Abstract
Genome-sequencing projects yield enormous amounts of information that can lead to revolutions in our understanding of life and provide new platforms for the treatment of human diseases. However, DNA sequencing alone does not provide enough information to determine the molecular pathways of an organism in healthy and disease states. A huge number of gene products await functional characterization. Hence, there is a strong demand for technological solutions that help to assign the functions of proteins and genes. This review discusses high-throughput molecular biology methods, which promise to meet the challenges of the post-genomic era.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Amarzguioui M, Rossi JJ, Kim D (2005) Approaches for chemically synthesized siRNA and vector-mediated RNAi. FEBS Lett 579:5974–5981
Angenendt P, Glokler J, Sobek J, Lehrach H, Cahill DJ (2003) Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. J Chromatogr A 1009:97–104
Armour CD, Lum PY (2005) From drug to protein: using yeast genetics for high-throughput target discovery. Curr Opin Chem Biol 9:20–24
Arts GJ, Langemeijer E, Tissingh R, Ma L, Pavliska H, Dokic K, Dooijes R, Mesic E, Clasen R, Michiels F, van der Schueren J, Lambrecht M, Herman S, Brys R, Thys K, Hoffmann M, Tomme P, van Es H (2003) Adenoviral vectors expressing siRNAs for discovery and validation of gene function. Genome Res 13:2325–2332
Ashkenazi A (2002) Targeting death and decoy receptors of the tumor necrosis factor superfamily. Nat Rev Cancer 2:420–430
Auburn RP, Kreil DP, Meadows LA, Fischer B, Matilla SS, Russell S (2005) Robotic spotting of cDNA and oligonucleotide microarrays. Trends Biotechnol 23:374–379
Bernards R, Brummelkamp TR, Beijersbergen RL (2006) shRNA libraries and their use in cancer genetics. Nat Methods 3:701–706
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
Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550–553
Carthew RW (2001) Gene silencing by double-stranded RNA. Curr Opin Cell Biol 13:244–248
Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G (1999) Making and reading microarrays. Nat Genet 21(Suppl):15–19
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 29:314–324
Cullen LM, Arndt GM (2005) Genome-wide screening for gene function using RNAi in mammalian cells. Immunol Cell Biol 83:217–223
Dang CV, Barrett J, Villa-Garcia M, Resar LM, Kato GJ, Fearon ER (1991) Intracellular leucine zipper interactions suggest c-Myc hetero-oligomerization. Mol Cell Biol 11:954–962
Ding DQ, Tomita Y, Yamamoto A, Chikashige Y, Haraguchi T, Hiraoka Y (2000) Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library. Genes Cells 5:169–190
Dixon EP, Johnstone EM, Liu X, Little SP (1997) An inverse mammalian two-hybrid system for beta secretase and other proteases. Anal Biochem 249:239–241
Duggan DJ (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10–14
Erfle H, Simpson JC, Bastiaens PI, Pepperkok R (2004) siRNA cell arrays for high-content screening microscopy. Biotechniques 37:454–458, 460, 462
Fan JB, Chee MS, Gunderson KL (2006a) Highly parallel genomics assays. Nat Rev Genet 7:632–644
Fan JB, Gunderson KL, Bibikova M, Yeakley JM, Chen J, Wickham Garcia E, Lebruska LL, Laurent M, Shen R, Barker D (2006b) Illumina universal bead arrays. Methods Enzymol 410:57–73
Feng XH, Dernyck R (2001) Mammalian two-hybrid assays. Analyzing protein-protein interactions in transforming growth factor-beta signaling pathway. Mol Biol 177:221–239
Fields S (2005) High-throughput two-hybrid analysis. The promise and the peril. FEBS J 272:5391–5399
Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, Worm U, Droege A, Lindenberg KS, Knoblich M, Haenig C, Herbst M, Suopanki J, Scherzinger E, Abraham C, Bauer B, Hasenbank R, Fritzsche A, Ludewig AH, Bussow K, Coleman SH, Gutekunst CA, Landwehrmeyer BG, Lehrach H, Wanker EE (2004) A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell 15:853–865
Hu YH, Warnatz HJ, Vanhecke D, Wagner F, Fiebitz A, Thamm S, Kahlem P, Lehrach H, Yaspo ML, Janitz M (2006) Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins. BMC Genomics 7:155
Igney FH, Krammer P (2002) Death and anti-death: tumor resistance to apoptosis. Nat Rev Cancer 2:277–288
Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Khvorova A, Linsley PS (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA 12:1179–1187
Jackson AL, Linsley PS (2004) Noise amidst the silence: off-target effects of siRNA? Trends Genet 20:521–524
Jin F, Hazbun T, Michaud GA, Salcius M, Predki PF, Fields S, Huang J (2006) A pooling-deconvolution strategy for biological network elucidation. Nat Methods 3:183–189
Kaller M, Lundeberg J, Ahmadian A (2007) Arrayed identification of DNA signatures. Expert Rev Mol Diagn 7:65–76
Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, Welchman DP, Zipperlen P, Ahringer J (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231–237
Kato K, Umezawa K, Miyake M, Miyake J, Nagamune T (2004) Transfection microarray of nonadherent cells on an oleyl poly(ethylene glycol) ether-modified glass slide. Biotechniques 37:444–452
Krishna RG, Wold F (1993) Post-translational modification of proteins. Adv Enzymol Relat Areas Mol Biol 67:265–298
Kumar R, Conklin DS, Mittal V (2003) High-throughput selection of effective RNAi probes for gene silencing. Genome Res 13:2333–2340
Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M (2002) Subcellular localization of the yeast proteome. Genes Dev 16:707–719
Kuttenkeuler D, Boutros M (2004) Genome-wide RNAi as a route to gene function in Drosophila. Brief Funct Genomic Proteomic 3:168–176
Kwon M, Scholey JM (2004) Spindle mechanics and dynamics during mitosis in Drosophila. Trends Cell Biol 14:194–205
Lamitina T (2006) Functional genomic approaches in C. elegans. Methods Mol Biol 351:127–138
Lander ES, Linton LM, Birren B, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Lee JW, Lee SK (2004) Mammalian two-hybrid assay for detecting protein-protein interactions in vivo. Methods Mol Biol 261:327–336
Legrain P, Selig L (2000) Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett 480:32–36
Lehner B, Semple JI, Brown SE, Counsell D, Campbell RD, Sanderson CM (2004) Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region. Genomics 83:153–167
Leonhardt SA, Altmann M, Edwards DP (1998) Agonist and antagonists induce homodimerization and mixed ligand heterodimerization of human progesterone receptors in vivo by a mammalian two-hybrid assay. Mol Endocrinol 12:1914–1930
Lettre G, Hengartner MO (2006) Developmental apoptosis in C. elegans: a complex CEDnario. Nat Rev Mol Cell Biol 7:97–108
Li CX, Parker A, Menocal E, Xiang S, Borodyansky L, Fruehauf JH (2006) Delivery of RNA interference. Cell Cycle 5:2103–2109
Liebel U, Starkuviene V, Erfle H, Simpson JC, Poustka A, Wiemann S, Pepperkok R (2003) FEBS Lett 554:394–398
Lin X, Ruan X, Anderson MG, McDowell JA, Kroeger PE, Fesik SW, Shen Y (2005) siRNA mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res 33:4527–4535
Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21(Suppl 1):20–24
Mann M, Jensen ON (2003) Proteomic analysis of post-translational modifications. Nat Biotechnol 21:255–261
Mannherz O, Mertens D, Hahn M, Lichet P (2006) Functional screening for proapoptotic genes by reverse transfection cell array technology. Genomics 87:665–672
Miller J, Stagljar I (2004) Using the yeast two-hybrid system to identify interacting proteins. Methods Mol Biol 261:247–262
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 (2006) A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124:1283–1298
Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34:267–273
Mousses S, Caplen NJ, Cornelison R, Weaver D, Basik M, Hauteniemi S, Elkahloun AG, Lotfuo RA, Choudary A, Dougherty ER, Suh E, Kallioniemi O (2003) RNAi microarray analysis in cultured mammalian cells. Genome Res 13:2341–2347
Murakami Y, Fukazawa H, Kobatake T, Yamagoe S, Takebe Y, Tobiume M, Matsuda M, Uehara Y (2002) A mammalian two-hybrid screening system for inhibitors of interaction between HIV Nef and the cellular tyrosine kinase Hck. Antiviral Res 55:161–168
Musacchio A (2002) How SH3 domains recognize proline. Adv Protein Chem 61:211–268
Narvaiza I, Aparicio O, Vera M, Razquin N, Bortolanza S, Prieto J, Fortes P (2006) Effect of adenovirus-mediated RNA interference on endogenous microRNAs in a mouse model of multidrug resistance protein 2 gene silencing. J Virol 80:12236–12247
Nicholson DW (2000) From bench to clinic with apoptosis-based therapeutic agents. Nature 407:810–816
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 (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature 428:427–431
Palmer EL, Miller AD, Freeman TC (2006) Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis. BMC Genomics 7:145
Pei Y, Tuschl T (2006) On the art of identifying effective and specific siRNAs. Nat Methods 3:670–676
Sandy P, Ventura A, Jacks T (2005) Mammalian RNAi: a practical guide. Biotechniques 39:215–224
Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S (2000) Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep 1:287–292
Sontheimer EJ (2005) Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 6:127–138
Talapatra A, Rouse R, Hardiman G (2002) Protein microarrays: challenges and promises. Pharmacogenomics 3:527–536
Tavernier J, Eyckerman S, Lemmens I, Van der Heyden J, Vandekerckhove J, Van Ostade X (2002) MAPPIT: a cytokine receptor-based two-hybrid method in mammalian cells. Clin Exp Allergy 32:1397–1404
Thierry-Mieg N (2006) A new pooling strategy for high-throughput screening: the Shifted Transversal Design. BMC Bioinformatics 7:28
Vanhecke D, Janitz M (2004) High-throughput gene silencing using cell arrays. Oncogene 23:8353–8358
Venter JC, Adams MD, Myers EW, et al. (2001) The sequence of the human genome. Science 291:1304–1351
Wolber PK, Collins PJ, Lucas AB, De Witte A, Shannon KW (2006) The Agilent in situ-synthesized microarray platform. Methods Enzymol 410:28–57
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
Zhang Y, Feng XH, Derynck R (1998) Smad3 and Smad4 cooperate with c-Jun/c-Fos to mediate TGF-beta-induced transcription. Nature 394:909–913
Zhao HF, Kiyota T, Chowdhury S, Purisima E, Banville D, Konishi Y, Shen SH (2004) A mammalian genetic system to screen for small molecules capable of disrupting protein-protein interactions. Anal Chem 76:2922–2927
Zhong J, Zhang H, Stanyon CA, Tromp G, and Finley RL Jr (2003) A strategy for constructing large protein interaction maps using the yeast two-hybrid system: regulated expression arrays and two-phase mating. Genome Res 13:2691–2699
Ziauddin J, Sabatini DM (2001) Microarrays of cells expressing defined cDNAs. Nature 411:107–110
Acknowledgements
The author would like to acknowledge members of his laboratory: Dominique Vanhecke, Anna Guerasimova, Andrea Fiebitz, Yu-Hui Hu, Jian-Ping Liu, Xi Cheng, Irina Girnus, and Sabine Thamm. The author also thanks the following organizations for support: the European Commission (integrated project MolTools) and the German Federal Ministry of Education and Research (grant no. 0313068, 01GS0416, 01GR0414, 31P3674).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer-Verlag
About this chapter
Cite this chapter
Janitz, M. (2007). Assigning functions to genes—the main challenge of the post-genomics era. In: Amara, S., et al. Reviews of Physiology, Biochemistry and Pharmacology. Reviews of Physiology, Biochemistry and Pharmacology, vol 159. Springer, Berlin, Heidelberg. https://doi.org/10.1007/112_2007_0703
Download citation
DOI: https://doi.org/10.1007/112_2007_0703
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73799-5
Online ISBN: 978-3-540-73800-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)