 7 (2012),pp. 171-192
    [78]
    Sebo, Z.L., Lee, H.B., Peng, Y. et al. Fly (Austin), 8 (2013)
    [79]
    Shalem, O., Sanjana, N.E., Hartenian, E. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells Science, 343 (2014),pp. 84-87
    [80]
    Shan, Q., Wang, Y., Li, J. et al. Targeted genome modification of crop plants using a CRISPR-Cas system Nat. Biotechnol., 31 (2013),pp. 686-688
    [81]
    Skennerton, C.T., Imelfort, M., Tyson, G.W. Crass: identification and reconstruction of CRISPR from unassembled metagenomic data Nucleic Acids Res., 41 (2013),p. e105
    [82]
    Smih, F., Rouet, P., Romanienko, P.J. et al. Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells Nucleic Acids Res., 23 (1995),pp. 5012-5019
    [83]
    Wang, H., Yang, H., Shivalila, C.S. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering Cell, 153 (2013),pp. 910-918
    [84]
    Wang, T., Wei, J.J., Sabatini, D.M. et al. Genetic screens in human cells using the CRISPR-Cas9 system Science, 343 (2014),pp. 80-84
    [85]
    Wei, C., Liu, J., Yu, Z. et al. TALEN or Cas9 - rapid, efficient and specific choices for genome modifications J. Genet. Genomics, 40 (2013),pp. 281-289
    [86]
    Xiao, A., Wang, Z., Hu, Y. et al. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish Nucleic Acids Res., 41 (2013),p. e141
    [87]
    Yu, Z., Ren, M., Wang, Z. et al. Genetics, 195 (2013),pp. 289-291
    [88]
    Zhao, J., Ohsumi, T.K., Kung, J.T. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq Mol. Cell, 40 (2010),pp. 939-953
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