Abstract
RNA interference (RNAi) refers to post-transcriptional silencing of gene expression as a result of the introduction of double-stranded RNA into cells. The application of RNAi in experimental systems has significantly accelerated elucidation of gene functions. In order to facilitate large-scale functional genomics studies using RNAi, several high-throughput approaches have been developed based on microarray or microwell assays. The recent establishment of large libraries of RNAi reagents combined with a variety of detection assays has further improved the performance of functional genome-wide screens in mammalian cells.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ashrafi K, Chang FY, Watts JL, Fraser AG, Kamath RS, Ahringer J, Ruvkun G (2003) Genomewide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421:268–272
Baghdoyan S, Roupioz Y, Pitaval A, Castel D, Khomyakova E, Papine A, Soussaline F, Gidrol X (2004) Quantitative analysis of highly parallel transfection in cell microarrays. Nucleic Acids Res 32:e77
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 (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428:431–437
Boer JM, Huber WK, Sultmann H, Wilmer F, von Heydebreck A, Haas S, Korn B, Gunawan B, Vente A, Fuzesi L, Vingron M, Poustka A (2001) Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array. Genome Res 11:1861–1870
Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550–553
Carpenter AE, Sabatini DM (2004) Systematic genome-wide screens of gene function. Nat Rev Genet 5:11–22
Chittur SV (2004) DNA microarrays: tools for the 21st century. Comb Chem High Throughput Screen 7:531–537
Colosimo A, Goncz KK, Holmes AR, Kunzelmann K, Novelli G, Malone RW, Bennett MJ, Gruenert DC (2000) Transfer and expression of foreign genes in mammalian cells. Biotechniques 29:314–318
Conrad C, Erfle H, Warnat P, Daigle N, Lorch T, Ellenberg J, Pepperkok R, Eils R (2004) Automatic identification of subcellular phenotypes on human cell arrays. Genome Res 14:1130–1136
Erfle H, Simpson JC, Bastiaens PI, Pepperkok R (2004) siRNA cell arrays for high-content screening microscopy. Biotechniques 37:454–462
Grzeskowiak R, Witt H, Drungowski M, Thermann R, Hennig S, Perrot A, Osterziel KJ, Klingbiel D, Scheid S, Spang R, Lehrach H, Ruiz P (2003) Expression profiling of human idiopathic dilated cardiomyopathy. Cardiovasc Res 59:400–411
Gutjahr C, Murphy D, Lueking A, Koenig A, Janitz M, O’Brien J, Korn B, Horn S, Lehrach H, Cahill DJ (2005) Mouse protein arrays from a TH1 cell cDNA library for antibody screening and serum profiling. Genomics 85:285–296
Kaynak B, von Heydebreck A, Mebus S, Seelow D, Hennig S, Vogel J, Sperling HP, Pregla R, Alexi-Meskishvili V, Hetzer R, Lange PE, Vingron M, Lehrach H, Sperling S (2003) Genome-wide array analysis of normal and malformed human hearts. Circulation 107:2467–2474
Kittler R, Putz G, Pelletier L, Poser I, Heninger AK, Drechsel D, Fischer S, Konstantinova I, Habermann B, Grabner H, Yaspo ML, Himmelbauer H, Korn B, Neugebauer K, Pisabarro MT, Buchholz F (2004) An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432:1036–1040
Kumar R, Conklin DS, Mittal V (2003) High-throughput selection of effective RNAi probes for gene silencing. Genome Res 13:2333–2340
Lum L, Yao S, Mozer B, Rovescalli A, Von Kessler D, Nirenberg M, Beachy PA (2003) Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299:2039–2045
Mishina YM, Wilson CJ, Bruett L, Smith JJ, Stoop-Myer C, Jong S, Amaral LP, Pedersen R, Lyman SK, Myer VE, Kreider BL, Thompson CM (2004) Multiplex GPCR assay in reverse transfection cell microarrays. J Biomol Screen 9:196–207
Mousses S, Caplen NJ, Cornelison R, Weaver D, Basik M, Hautaniemi S, Elkahloun AG, Lotufo RA, Choudary A, Dougherty ER, Suh E, Kallioniemi O (2003) RNAi microarray analysis in cultured mammalian cells. Genome Res 13:2341–2347
Paddison PJ, Hannon GJ (2003) siRNAs and shRNAs: skeleton keys to the human genome. Curr Opin Mol Ther 5:217–224
Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ (2004) RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. Proc Natl Acad Sci USA 101:6548–6552
Stoll D, Templin MF, Bachmann J, Joos TO (2005) Protein microarrays: applications and future challenges. Curr Opin Drug Discov Devel 8:239–252
van de Wetering M, Oving I, Muncan V, Pon Fong MT, Brantjes H, van Leenen D, Holstege FC, Brummelkamp TR, Agami R, Clevers H (2003) Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector. EMBO Rep 4:609–615
Walter G, Bussow K, Cahill D, Lueking A, Lehrach H(2000) Protein arrays for gene expression and molecular interaction screening. Curr Opin Microbiol 3:298–302
Wang JC, Walker A, Blackwell TK, Yamamoto KR (2004) The Caenorhabditis elegans ortholog of TRAP240, CeTRAP240/let-19, selectively modulates gene expression and is essential for embryogenesis. J Biol Chem 279:29270–29277
Wheeler DB, Bailey SN, Guertin DA, Carpenter AE, Higgins CO, Sabatini DM (2004) RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nat Methods 1:127–132
Wiemann S, Bechtel S, Bannasch D, Pepperkok R, Poustka A, German cDNA Network (2003) The German cDNA network: cDNAs, functional genomics and proteomics. J Struct Funct Genomics 4:87–96
Yoshikawa T, Uchimura E, Kishi M, Funeriu DP, Miyake M, Miyake J (2004) Transfection microarray of human mesenchymal stem cells and on-chip siRNA gene knockdown. J Control Release 96:227–232
Zheng L, Liu J, Batalov S, Zhou D, Orth A, Ding S, Schultz PG (2004) An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc Natl Acad Sci USA 101:135–140
Ziauddin J, Sabatini DM (2001) Microarrays of cells expressing defined cDNAs. Nature 411:107–110
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Janitz, M., Vanhecke, D., Lehrach, H. (2006). High-Throughput RNA Interference in Functional Genomics. In: Erdmann, V., Barciszewski, J., Brosius, J. (eds) RNA Towards Medicine. Handbook of Experimental Pharmacology, vol 173. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-27262-3_5
Download citation
DOI: https://doi.org/10.1007/3-540-27262-3_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-27261-8
Online ISBN: 978-3-540-27262-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)