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Assigning functions to genes—the main challenge of the post-genomics era

  • M. JanitzEmail author
Chapter
Part of the Reviews of Physiology, Biochemistry and Pharmacology book series (REVIEWS, volume 159)

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.

Keywords

cDNA Microarrays Cell Array Array Format Prey Protein MyoD Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

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).

References

  1. Amarzguioui M, Rossi JJ, Kim D (2005) Approaches for chemically synthesized siRNA and vector-mediated RNAi. FEBS Lett 579:5974–5981PubMedCrossRefGoogle Scholar
  2. 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 1009:97–104PubMedCrossRefGoogle Scholar
  3. Armour CD, Lum PY (2005) From drug to protein: using yeast genetics for high-throughput target discovery. Curr Opin Chem Biol 9:20–24PubMedCrossRefGoogle Scholar
  4. 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 13:2325–2332PubMedCrossRefGoogle Scholar
  5. Ashkenazi A (2002) Targeting death and decoy receptors of the tumor necrosis factor superfamily. Nat Rev Cancer 2:420–430PubMedCrossRefGoogle Scholar
  6. Auburn RP, Kreil DP, Meadows LA, Fischer B, Matilla SS, Russell S (2005) Robotic spotting of cDNA and oligonucleotide microarrays. Trends Biotechnol 23:374–379PubMedCrossRefGoogle Scholar
  7. Bernards R, Brummelkamp TR, Beijersbergen RL (2006) shRNA libraries and their use in cancer genetics. Nat Methods 3:701–706PubMedCrossRefGoogle Scholar
  8. 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 428:431–437PubMedCrossRefGoogle Scholar
  9. Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550–553PubMedCrossRefGoogle Scholar
  10. Carthew RW (2001) Gene silencing by double-stranded RNA. Curr Opin Cell Biol 13:244–248PubMedCrossRefGoogle Scholar
  11. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G (1999) Making and reading microarrays. Nat Genet 21(Suppl):15–19PubMedCrossRefGoogle Scholar
  12. 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 29:314–324PubMedGoogle Scholar
  13. Cullen LM, Arndt GM (2005) Genome-wide screening for gene function using RNAi in mammalian cells. Immunol Cell Biol 83:217–223PubMedCrossRefGoogle Scholar
  14. 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 11:954–962PubMedGoogle Scholar
  15. 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 5:169–190PubMedCrossRefGoogle Scholar
  16. Dixon EP, Johnstone EM, Liu X, Little SP (1997) An inverse mammalian two-hybrid system for beta secretase and other proteases. Anal Biochem 249:239–241PubMedCrossRefGoogle Scholar
  17. Duggan DJ (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10–14PubMedCrossRefGoogle Scholar
  18. Erfle H, Simpson JC, Bastiaens PI, Pepperkok R (2004) siRNA cell arrays for high-content screening microscopy. Biotechniques 37:454–458, 460, 462PubMedGoogle Scholar
  19. Fan JB, Chee MS, Gunderson KL (2006a) Highly parallel genomics assays. Nat Rev Genet 7:632–644PubMedCrossRefGoogle Scholar
  20. 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 410:57–73PubMedCrossRefGoogle Scholar
  21. Feng XH, Dernyck R (2001) Mammalian two-hybrid assays. Analyzing protein-protein interactions in transforming growth factor-beta signaling pathway. Mol Biol 177:221–239Google Scholar
  22. Fields S (2005) High-throughput two-hybrid analysis. The promise and the peril. FEBS J 272:5391–5399PubMedCrossRefGoogle Scholar
  23. 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 15:853–865PubMedCrossRefGoogle Scholar
  24. 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 7:155PubMedCrossRefGoogle Scholar
  25. Igney FH, Krammer P (2002) Death and anti-death: tumor resistance to apoptosis. Nat Rev Cancer 2:277–288PubMedCrossRefGoogle Scholar
  26. 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 12:1179–1187PubMedCrossRefGoogle Scholar
  27. Jackson AL, Linsley PS (2004) Noise amidst the silence: off-target effects of siRNA? Trends Genet 20:521–524PubMedCrossRefGoogle Scholar
  28. 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 3:183–189PubMedCrossRefGoogle Scholar
  29. Kaller M, Lundeberg J, Ahmadian A (2007) Arrayed identification of DNA signatures. Expert Rev Mol Diagn 7:65–76PubMedCrossRefGoogle Scholar
  30. 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 421:231–237PubMedCrossRefGoogle Scholar
  31. 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 37:444–452PubMedGoogle Scholar
  32. Krishna RG, Wold F (1993) Post-translational modification of proteins. Adv Enzymol Relat Areas Mol Biol 67:265–298PubMedGoogle Scholar
  33. Kumar R, Conklin DS, Mittal V (2003) High-throughput selection of effective RNAi probes for gene silencing. Genome Res 13:2333–2340PubMedCrossRefGoogle Scholar
  34. 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 16:707–719PubMedCrossRefGoogle Scholar
  35. Kuttenkeuler D, Boutros M (2004) Genome-wide RNAi as a route to gene function in Drosophila. Brief Funct Genomic Proteomic 3:168–176PubMedCrossRefGoogle Scholar
  36. Kwon M, Scholey JM (2004) Spindle mechanics and dynamics during mitosis in Drosophila. Trends Cell Biol 14:194–205PubMedCrossRefGoogle Scholar
  37. Lamitina T (2006) Functional genomic approaches in C. elegans. Methods Mol Biol 351:127–138PubMedGoogle Scholar
  38. Lander ES, Linton LM, Birren B, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921PubMedCrossRefGoogle Scholar
  39. Lee JW, Lee SK (2004) Mammalian two-hybrid assay for detecting protein-protein interactions in vivo. Methods Mol Biol 261:327–336PubMedGoogle Scholar
  40. Legrain P, Selig L (2000) Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett 480:32–36PubMedCrossRefGoogle Scholar
  41. 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 83:153–167PubMedCrossRefGoogle Scholar
  42. 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 12:1914–1930PubMedCrossRefGoogle Scholar
  43. Lettre G, Hengartner MO (2006) Developmental apoptosis in C. elegans: a complex CEDnario. Nat Rev Mol Cell Biol 7:97–108PubMedCrossRefGoogle Scholar
  44. Li CX, Parker A, Menocal E, Xiang S, Borodyansky L, Fruehauf JH (2006) Delivery of RNA interference. Cell Cycle 5:2103–2109PubMedCrossRefGoogle Scholar
  45. Liebel U, Starkuviene V, Erfle H, Simpson JC, Poustka A, Wiemann S, Pepperkok R (2003) FEBS Lett 554:394–398PubMedCrossRefGoogle Scholar
  46. 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 33:4527–4535PubMedCrossRefGoogle Scholar
  47. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21(Suppl 1):20–24PubMedCrossRefGoogle Scholar
  48. Mann M, Jensen ON (2003) Proteomic analysis of post-translational modifications. Nat Biotechnol 21:255–261PubMedCrossRefGoogle Scholar
  49. Mannherz O, Mertens D, Hahn M, Lichet P (2006) Functional screening for proapoptotic genes by reverse transfection cell array technology. Genomics 87:665–672PubMedCrossRefGoogle Scholar
  50. Miller J, Stagljar I (2004) Using the yeast two-hybrid system to identify interacting proteins. Methods Mol Biol 261:247–262PubMedGoogle Scholar
  51. 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 124:1283–1298PubMedCrossRefGoogle Scholar
  52. 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 34:267–273PubMedCrossRefGoogle Scholar
  53. 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 13:2341–2347PubMedCrossRefGoogle Scholar
  54. 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 55:161–168PubMedCrossRefGoogle Scholar
  55. Musacchio A (2002) How SH3 domains recognize proline. Adv Protein Chem 61:211–268PubMedCrossRefGoogle Scholar
  56. 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 80:12236–12247PubMedCrossRefGoogle Scholar
  57. Nicholson DW (2000) From bench to clinic with apoptosis-based therapeutic agents. Nature 407:810–816PubMedCrossRefGoogle Scholar
  58. 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 428:427–431PubMedCrossRefGoogle Scholar
  59. 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 7:145PubMedCrossRefGoogle Scholar
  60. Pei Y, Tuschl T (2006) On the art of identifying effective and specific siRNAs. Nat Methods 3:670–676PubMedCrossRefGoogle Scholar
  61. Sandy P, Ventura A, Jacks T (2005) Mammalian RNAi: a practical guide. Biotechniques 39:215–224PubMedCrossRefGoogle Scholar
  62. 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 1:287–292PubMedCrossRefGoogle Scholar
  63. Sontheimer EJ (2005) Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 6:127–138PubMedCrossRefGoogle Scholar
  64. Talapatra A, Rouse R, Hardiman G (2002) Protein microarrays: challenges and promises. Pharmacogenomics 3:527–536PubMedCrossRefGoogle Scholar
  65. 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 32:1397–1404PubMedCrossRefGoogle Scholar
  66. Thierry-Mieg N (2006) A new pooling strategy for high-throughput screening: the Shifted Transversal Design. BMC Bioinformatics 7:28PubMedCrossRefGoogle Scholar
  67. Vanhecke D, Janitz M (2004) High-throughput gene silencing using cell arrays. Oncogene 23:8353–8358PubMedCrossRefGoogle Scholar
  68. Venter JC, Adams MD, Myers EW, et al. (2001) The sequence of the human genome. Science 291:1304–1351PubMedCrossRefGoogle Scholar
  69. Wolber PK, Collins PJ, Lucas AB, De Witte A, Shannon KW (2006) The Agilent in situ-synthesized microarray platform. Methods Enzymol 410:28–57PubMedCrossRefGoogle Scholar
  70. 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 96:227–232PubMedCrossRefGoogle Scholar
  71. Zhang Y, Feng XH, Derynck R (1998) Smad3 and Smad4 cooperate with c-Jun/c-Fos to mediate TGF-beta-induced transcription. Nature 394:909–913PubMedCrossRefGoogle Scholar
  72. 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 76:2922–2927PubMedCrossRefGoogle Scholar
  73. 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 13:2691–2699PubMedCrossRefGoogle Scholar
  74. Ziauddin J, Sabatini DM (2001) Microarrays of cells expressing defined cDNAs. Nature 411:107–110PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  1. 1.Max Planck Institute for Molecular GeneticsBerlinGermany

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