The living microarray: A high-throughput platform for measuring transcription dynamics in single cells

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Rajan, Saravanan ^a   Djambazian, Haig ^a   Dang, Huan C P ^a   Sladek, Rob ^a   Hudson, Thomas J ^b,c  

^a MCGILL UNIVERSITY   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; CELL ASSAY; CELL HETEROGENEITY; CELL POPULATION; FLUORESCENCE ANALYSIS; GENE INDUCTION; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; LIVING MICROARRAY; MAMMAL CELL; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; PROMOTER REGION; REPORTER GENE; ANIMAL; CELL LINE; DNA MICROARRAY; FLUORESCENCE MICROSCOPY; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; PLASMID; SINGLE CELL ANALYSIS;

MAMMALIA;

ANIMALS; CELL LINE; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSCOPY, FLUORESCENCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMIDS; PROMOTER REGIONS, GENETIC; SINGLE-CELL ANALYSIS; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 79951553274     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-115     Document Type: Article

References (51)

1. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne J, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104. 10.1038/nature02800, 3006441, 15343339.
2. Workman CT, Mak HC, McCuine S, Tagne J, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways. Science 2006, 312:1054-1059. 10.1126/science.1122088, 2811083, 16709784.
3. Simonis N, Rual J, Carvunis A, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet A, Kao H, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, Vidal M. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods 2009, 6:47-54. 10.1038/nmeth.1279, 19123269.
4. Suzuki H, Forrest ARR, van Nimwegen E, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 2009, 41:553-562. 10.1038/ng.375, 19377474.
5. Ziauddin J, Sabatini DM. Microarrays of cells expressing defined cDNAs. Nature 2001, 411:107-10. 10.1038/35075114, 11333987.
6. Redmond TM, Ren X, Kubish G, Atkins S, Low S, Uhler MD. Microarray transfection analysis of transcriptional regulation by cAMP-dependent protein kinase. Mol Cell Proteomics 2004, 3:770-9. 10.1074/mcp.M400018-MCP200, 15118071.
7. Yoshikawa T, Uchimura E, Kishi M, Funeriu DP, Miyake M, Miyake J. Transfection microarray of human mesenchymal stem cells and on-chip siRNA gene knockdown. J Control Release 2004, 96:227-32. 10.1016/j.jconrel.2004.01.024, 15081214.
8. Reinisalo M, Urtti A, Honkakoski P. Freeze-drying of cationic polymer DNA complexes enables their long-term storage and reverse transfection of post-mitotic cells. J Control Release 2006, 110:437-43. 10.1016/j.jconrel.2005.10.003, 16297485.
9. Isalan M, Santori MI, Gonzalez C, Serrano L. Localized transfection on arrays of magnetic beads coated with PCR products. Nat Methods 2005, 2:113-8. 10.1038/nmeth732, 2666273, 15782208.
10. Bailey SN, Ali SM, Carpenter AE, Higgins CO, Sabatini DM. Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nat Methods 2006, 3:117-22. 10.1038/nmeth848, 16432521.
11. Oehmig A, Klotzbucher A, Thomas M, Weise F, Hagner U, Brundiers R, Waldherr D, Lingnau A, Knappik A, Kubbutat M, Joos T, Volkmer H. A novel reverse transduction adenoviral array for the functional analysis of shRNA libraries. BMC Genomics 2008, 9:441. 10.1186/1471-2164-9-441, 2559852, 18816379.
12. Honma K, Ochiya T, Nagahara S, Sano A, Yamamoto H, Hirai K, Aso Y, Terada M. Atelocollagen-based gene transfer in cells allows high-throughput screening of gene functions. Biochem Biophys Res Commun 2001, 289:1075-1081. 10.1006/bbrc.2001.6133, 11741301.
13. Mousses S, Caplen NJ, Cornelison R, Weaver D, Basik M, Hautaniemi S, Elkahloun AG, Lotufo RA, Choudary A, Dougherty ER, Suh E, Kallioniemi O. RNAi microarray analysis in cultured mammalian cells. Genome Res 2003, 13:2341-7. 10.1101/gr.1478703, 403721, 14525932.
14. Minakuchi Y, Takeshita F, Kosaka N, Sasaki H, Yamamoto Y, Kouno M, Honma K, Nagahara S, Hanai K, Sano A, Kato T, Terada M, Ochiya T. Atelocollagenmediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo. Nucleic Acids Res 2004, 32:e109. 10.1093/nar/gnh093, 506824, 15272050.
15. Neumann B, Held M, Liebel U, Erfle H, Rogers P, Pepperkok R, Ellenberg J. High-throughput RNAi screening by time-lapse imaging of live human cells. Nat Methods 2006, 3:385-390. 10.1038/nmeth876, 16628209.
16. Simpson JC, Cetin C, Erfle H, Joggerst B, Liebel U, Ellenberg J, Pepperkok R. An RNAi screening platform to identify secretion machinery in mammalian cells. J Biotechnol 2007, 129:352-365. 10.1016/j.jbiotec.2006.12.027, 17275941.
17. Neumann B, Walter T, Hériché J, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wünsche A, Satagopam V, Schmitz MHA, Chapuis C, Gerlich DW, Schneider R, Eils R, Huber W, Peters J, Hyman AA, Durbin R, Pepperkok R, Ellenberg J. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 2010, 464:721-727. 10.1038/nature08869, 20360735.
18. Webb BL, Diaz B, Martin GS, Lai F. A Reporter System for Reverse Transfection Cell Arrays. J Biomol Screen 2003, 8:620-623. 10.1177/1087057103259324, 14711387.
19. Nagoshi E, Saini C, Bauer C, Laroche T, Naef F, Schibler U. Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell 2004, 119:693-705. 10.1016/j.cell.2004.11.015, 15550250.
20. Nagai T, Ibata K, Park ES, Kubota M, Mikoshiba K, Miyawaki A. A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nat Biotechnol 2002, 20:87-90. 10.1038/nbt0102-87, 11753368.
21. Li X, Zhao X, Fang Y, Jiang X, Duong T, Fan C, Huang CC, Kain SR. Generation of destabilized green fluorescent protein as a transcription reporter. J Biol Chem 1998, 273:34970-5. 10.1074/jbc.273.52.34970, 9857028.
22. Roysam B, Lin G, Abdul-Karim MA, Al-Kofahi O, Al-Kofahi K, Shain W, Szarowsk DH, Turner JN. Automated three dimensional image analysis methods for confocal microscopy. Handbook of Biological Confocal Microscopy 2006, 316-337. Springer, 3.
23. Pannier A, Ariazi E, Bellis A, Bengali Z, Jordan V, Shea L. Bioluminescence imaging for assessment and normalization in transfected cell arrays. Biotechnol Bioeng 2007, 98:486-497. 10.1002/bit.21477, 2648395, 17486653.
24. Kim DW, Uetsuki T, Kaziro Y, Yamaguchi N, Sugano S. Use of the human elongation factor 1 alpha promoter as a versatile and efficient expression system. Gene 1990, 91:217-223. 10.1016/0378-1119(90)90091-5, 2210382.
25. Gopalkrishnan RV, Christiansen KA, Goldstein NI, DePinho RA, Fisher PB. Use of the human EF-1alpha promoter for expression can significantly increase success in establishing stable cell lines with consistent expression: a study using the tetracycline-inducible system in human cancer cells. Nucleic Acids Res 1999, 27:4775-4782. 10.1093/nar/27.24.4775, 148778, 10572178.
26. Pfau A, Grossmann C, Freudinger R, Mildenberger S, Benesic A, Gekle M. Ca2+ but not H2O2 modulates GRE-element activation by the human mineralocorticoid receptor in HEK cells. Mol Cell Endocrinol 2007, 264:35-43. 10.1016/j.mce.2006.10.002, 17113706.
27. Romanov S, Medvedev A, Gambarian M, Poltoratskaya N, Moeser M, Medvedeva L, Gambarian M, Diatchenko L, Makarov S. Homogeneous reporter system enables quantitative functional assessment of multiple transcription factors. Nat Methods 2008, 5:253-260. 10.1038/nmeth.1186, 18297081.
28. Megason SG, Fraser SE. Imaging in systems biology. Cell 2007, 130:784-795. 10.1016/j.cell.2007.08.031, 17803903.
29. Verveer PJ, Bastiaens PIH. Quantitative microscopy and systems biology: seeing the whole picture. Histochem Cell Biol 2008, 130:833-843. 10.1007/s00418-008-0517-5, 18830616.
30. Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N, Alon U. Dynamic Proteomics of Individual Cancer Cells in Response to a Drug. Science 2008, 322:1511-1516. 10.1126/science.1160165, 19023046.
31. Bellis AD, Peňalver-Bernabé B, Weiss MS, Yarrington ME, Barbolina MV, Pannier AK, Jeruss JS, Broadbelt LJ, Shea LD. Cellular arrays for large-scale analysis of transcription factor activity. Biotechnol Bioeng 2011, 108:395-403. 10.1002/bit.22916, 20812256.
32. Muller R. Transcriptional regulation during the mammalian cell cycle. Trends in Genetics 1995, 11:173-178. 10.1016/S0168-9525(00)89039-3, 7785076.
33. Dynlacht BD. Regulation of transcription by proteins that control the cell cycle. Nature 1997, 389:149-152. 10.1038/38225, 9296491.
34. Lania L, Majello B, Napolitano G. Transcriptional control by cell-cycle regulators: a review. J Cell Physiol 1999, 179:134-141. 10.1002/(SICI)1097-4652(199905)179:2<134::AID-JCP3>3.0.CO;2-O, 10199552.
35. Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhart DJ. Transcriptional regulation and function during the human cell cycle. Nat Genet 2001, 27:48-54.
36. Van der Meijden C, Lapointe D, Luong M, Peric-Hupkes D, Cho B, Stein J, Van Wijnen A, Stein G. Gene profiling of cell cycle progression through S-phase reveals sequential expression of genes required for DNA replication and nucleosome assembly. Cancer Res 2002, 62:3233-3243.
37. Whitfield M, Sherlock G, Saldanha A, Murray J, Ball C, Alexander K, Matese J, Perou C, Hurt M, Brown P, Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 2002, 13:1977-2000. 10.1091/mbc.02-02-0030., 117619, 12058064.
38. Cooper S, Shedden K. Microarray analysis of gene expression during the cell cycle. Cell Chromosome 2003, 2:1. 10.1186/1475-9268-2-1, 239863, 14577836.
39. Swain PS, Elowitz MB, Siggia ED. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci USA 2002, 99:12795-800. 10.1073/pnas.162041399, 130539, 12237400.
40. Wilkinson D. Stochastic modelling for quantitative description of heterogeneous biological systems. Nat Rev Genet 2009, 10:122-133. 10.1038/nrg2509, 19139763.
41. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 2008, 453:544-547. 10.1038/nature06965, 18497826.
42. Colman-Lerner A, Gordon A, Serra E, Chin T, Resnekov O, Endy D, Pesce CG, Brent R. Regulated cell-to-cell variation in a cell-fate decision system. Nature 2005, 437:699-706. 10.1038/nature03998, 16170311.
43. Norris A, Stirland J, McFerran D, Seymour Z, Spiller D, Loudon A, White M, Davis J. Dynamic patterns of growth hormone gene transcription in individual living pituitary cells. Mol Endocrinol 2003, 17:193-202. 10.1210/me.2002-0201, 12554747.
44. Takasuka N, White MRH, Wood CD, Robertson WR, Davis JRE. Dynamic Changes in Prolactin Promoter Activation in Individual Living Lactotrophic Cells. Endocrinology 1998, 139:1361-1368. 10.1210/en.139.3.1361, 9492073.
45. Villalobos C, Faught W, Frawley L. Dynamics of stimulus-expression coupling as revealed by monitoring of prolactin promoter-driven reporter activity in individual, living mammotropes. Mol Endocrinol 1999, 13:1718-1727. 10.1210/me.13.10.1718, 10517673.
46. Harper CV, Featherstone K, Semprini S, Friedrichsen S, McNeilly J, Paszek P, Spiller DG, McNeilly AS, Mullins JJ, Davis JRE, White MRH. Dynamic organisation of prolactin gene expression in living pituitary tissue. J Cell Sci 2010, 123:424-430. 10.1242/jcs.060434, 2816187, 20130141.
47. Hood L, Heath JR, Phelps ME, Lin B. Systems Biology and New Technologies Enable Predictive and Preventative Medicine. Science 2004, 306:640-643. 10.1126/science.1104635, 15499008.
48. Kitano H. Systems Biology: A Brief Overview. Science 2002, 295:1662-1664. 10.1126/science.1069492, 11872829.
49. Vass G, Perlaki T. Applying and removing lens distortion in post production. Second Hungarian Conference on Computer Graphics and Geometry 2003,
50. Sun Y, Duthaler S, Nelson BJ. Autofocusing in computer microscopy: Selecting the optimal focus algorithm. Microsc Res Tech 2004, 65.
51. Motwani MC, Gadiya MC, Motwani RC, Harris FC. Survey of image denoising techniques. Proceedings of the Global Signal Processing Expo and Conference 2004,