Cell microarrays and RNA interference chip away at gene function

The recent development of cell microarrays offers the potential to accelerate high-throughput functional genetic studies. The widespread use of RNA interference (RNAi) has prompted several groups to fabricate RNAi cell microarrays that make possible discrete, in-parallel transfection with thousands of RNAi reagents on a microarray slide. Though still a budding technology, RNAi cell microarrays promise to increase the efficiency, economy and ease of genome-wide RNAi screens in metazoan cells.

[1]  P. I. Marcus.  Interferon Induction by Viruses , 1984 .

[2]  P. I. Marcus,et al.  Interferon induction by viruses. XIII. Detection and assay of interferon induction-suppressing particles. , 1985, Virology.

[3]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[4]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[5]  L. Hartwell,et al.  Integrating genetic approaches into the discovery of anticancer drugs. , 1997, Science.

[6]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[7]  J. Kononen,et al.  Tissue microarrays for high-throughput molecular profiling of tumor specimens , 1998, Nature Medicine.

[8]  T. Lörch,et al.  Quantitative analysis of disseminated tumor cells in the bone marrow by automated fluorescence image analysis. , 2000, Cytometry.

[9]  Robert F. Murphy,et al.  Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images , 2000, ISMB.

[10]  M. Gerstein,et al.  Analysis of yeast protein kinases using protein chips , 2000, Nature Genetics.

[11]  T. Hirano,et al.  The development of a cell array and its combination with laser-scanning cytometry allows a high-throughput analysis of nuclear DNA content. , 2000, The American journal of pathology.

[12]  J. C. Clemens,et al.  Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  D. Sabatini,et al.  Microarrays of cells expressing defined cDNAs , 2001, Nature.

[14]  M K Cheezum,et al.  Quantitative comparison of algorithms for tracking single fluorescent particles. , 2001, Biophysical journal.

[15]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[16]  D. Rimm,et al.  Automated subcellular localization and quantification of protein expression in tissue microarrays , 2002, Nature Medicine.

[17]  W. Huttner,et al.  Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNA , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[18]  P. V. van Diest,et al.  Confocal DNA cytometry: a contour-based segmentation algorithm for automated three-dimensional image segmentation. , 2002, Cytometry.

[19]  Milan Mrksich,et al.  Carbohydrate arrays for the evaluation of protein binding and enzymatic modification. , 2002, Chemistry & biology.

[20]  Michael T. McManus,et al.  Gene silencing using micro-RNA designed hairpins. , 2002, RNA.

[21]  Stuart L. Schreiber,et al.  Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays , 2002, Nature.

[22]  R. Eils,et al.  Computational imaging in cell biology , 2003, The Journal of cell biology.

[23]  D. Dykxhoorn,et al.  Killing the messenger: short RNAs that silence gene expression , 2003, Nature Reviews Molecular Cell Biology.

[24]  Lawrence Lum,et al.  Identification of Hedgehog Pathway Components by RNAi in Drosophila Cultured Cells , 2003, Science.

[25]  Peter G Schultz,et al.  An approach to genomewide screens of expressed small interfering RNAs in mammalian cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[26]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[27]  A. Coulson,et al.  A functional genomic analysis of cell morphology using RNA interference , 2003, Journal of biology.

[28]  J. Kurreck.  Improvement through novel chemical modifications , 2003 .

[29]  Fang Lai,et al.  A Reporter System for Reverse Transfection Cell Arrays , 2003, Journal of biomolecular screening.

[30]  Robert F. Murphy,et al.  Robust Numerical Features for Description and Classification of Subcellular Location Patterns in Fluorescence Microscope Images , 2003, J. VLSI Signal Process..

[31]  Jens Kurreck,et al.  Antisense technologies. Improvement through novel chemical modifications. , 2003, European journal of biochemistry.

[32]  Erik Brauner,et al.  Informatics and Quantitative Analysis in Biological Imaging , 2003, Science.

[33]  A. Poustka,et al.  A microscope‐based screening platform for large‐scale functional protein analysis in intact cells , 2003, FEBS letters.

[34]  E. Dougherty,et al.  RNAi microarray analysis in cultured mammalian cells. , 2003, Genome research.

[35]  Vivek Mittal,et al.  High-throughput selection of effective RNAi probes for gene silencing. , 2003, Genome research.

[36]  Norbert Perrimon,et al.  Parallel Chemical Genetic and Genome-Wide RNAi Screens Identify Cytokinesis Inhibitors and Targets , 2004, PLoS biology.

[37]  Robert Lucito,et al.  RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Masato Miyake,et al.  Transfection microarray of human mesenchymal stem cells and on-chip siRNA gene knockdown. , 2004, Journal of controlled release : official journal of the Controlled Release Society.

[39]  Joakim Lindblad,et al.  Image analysis for automatic segmentation of cytoplasms and classification of Rac1 activation , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[40]  Reuven Agami,et al.  A large-scale RNAi screen in human cells identifies new components of the p53 pathway , 2004, Nature.

[41]  M. Uhler,et al.  Microarray Transfection Analysis of Transcriptional Regulation by cAMP-dependent Protein Kinase* , 2004, Molecular & Cellular Proteomics.

[42]  D. M. Glover,et al.  Genome-wide survey of protein kinases required for cell cycle progression , 2004, Nature.

[43]  Fu-Hsiung Chang,et al.  Surfection: a new platform for transfected cell arrays. , 2004, Nucleic acids research.

[44]  Yoann Roupioz,et al.  Quantitative analysis of highly parallel transfection in cell microarrays. , 2004, Nucleic acids research.

[45]  Lani F. Wu,et al.  Multidimensional Drug Profiling By Automated Microscopy , 2004, Science.

[46]  Michael D. Abràmoff,et al.  Image processing with ImageJ , 2004 .

[47]  T. Mitchison,et al.  A high-throughput cell migration assay using scratch wound healing, a comparison of image-based readout methods , 2004, BMC biotechnology.

[48]  Anne E Carpenter,et al.  RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells , 2004, Nature Methods.

[49]  T. Freeman,et al.  Investigation Into the use of C- and N-terminal GFP Fusion Proteins for Subcellular Localization Studies Using Reverse Transfection Microarrays , 2004, Comparative and functional genomics.

[50]  Oleg Lapets,et al.  A quantitative cell-based high-content screening assay for the epidermal growth factor receptor-specific activation of mitogen-activated protein kinase. , 2004, Assay and drug development technologies.

[51]  N. Perrimon,et al.  Genome-Wide RNAi Analysis of Growth and Viability in Drosophila Cells , 2004, Science.

[52]  H. Himmelbauer,et al.  An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division , 2004, Nature.

[53]  C. Conrad,et al.  Automatic identification of subcellular phenotypes on human cell arrays. , 2004, Genome research.

[54]  R. Eils,et al.  4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin – poor tracks , 2004, BMC Cell Biology.

[55]  Anne E Carpenter,et al.  Automated microscopy identifies estrogen receptor subdomains with large‐scale chromatin structure unfolding activity , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[56]  Patrick J. Paddison,et al.  A resource for large-scale RNA-interference-based screens in mammals , 2004, Nature.

[57]  Teruyuki Nagamune,et al.  Transfection microarray of nonadherent cells on an oleyl poly(ethylene glycol) ether-modified glass slide. , 2004, BioTechniques.

[58]  Holger Erfle,et al.  siRNA cell arrays for high-content screening microscopy. , 2004, BioTechniques.

[59]  Christopher J Wilson,et al.  Multiplex GPCR Assay in Reverse Transfection Cell Microarrays , 2004, Journal of biomolecular screening.

[60]  Anne E Carpenter,et al.  Systematic genome-wide screens of gene function , 2004, Nature Reviews Genetics.

[61]  S. Haggarty,et al.  Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[62]  M. Grace,et al.  Use of an Automated Image Processing Program to Quantify Recombinant Adenovirus Particles , 2005, Microscopy and Microanalysis.

[63]  Anne E Carpenter,et al.  Common Effects of Acidic Activators on Large-Scale Chromatin Structure and Transcription , 2005, Molecular and Cellular Biology.

[64]  Norbert Perrimon,et al.  High-throughput RNA interference screens in Drosophila tissue culture cells. , 2005, Methods in enzymology.

[65]  Stefan Seeger,et al.  Confocal reader for biochip screening and fluorescence microscopy. , 2005, Biosensors & bioelectronics.

[66]  Timothy J Mitchison,et al.  High‐Content Screening and Profiling of Drug Activity in an Automated Centrosome‐Duplication Assay , 2005, Chembiochem : a European journal of chemical biology.

[67]  David B. Searls,et al.  Data integration: challenges for drug discovery , 2005, Nature Reviews Drug Discovery.