Cell microarrays and rna interference chip away at gene function

Nature Genetics

Volumn 37, Issue 6S, 2005, Pages S25-S30

  Wheeler, Douglas B ^a   Carpenter, Anne E ^a   Sabatini, David M ^a  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

8 CHLORO 2,3,4,5 TETRAHYDRO 3 METHYL 5 PHENYL 1H 3 BENZAZEPIN 7 OL HYDROGEN MALEATE; CYCLIC AMP; DOUBLE STRANDED RNA; F ACTIN; FK 506 BINDING PROTEIN; GREEN FLUORESCENT PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MESSENGER RNA; MYOD PROTEIN; PROTEIN KINASE B; PROTEIN P53; RIBONUCLEASE III; RNA; TACROLIMUS;

APOPTOSIS; CAENORHABDITIS ELEGANS; CELL ADHESION; CELL STRAIN K 562; DNA MICROARRAY; DROSOPHILA MELANOGASTER; GENE FUNCTION; HELA CELL; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; IMAGE ANALYSIS; IMMUNOFLUORESCENCE; IN SITU HYBRIDIZATION; NICK END LABELING; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; REVIEW; RNA INTERFERENCE;

ANIMALS; CELLS, CULTURED; GENE SILENCING; GENOMICS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA INTERFERENCE;

METAZOA;

EID: 20044366920     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1560     Document Type: Article

References (65)

1. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998).
2. Carpenter, A.E. & Sabatini, D.M. Systematic genome-wide screens of gene function. Nat. Rev. Genet. 5, 11-22 (2004).
3. Armknecht, S. et al. High-throughput RNA interference screens in Drosophila tissue culture cells. Methods Enzymol. 392, 55-73 (2005).
4. Boutros, M. et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303, 832-835 (2004).
5. Ziauddin, J. & Sabatini, D.M. Microarrays of cells expressing defined cDNAs. Nature 411, 107-110 (2001).
6. Mishina, Y.M. et al. Multiplex GPCR assay in reverse transfection cell microarrays. J. Biomo. Screen. 9, 196-207 (2004).
7. Kumar, R., Conklin, D.S. & Mittal, V. High-throughput selection of effective RNAi probes for gene silencing. Genome Res. 13, 2333-2340 (2003).
8. Baghdoyan, S. et al. Quantitative analysis of highly parallel transfection in cell microarrays. Nucleic Acids Res. 32, e77 (2004).
9. Yoshikawa, T. et al. Transfection microarray of human mesenchymal stem cells and on-chip siRNA gene knockdown. J. Control. Release 96, 227-232 (2004).
10. Erfle, H., Simpson, J.C., Bastiaens, P.I. & Pepperkok, R. siRNA cell arrays for highcontent screening microscopy. Biotechniques 37, 454-458, 460, 462 (2004).
11. Kato, K., Umezawa, K., Miyake, M., Miyake, J. & Nagamune, T. Transfection microarray of nonadherent cells on an oleyl poly(ethylene glycol) ether-modified glass slide. Biotechniques 37, 444-452 (2004).
12. Silva, J.M., Mizuno, H., Brady, A., Lucito, R. & Hannon, G.J. RNA interference microarrays: High-throughput loss-of-function genetics in mammalian cells. Proc. Natl. Acad. Sci. USA 101, 6548-6552 (2004).
13. Mousses, S. et al. RNAi microarray analysis in cultured mammalian cells. Genome Res. 13, 2341-2347 (2003).
14. Chang, F.H. et al. Surfection: A new platform for transfected cell arrays. Nucleic Acids Res. 32, e33 (2004).
15. Wheeler, D.B. et al. RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogastercells. Nat. Methods 1, 127-132 (2004).
16. Fodor, S.P. et al. Light-directed, spatially addressable parallel chemical synthesis. Science 251, 767-773 (1991).
17. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
18. Huang, J. et al. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc. Natl. Acad. Sci. USA 101, 16594-16599 (2004).
19. Zhu, H. et al. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26, 283-289 (2000).
20. Houseman, B.T. & Mrksich, M. Carbohydrate arrays for the evaluation of protein bind- I ing and enzymatic modification. Chem. Biol. 9, 443-454 (2002).
21. Kononen, J. et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4, 844-847 (1998).
22. Kuruvilla, F.G., Shamji, A.F., Sternson, S.M., Hergenrother, P.J. & Schreiber, S.L. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416, 653-657 (2002).
23. Redmond, T.M. et al. Microarray transfection analysis of transcriptional regulation by cAMP-dependent protein kinase. Mol. Cell. Proteomics 3, 770-779 (2004).
24. Conrad, C. et al. Automatic identification of subcellular phenotypes on human cell arrays. Genome Res. 14, 1130-1136 (2004).
25. Palmer, E. & Freeman, T. Investigation into the use of C- and N-terminal GFP fusion proteins for subcellular localization studies using reverse transfection microarrays. Comp. Funct. Genomics 5, 342-353 (2004).
26. Webb, B.L., Diaz, B., Martin, G.S. & Lai, F. A reporter system for reverse transfection cell arrays. J. Biomol. Screen. 8, 620-623 (2003).
27. Clemens, J.C. et al. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc. Natl. Acad. Sci. USA 97, 6499-6503 (2000).
28. Marcus, P.I. & Sekellick, M.J. Interferon induction by viruses. XIII. Detection and assay of interferon induction-suppressing particles. Virology 142, 411-415(1985).
29. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498 (2001).
30. Dykxhoorn, D.M., Novina, C.D. & Sharp, P.A. Killing the messenger: Short RNAs that silence gene expression. Nat. Rev. Mol. Cell Biol. 4, 457-467 (2003).
31. McManus, M.T., Petersen, C.P., Haines, B.B., Chen, J. & Sharp, P.A. Gene silencing using micro-RNA designed hairpins. RNA 8, 842-850 (2002).
32. Berns, K. et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431-437 (2004).
33. Paddison, P.J. et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428, 427-431 (2004).
34. Zheng, L. et al. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 101, 135-140 (2004).
35. Calegari, F., Haubensak, W., Yang, D., Huttner, W.B. & Buchholz, F. Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNA. Proc. Natl. Acad. Sci. USA 99, 14236-14240 (2002).
36. Kittler, R. et al. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432, 1036-1040 (2004).
37. Lum, L. et al. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299, 2039-2045 (2003).
38. Kiger, A. et al. A functional genomic analysis of cell morphology using RNA interference. J. Biol. 2, 27 (2003).
39. Eggert, U.S. et al. Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol. 2, e379 (2004).
40. Bettencourt-Dias, M. et al. Genome-wide survey of protein kinases required for cell cycle progression. Nature 432, 980-987 (2004).
41. Yarrow, J.C., Perlman, Z.E., Westwood, N.J. & Mitchison, T.J. A high-throughput cell migration assay using scratch wound healing, a comparison of image-based readout methods. BMC Biotechnol. 4, 21 (2004).
42. Ruckstuhl, T., Walser, A., Verdes, D. & Seeger S. Confocal reader for biochip screening and fluorescence microscopy. Biosens. Bioelectron. 20, 1872-1877 (2005).
43. Liebel, U. et al. A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Lett. 554, 394-398 (2003).
44. Huh, W.K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686-691 (2003).
45. Murphy, R.F., Boland, M.V. & Velliste, M. Towards a systematics for protein subcellular location: Quantitative description of protein localization patterns and automated analysis of fluorescence microscope images. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 251-259 (2000).
46. Murphy, R.F., Velliste, M. & Porreca, G. Robust numerical features for description and classification of subcellular location patterns in fluorescence microscope images. J. VLSI Signal Process. 35, 311-321 (2003).
47. Eils, R. & Athale, C. Computational imaging in cell biology. J. Cell. Biol. 161, 477-481 (2003).
48. Lindblad, J., Wahlby, C., Bengtsson, E. & Zaltsman, A. Image analysis for automatic segmentation of cytoplasms and classification of Rac1 activation. Cytometry A 57, 22-33 (2004).
49. Mehes, G., Lorch, T. & Ambros, P.F. Quantitative analysis of disseminated tumor cells in the bone marrow by automated fluorescence image analysis. Cytometry 42, 357-362 (2000).
50. Carpenter, A.E., Memedula, S., Plutz, M.J. & Belmont, A.S. Common effects of acidic activators on large-scale chromatin structure and transcription. Mol. Cell. Biol. 25, 958-968 (2005).
51. Carpenter, A.E., Ashouri, A. & Belmont, A.S. Automated microscopy identifies estrogen receptor subdomains with large-scale chromatin structure unfolding activity. Cytometry A 58A, 157-166 (2004).
52. Perlman, Z.E. et al. Multidimensional drug profiling by automated microscopy. Science 306, 1194-1198 (2004).
53. Perlman, Z.E., Mitchison, T.J. & Mayer, T.U. High-content screening and profiling of drug activity in an automated centrosome-duplication assay. Chembiochemistry 6, 145-151 (2005).
54. Obenauer-Kutner, L.J. et al. Use of an automated image processing program to quantify recombinant adenovirus particles. Microsc. Microanal. 11, 37-41 (2005).
55. Camp, R.L., Chung, G.G. & Rimm, D.L. Automated subcellular localization and quantification of protein expression in tissue microarrays. Nat. Med. 8, 1323-1327 (2002).
56. Abramoff, M.D., Magalhaes, P.J. & Ram, S.J. Image processing with ImageJ. Biophotonics Int. 11, 36-42 (2004).
57. Ghosh, R.N., Grove, L. & Lapets, O. A quantitative cell-based high-content screening assay for the epidermal growth factor receptor-specific activation of mitogen-activated protein kinase. Assay Drug. Dev. Technol. 2, 473-481 (2004).
58. Oode, K. et al. The development of a cell array and its combination with laser-scanning cytometry allows a high-throughput analysis of nuclear DNA content. Am. J. Pathol. 157, 723-728 (2000).
59. Belien, J.A. et al. Confocal DNA cytometry: A contour-based segmentation algorithm for automated three-dimensional image segmentation. Cytometry 49, 12-21 (2002).
60. Searls, D.B. Data integration: Challenges for drug discovery. Nat. Rev. DrugDiscov. 4, 45-58 (2005).
61. Swedlow, J.R., Goldberg, I., Brauner, E. & Sorger, P.K. Informatics and quantitative analysis in biological imaging. Science 300, 100-102 (2003).
62. Swayne, D.F., Buja, A. & Temple-Lang, D. Exploratory visual analysis of graphs. Proceedings of the Third Annual Workshop on Distributed Statistical Computing (Technische Universität Wien, Vienna, 2003).
63. Cheezum, M.K., Walker, W.F. & Guilford, W.H. Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys. J. 81, 2378-2388 (2001).
64. Bacher, C.P., Reichenzeller, M., Athale, C., Herrmann, H. & Eils, R. 4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin-poor tracks. BMC Cell. Biol. 5, 45 (2004).
65. Hartwell, L.H., Szankasi, P., Roberts, C.J., Murray, A.W. & Friend, S.H. Integrating genetic approaches into the discovery of anticancer drugs. Science 278, 1064-1068 (1997).