A comprehensive platform for highly multiplexed mammalian functional genetic screens
详细信息 查看全文
- 作者：Troy Ketela (1)
Lawrence E Heisler (1)
Kevin R Brown (1)
Ron Ammar (1) (2)
Dahlia Kasimer (1)
Anuradha Surendra (1)
Elke Ericson (1)
Kim Blakely (1) (2)
Dina Karamboulas (1)
Andrew M Smith (1) (2)
Tanja Durbic (1)
Anthony Arnoldo (1)
Kahlin Cheung-Ong (1)
Judice LY Koh (1)
Shuba Gopal (3)
Glenn S Cowley (3)
Xiaoping Yang (3)
Jennifer K Grenier (3)
Guri Giaever (1) (2) (4)
David E Root (3)
Jason Moffat (1) (2)
Corey Nislow (1) (2) - 刊名：BMC Genomics
- 出版年：2011
- 出版时间：December 2011
- 年：2011
- 卷：12
- 期：1
- 全文大小：1872KB
- 参考文献：1. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, / et al.: Functional profiling of the Saccharomyces cerevisiae genome. / Nature 2002, 418:387鈥?91. CrossRef
2. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, / et al.: Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. / Science 1999, 285:901鈥?06. CrossRef
3. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, / et al.: The genetic landscape of a cell. / Science 327:425鈥?31.
4. Giaever G, Shoemaker DD, Jones TW, Liang H, Winzeler EA, Astromoff A, Davis RW: Genomic profiling of drug sensitivities via induced haploinsufficiency. / Nat Genet 1999, 21:278鈥?83. CrossRef
5. Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G: The chemical genomic portrait of yeast: uncovering a phenotype for all genes. / Science 2008, 320:362鈥?65. CrossRef
6. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C: Systematic genetic analysis with ordered arrays of yeast deletion mutants. / Science 2001, 294:2364鈥?368. CrossRef
7. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, / et al.: Global mapping of the yeast genetic interaction network. / Science 2004, 303:808鈥?13. CrossRef
8. Bernards R, Brummelkamp TR, Beijersbergen RL: shRNA libraries and their use in cancer genetics. / Nat Methods 2006, 3:701鈥?06. CrossRef
9. Chang K, Elledge SJ, Hannon GJ: Lessons from Nature: microRNA-based shRNA libraries. / Nat Methods 2006, 3:707鈥?14. CrossRef
10. Moffat J, Sabatini DM: Building mammalian signalling pathways with RNAi screens. / Nat Rev Mol Cell Biol 2006, 7:177鈥?87. CrossRef
11. Root DE, Hacohen N, Hahn WC, Lander ES, Sabatini DM: Genome-scale loss-of-function screening with a lentiviral RNAi library. / Nat Methods 2006, 3:715鈥?19. CrossRef
12. Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R: A large-scale RNAi screen in human cells identifies new components of the p53 pathway. / Nature 2004, 428:431鈥?37. CrossRef
13. Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ: A resource for large-scale RNA-interference-based screens in mammals. / Nature 2004, 428:427鈥?31. CrossRef
14. Luo B, Cheung HW, Subramanian A, Sharifnia T, Okamoto M, Yang X, Hinkle G, Boehm JS, Beroukhim R, Weir BA, Mermel C, Barbie DA, Awad T, Zhou X, Nguyen T, Piqani B, Li C, Golub TR, Meyerson M, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE: Highly parallel identification of essential genes in cancer cells. / Proc Natl Acad Sci USA 2008, 105:20380鈥?0385. CrossRef
15. Luo J, Emanuele MJ, Li D, Creighton CJ, Schlabach MR, Westbrook TF, Wong KK, Elledge SJ: A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. / Cell 2009, 137:835鈥?48. CrossRef
16. Schlabach MR, Luo J, Solimini NL, Hu G, Xu Q, Li MZ, Zhao Z, Smogorzewska A, Sowa ME, Ang XL, Westbrook TF, Liang AC, Chang K, Hackett JA, Harper JW, Hannon GJ, Elledge SJ: Cancer proliferation gene discovery through functional genomics. / Science 2008, 319:620鈥?24. CrossRef
17. Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ, Chang K: Profiling essential genes in human mammary cells by multiplex RNAi screening. / Science 2008, 319:617鈥?20. CrossRef
18. Ngo VN, Davis RE, Lamy L, Yu X, Zhao H, Lenz G, Lam LT, Dave S, Yang L, Powell J, Staudt LM: A loss-of-function RNA interference screen for molecular targets in cancer. / Nature 2006, 441:106鈥?10. CrossRef
19. Pierce SE, Davis RW, Nislow C, Giaever G: Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. / Nat Protoc 2007, 2:2958鈥?974. CrossRef
20. Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, Chee M, Roth FP, Giaever G, Nislow C: Quantitative phenotyping via deep barcode sequencing. / Genome Res 2009, 19:1836鈥?842. CrossRef
21. Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, Bodeau J, Harris AN, Perry KM, Giaever G, Pourmand N, Nislow C: Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. / Nucleic Acids Res
22. Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE: A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. / Cell 2006, 124:1283鈥?298. CrossRef
23. Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M: hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. / Genomics 2007, 89:307鈥?15. CrossRef
24. Rual JF, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, Dricot A, Li N, Rosenberg J, Lamesch P, Vidalain PO, Clingingsmith TR, Hartley JL, Esposito D, Cheo D, Moore T, Simmons B, Sequerra R, Bosak S, Doucette-Stamm L, Le Peuch C, Vandenhaute J, Cusick ME, Albala JS, Hill DE, Vidal M: Human ORFeome version 1.1: a platform for reverse proteomics. / Genome Res 2004, 14:2128鈥?135. CrossRef
25. Hoon S, Smith AM, Wallace IM, Suresh S, Miranda M, Fung E, Proctor M, Shokat KM, Zhang C, Davis RW, Giaever G, St Onge RP, Nislow C: An integrated platform of genomic assays reveals small-molecule bioactivities. / Nat Chem Biol 2008, 4:498鈥?06. CrossRef
26. Ammar R, Smith AM, Heisler LE, Giaever G, Nislow C: A comparative analysis of DNA barcode microarray feature size. / BMC Genomics 2009, 10:471. CrossRef
27. Pierce SE, Fung EL, Jaramillo DF, Chu AM, Davis RW, Nislow C, Giaever G: A unique and universal molecular barcode array. / Nat Methods 2006, 3:601鈥?03. CrossRef
28. Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S: Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. / J Biotechnol 2004, 112:225鈥?45. CrossRef
29. Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, / et al.: The completion of the Mammalian Gene Collection (MGC). / Genome Res 2009, 19:2324鈥?333. CrossRef
30. Rouillard JM, Zuker M, Gulari E: OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. / Nucleic Acids Res 2003, 31:3057鈥?062. CrossRef
31. Le Novere N: MELTING, computing the melting temperature of nucleic acid duplex. / Bioinformatics 2001, 17:1226鈥?227. CrossRef
32. Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. / Genome Res 2008, 18:1851鈥?858. CrossRef - 作者单位：Troy Ketela (1)
Lawrence E Heisler (1)
Kevin R Brown (1)
Ron Ammar (1) (2)
Dahlia Kasimer (1)
Anuradha Surendra (1)
Elke Ericson (1)
Kim Blakely (1) (2)
Dina Karamboulas (1)
Andrew M Smith (1) (2)
Tanja Durbic (1)
Anthony Arnoldo (1)
Kahlin Cheung-Ong (1)
Judice LY Koh (1)
Shuba Gopal (3)
Glenn S Cowley (3)
Xiaoping Yang (3)
Jennifer K Grenier (3)
Guri Giaever (1) (2) (4)
David E Root (3)
Jason Moffat (1) (2)
Corey Nislow (1) (2)
1. Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
2. Department of Molecular Genetics, University of Toronto, Toronto, Canada
3. Broad Institute, Cambridge, USA
4. Department of Pharmaceutical Sciences, University of Toronto, Toronto, Canada
文摘
Background Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens. Results Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens. Conclusion Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.