Links & References


CRISPR/Cas9 in Drosophila:

flyCRISPR discussion group

CRISPRflydesign website

OXfCRISPR website

FlyCas9 website

Drosophila CRISPR target finders:

flyCRISPR Optimal Target Finder




General CRISPR/Cas9 resources:

CRISPR discussion group

Zhang lab CRISPR website

Joung lab CRISPR website

Goldstein lab CRISPR website





Bassett, A.R., and Liu, J.L. (2014). CRISPR/Cas9 and Genome Editing in Drosophila. J Genet Genomics 41, 7-19.

Bassett, A.R., Tibbit, C., Ponting, C.P., and Liu, J.L. (2014). Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9. Biology open 3, 42-49.

Beumer, K.J., and Carroll, D. (2014). Targeted genome engineering techniques in Drosophila. Methods.

Gratz, S.J., Ukken, F.P., Rubinstein, C.D., Thiede, G., Donohue, L.K., Cummings, A.M., and O'Connor-Giles, K.M. (2014). Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila. Genetics 196, 961-971.



Baena-Lopez, L.A., Alexandre, C., Mitchell, A., Pasakarnis, L., and Vincent, J.P. (2013). Accelerated homologous recombination and subsequent genome modification in Drosophila. Development.

Bassett, A.R., Tibbit, C., Ponting, C.P., and Liu, J.L. (2013). Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 4, 220-228.

Gratz, S.J., Cummings, A.M., Nguyen, J.N., Hamm, D.C., Donohue, L.K., Harrison, M.M., Wildonger, J., and O'Connor-Giles, K.M. (2013a). Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194, 1029-1035.

Gratz, S.J., Wildonger, J., Harrison, M.M., and O'Connor-Giles, K.M. (2013b). CRISPR/Cas9-mediated genome engineering and the promise of designer flies on demand. Fly (Austin) 7.

Kondo, S., and Ueda, R. (2013). Highly Improved Gene Targeting by Germline-Specific Cas9 Expression in Drosophila. Genetics.

Ren, X., Sun, J., Housden, B.E., Hu, Y., Roesel, C., Lin, S., Liu, L.P., Yang, Z., Mao, D., Sun, L., et al. (2013). Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci U S A.

Sebo, Z.L., Lee, H.B., Peng, Y., and Guo, Y. (2013). A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering. Fly (Austin) 8.

Yu, Z., Ren, M., Wang, Z., Zhang, B., Rong, Y.S., Jiao, R., and Gao, G. (2013). Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics 195, 289-291.


Other systems:


Auer, T.O., Duroure, K., De Cian, A., Concordet, J.P., and Del Bene, F. (2013). Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res.

Belhaj, K., Chaparro-Garcia, A., Kamoun, S., and Nekrasov, V. (2013). Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant methods 9, 39.

Blitz, I.L., Biesinger, J., Xie, X., and Cho, K.W. (2013). Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system. Genesis.

Carroll, D. (2013). Staying on target with CRISPR-Cas. Nat Biotechnol 31, 807-809.

Chang, N., Sun, C., Gao, L., Zhu, D., Xu, X., Zhu, X., Xiong, J.W., and Xi, J.J. (2013). Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23, 465-472.

Cho, S.W., Kim, S., Kim, J.M., and Kim, J.S. (2013a). Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31, 230-232.

Cho, S.W., Lee, J., Carroll, D., Kim, J.S., and Lee, J. (2013b). Heritable Gene Knockout in Caenorhabditis elegans by Direct Injection of Cas9-sgRNA Ribonucleoproteins. Genetics.

Chylinski, K., Le Rhun, A., and Charpentier, E. (2013). The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol 10, 726-737.

Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823.

Cradick, T.J., Fine, E.J., Antico, C.J., and Bao, G. (2013). CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res.

Dickinson, D.J., Ward, J.D., Reiner, D.J., and Goldstein, B. (2013). Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods 10, 1028-1034.

Ebina, H., Misawa, N., Kanemura, Y., and Koyanagi, Y. (2013). Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Scientific reports 3, 2510.

Esvelt, K.M., Mali, P., Braff, J.L., Moosburner, M., Yaung, S.J., and Church, G.M. (2013). Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 10, 1116-1121.

Feng, Z., Zhang, B., Ding, W., Liu, X., Yang, D.L., Wei, P., Cao, F., Zhu, S., Zhang, F., Mao, Y., et al. (2013). Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23, 1229-1232.

Friedland, A.E., Tzur, Y.B., Esvelt, K.M., Colaiacovo, M.P., Church, G.M., and Calarco, J.A. (2013). Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10, 741-743.

Frokjaer-Jensen, C. (2013). Exciting Prospects for Precise Engineering of Caenorhabditis elegans Genomes with CRISPR/Cas9. Genetics 195, 635-642.

Fujii, W., Kawasaki, K., Sugiura, K., and Naito, K. (2013). Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res.

Gasiunas, G., and Siksnys, V. (2013). RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing? Trends Microbiol.

Heidrich, N., and Vogel, J. (2013). CRISPRs extending their reach: prokaryotic RNAi protein Cas9 recruited for gene regulation. EMBO J 32, 1802-1804.

Hou, Z., Zhang, Y., Propson, N.E., Howden, S.E., Chu, L.F., Sontheimer, E.J., and Thomson, J.A. (2013). Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A 110, 15644-15649.

Hsu, P.D., Scott, D.A., Weinstein, J.A., Ran, F.A., Konermann, S., Agarwala, V., Li, Y., Fine, E.J., Wu, X., Shalem, O., et al. (2013). DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31, 827-832.

Hu, X., Chang, N., Wang, X., Zhou, F., Zhou, X., Zhu, X., and Xiong, J.W. (2013). Heritable gene-targeting with gRNA/Cas9 in rats. Cell Res.

Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B., and Weeks, D.P. (2013). Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., and Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821.

Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., and Doudna, J. (2013). RNA-programmed genome editing in human cells. Elife 2, e00471.

Karvelis, T., Gasiunas, G., Miksys, A., Barrangou, R., Horvath, P., and Siksnys, V. (2013). crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol 10, 841-851.

Katic, I., and Grosshans, H. (2013). Targeted Heritable Mutation and Gene Conversion by Cas9-CRISPR in Caenorhabditis elegans. Genetics.

Li, D., Qiu, Z., Shao, Y., Chen, Y., Guan, Y., Liu, M., Li, Y., Gao, N., Wang, L., Lu, X., et al. (2013a). Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat Biotechnol 31, 681-683.

Li, J.F., Norville, J.E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G.M., and Sheen, J. (2013b). Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 31, 688-691.

Lo, T.W., Pickle, C.S., Lin, S., Ralston, E.J., Gurling, M., Schartner, C.M., Bian, Q., Doudna, J.A., and Meyer, B.J. (2013). Precise and Heritable Genome Editing in Evolutionarily Diverse Nematodes Using TALENs and CRISPR/Cas9 to Engineer Insertions and Deletions. Genetics 195, 331-348.

Mali, P., Aach, J., Stranges, P.B., Esvelt, K.M., Moosburner, M., Kosuri, S., Yang, L., and Church, G.M. (2013a). CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31, 833-838.

Mali, P., Esvelt, K.M., and Church, G.M. (2013b). Cas9 as a versatile tool for engineering biology. Nat Methods 10, 957-963.

Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., Norville, J.E., and Church, G.M. (2013c). RNA-guided human genome engineering via Cas9. Science 339, 823-826.

Mao, Y., Zhang, H., Xu, N., Zhang, B., Gou, F., and Zhu, J.K. (2013). Application of the CRISPR-Cas System for Efficient Genome Engineering in Plants. Mol Plant.

Miao, J., Guo, D., Zhang, J., Huang, Q., Qin, G., Zhang, X., Wan, J., Gu, H., and Qu, L.J. (2013). Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res 23, 1233-1236.

Nakayama, T., Fish, M.B., Fisher, M., Oomen-Hajagos, J., Thomsen, G.H., and Grainger, R.M. (2013). Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis. Genesis.

Nekrasov, V., Staskawicz, B., Weigel, D., Jones, J.D., and Kamoun, S. (2013). Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 31, 691-693.

Pattanayak, V., Lin, S., Guilinger, J.P., Ma, E., Doudna, J.A., and Liu, D.R. (2013). High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31, 839-843.

Perez-Pinera, P., Kocak, D.D., Vockley, C.M., Adler, A.F., Kabadi, A.M., Polstein, L.R., Thakore, P.I., Glass, K.A., Ousterout, D.G., Leong, K.W., et al. (2013). RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 10, 973-976.

Ran, F.A., Hsu, P.D., Lin, C.Y., Gootenberg, J.S., Konermann, S., Trevino, A.E., Scott, D.A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013a). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380-1389.

Ran, F.A., Hsu, P.D., Wright, J., Agarwala, V., Scott, D.A., and Zhang, F. (2013b). Genome engineering using the CRISPR-Cas9 system. Nature protocols 8, 2281-2308.

Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J.J., Qiu, J.L., et al. (2013). Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31, 686-688.

Shen, B., Zhang, J., Wu, H., Wang, J., Ma, K., Li, Z., Zhang, X., Zhang, P., and Huang, X. (2013). Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res 23, 720-723.

Straubeta, A., and Lahaye, T. (2013). Zinc fingers, TAL effectors, or Cas9-based DNA binding proteins: what's best for targeting desired genome loci? Mol Plant 6, 1384-1387.

Tzur, Y.B., Friedland, A.E., Nadarajan, S., Church, G.M., Calarco, J.A., and Colaiacovo, M.P. (2013). Heritable Custom Genomic Modifications in Caenorhabditis elegans via a CRISPR-Cas9 System. Genetics.

Waaijers, S., Portegijs, V., Kerver, J., Lemmens, B.B., Tijsterman, M., van den Heuvel, S., and Boxem, M. (2013). CRISPR/Cas9-Targeted Mutagenesis in Caenorhabditis elegans. Genetics.

Walsh, R.M., and Hochedlinger, K. (2013). A variant CRISPR-Cas9 system adds versatility to genome engineering. Proc Natl Acad Sci U S A 110, 15514-15515.

Wei, C., Liu, J., Yu, Z., Zhang, B., Gao, G., and Jiao, R. (2013). TALEN or Cas9 - rapid, efficient and specific choices for genome modifications. J Genet Genomics 40, 281-289.

Xie, K., and Yang, Y. (2013). RNA-Guided Genome Editing in Plants Using a CRISPR-Cas System. Mol Plant.


Gasiunas, G., Barrangou, R., Horvath, P., and Siksnys, V. (2012). Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109, E2579-2586.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., and Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821.