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Drosophila Genome EngineeringFor BestGene Drosophila Genome Editing Service, pls see here.
For currently available Cas9 stocks at BestGene, pls see here.
CRISPR/Cas9, TALEN, ZFN system are three powerful genome engineering tools that are composed of programmable, sequence-specific DNA-binding modules associated with a nonspecific DNA nuclease, which introduce DSB (DNA double-strand breaks) that stimulate NHEJ (non-homologous end joining) or HR (homologous recombination) repairing mechanisms at specific genomic locations. In the application of these technology in Drosophila, random indels can be introduced into DSB via NHEJ.
Currently, CRISPR/Cas9 has grown in popularity for Drosophila genome editing.
Drosophila CRISPR/Cas9 SystemCRISPR/Cas system (clustered regularly interspaced palindromic repeats/CRISPR associated) is a component of bacteria/archaea innate immunity system. Type II CRISPR/Cas9 system uses ~20 nt sequence of crRNA to bind its complementary sequence of exogenous DNA. Subsequently with the aid of trans-acting RNA (trancrRNA), Cas9 endonuclease is recruited to the sequence and cut off the DNA at both strands.
In the application of CRISPR/Cas9 system in Drosophila genome editing, the two RNAs that play key roles can be synthesized into a single chimeric RNA (chiRNA or gRNA). By editing the 20 nt targeting sequence of gRNA, the system introduces DSB on the target sequence followed by an NGG or NAG protospacer adjacent motif (PAM) required for Cas9 cleavage.
Since CRISPR/Cas9 works through RNA-DNA recognition, Cas9 can perform its function simultaneously with multiple gRNA target sites, thus facilitates precise deletion, insertion and sequence replacement between the space via HR repair mechanism.
Below are three main Drosophila CRISPR/Cas9 systems, please visit their websites for more info:
For selecting/designing CRISPR target, DRSC Find CRISPR Tool is a genome-wide resource based on D. melanogaster genome assembly 6, and CRISPR Efficiency Predictor reports predicted efficiency based on nucleotide sequence.
Considering polymorphisms between a chosen fly strain and the reference genome, flyCRISPR Optimal Target Finder identifies gRNA target sites in user-supplied DNA sequence, evaluated with the reference of genome sequences, including D. melanogaster release 6, D. melanogaster vas-Cas9(III) (BDSC#51324) whole-genome sequence and other Drosophila genomes, etc.
Reference: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. (2013). 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. (2013). CRISPR/Cas9-mediated genome engineering and the promise of designer flies on demand. Fly (Austin) 7
Bassett AR, Tibbit C, Ponting CP, Liu JL (2013). Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 4(1): 220
Kondo S, Ueda R (2013). Highly improved gene targeting by germline-specific Cas9 expression in Drosophila. Genetics 195(3): 715
Port F, Chen HM, Lee T, Bullock SL. (2014) Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. PNAS 111(29):E2967
Port F, Muschalik N, Bullock SL. (2015) Systematic evaluation of Drosophila CRISPR tools reveals safe and robust alternatives to autonomous gene drives in basic research. G3 5(7): 1493
Ren XJ, Sun J, Housden BE, Hu YH, Roesel C, Lin SL, Liu LP, Yang ZH, Mao DC, Sun LZ, Wu QJ, Ji JY, Xi JZ, Mohr SE, Xu J, Perrimon N, Ni JQ (2013). Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. PNAS 110(47):19012
Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB, Ni JQ. (2014) Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep 9(3):1151
Zhang X, Koolhaas WH, Schnorrer F. (2014) A Versatile Two-Step CRISPR- and RMCE-Based Strategy for Efficient Genome Engineering in Drosophila. G3 4(12): 2409
flyCRISPR Stocks from Kate O'Connor-Giles, Jill Wildonger and Melissa Harrison
#PCR for Cas9 sequence ok; VK00037 landing site PCRs failed. Use with caution.
FlyCas9 Stocks from Shu Kondo and Ryu Ueda
CRISPR fly design Stocks* from Fillip Port and Simon Bullock
nos-Cas9 Stocks from Jian-Quan Ni and Norbert Perrimon
Act5C-Cas9, Lig4 Stock from Frank Schnorrer
For BestGene Drosophila Genome Editing Service, pls see here.