A Genome-Wide CRISPR Library for High-Throughput Genetic Screening in Drosophila Cells

Journal of Genetics and Genomics

Volumn 42, Issue 6, 2015, Pages 301-309

  Bassett, Andrew R ^a,b   Kong, Lesheng ^a   Liu, Ji Long ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

CRISPR Cas9; Drosophila; Genome wide library

Indexed keywords

GUIDE RNA; SINGLE GUIDE RNA; UNCLASSIFIED DRUG;

ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DROSOPHILA; GENE DISRUPTION; GENE TARGETING; GENETIC SCREENING; HIGH THROUGHPUT SCREENING; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; LOSS OF FUNCTION MUTATION; NONHUMAN; PHENOTYPE; RNA INTERFERENCE; SIGNAL NOISE RATIO; ANIMAL; CRISPR CAS SYSTEM; GENE LIBRARY; GENETICS;

ANIMALS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; DROSOPHILA; GENOMIC LIBRARY;

EID: 84947039940     PISSN: 16738527     EISSN: 18735533     Source Type: Journal    
DOI: 10.1016/j.jgg.2015.03.011     Document Type: Article

References (39)

1. Bakal C. Drosophila RNAi screening in a postgenomic world. Brief. Funct. Genomics 2011, 10:197-205.
2. Bassett A.R., Liu J.L. CRISPR/Cas9 and genome editing in Drosophila. J. Genet. Genomics 2014, 41:7-19.
3. Bassett A.R., Tibbit C., Ponting C.P., Liu J.L. Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 2013, 4:220-228.
4. Bassett A.R., Tibbit C., Ponting C.P., Liu J.L. Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9. Biol. Open 2014, 3:42-49.
5. Bibikova M., Golic M., Golic K.G., Carroll D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 2002, 161:1169-1175.
6. Boutros M., Ahringer J. The art and design of genetic screens: RNA interference. Nat. Rev. Genet. 2008, 9:554-566.
7. Boutros M., Kiger A.A., Armknecht S., Kerr K., Hild M., Koch B., Haas S.A., Paro R., Perrimon N. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 2004, 303:832-835. Heidelberg Fly Array, C.
8. Brouns S.J., Jore M.M., Lundgren M., Westra E.R., Slijkhuis R.J., Snijders A.P., Dickman M.J., Makarova K.S., Koonin E.V., van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008, 321:960-964.
9. de Hoon M.J., Imoto S., Nolan J., Miyano S. Open source clustering software. Bioinformatics 2004, 20:1453-1454.
10. Doench J.G., Hartenian E., Graham D.B., Tothova Z., Hegde M., Smith I., Sullender M., Ebert B.L., Xavier R.J., Root D.E. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat. Biotechnol. 2014, 32:1262-1267.
11. Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014, 346:1258096.
12. Frock R.L., Hu J., Meyers R.M., Ho Y.J., Kii E., Alt F.W. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat. Biotechnol. 2015, 33:179-186.
13. Gasiunas G., Barrangou R., Horvath P., Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl. Acad. Sci. USA 2012, 109:E2579-2586.
14. Gratz S.J., Cummings A.M., Nguyen J.N., Hamm D.C., Donohue L.K., Harrison M.M., Wildonger J., O'Connor-Giles K.M. Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 2013, 194:1029-1035.
15. Gratz S.J., Ukken F.P., Rubinstein C.D., Thiede G., Donohue L.K., Cummings A.M., O'Connor-Giles K.M. Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics 2014, 196:961-971.
16. Groth A.C., Fish M., Nusse R., Calos M.P. Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics 2004, 166:1775-1782.
17. 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., Cradick T.J., Marraffini L.A., Bao G., Zhang F. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 2013, 31:827-832.
18. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
19. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
20. Koike-Yusa H., Li Y., Tan E.P., Velasco-Herrera Mdel C., Yusa K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat. Biotechnol. 2014, 32:267-273.
21. Kondo S., Ueda R. Highly improved gene targeting by germline-specific Cas9 expression in Drosophila. Genetics 2013, 195:715-721.
22. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
23. Lee D.F., Chen C.C., Hsu T.A., Juang J.L. A baculovirus superinfection system: efficient vehicle for gene transfer into Drosophila S2 cells. J. Virol. 2000, 74:11873-11880.
24. Lloyd T.E., Taylor J.P. Flightless flies: Drosophila models of neuromuscular disease. Ann. N. Y. Acad. Sci. 2010, 1184:e1-20.
25. Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014, 15:550.
26. Ma Y., Creanga A., Lum L., Beachy P.A. Prevalence of off-target effects in Drosophila RNA interference screens. Nature 2006, 443:359-363.
27. Pattanayak V., Lin S., Guilinger J.P., Ma E., Doudna J.A., Liu D.R. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 2013, 31:839-843.
28. Port F., Chen H.M., Lee T., Bullock S.L. Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc. Natl. Acad. Sci. USA 2014, 111:E2967-2976.
29. Reiter L.T., Potocki L., Chien S., Gribskov M., Bier E. A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster. Genome Res. 2001, 11:1114-1125.
30. Ren X., Yang Z., Xu J., Sun J., Mao D., Hu Y., Yang S.J., Qiao H.H., Wang X., Hu Q., Deng P., Liu L.P., Ji J.Y., Li J.B., Ni J.Q. Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep. 2014, 9:1151-1162.
31. Rouet P., Smih F., Jasin M. Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc. Natl. Acad. Sci. USA 1994, 91:6064-6068.
32. Saldanha A.J. Java Treeview-extensible visualization of microarray data. Bioinformatics 2004, 20:3246-3248.
33. Sebo Z.L., Lee H.B., Peng Y., Guo Y. A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering. Fly (Austin) 2014, 8:52-57.
34. Shalem O., Sanjana N.E., Hartenian E., Shi X., Scott D.A., Mikkelsen T.S., Heckl D., Ebert B.L., Root D.E., Doench J.G., Zhang F. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 2014, 343:84-87.
35. Shrivastav M., De Haro L.P., Nickoloff J.A. Regulation of DNA double-strand break repair pathway choice. Cell Res. 2008, 18:134-147.
36. Tsai S.Q., Zheng Z., Nguyen N.T., Liebers M., Topkar V.V., Thapar V., Wyvekens N., Khayter C., Iafrate A.J., Le L.P., Aryee M.J., Joung J.K. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 2015, 33:187-197.
37. Wang T., Wei J.J., Sabatini D.M., Lander E.S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014, 343:80-84.
38. Wei C., Liu J., Yu Z., Zhang B., Gao G., Jiao R. TALEN or Cas9-rapid, efficient and specific choices for genome modifications. J. Genet. Genomics 2013, 40:281-289.
39. Yu Z., Ren M., Wang Z., Zhang B., Rong Y.S., Jiao R., Gao G. Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics 2013, 195:289-291.