Cross-species studies for target validation

Briefings in Functional Genomics and Proteomics

Volumn 1, Issue 1, 2002, Pages 53-65

  Baumeister, Ralf ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

Animal models; Diseose genes; Functional genomics; Gene knock out gene replacement; Target validation; Transgene

Indexed keywords

ANIMAL; ANIMAL MODEL; ARTICLE; GENE EXPRESSION; MUTATION; PHENOTYPE; SPECIES DIFFERENCE; VALIDATION STUDY;

ANIMALS; GENE EXPRESSION; MODELS, ANIMAL; MUTATION; PHENOTYPE; SPECIES SPECIFICITY;

EID: 0038401618     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/1.1.53     Document Type: Article

References (82)

1. Lander, E. S., Linton, L. M., Birren, B. et al. (2001), 'Initial sequencing and analysis of the human genome', Nature, Vol. 409, pp. 860-921. (Pubitemid 32165345)
2. Venter, J. C, Adams, M. D., Myers, E. W. et al. (2001), 'The sequence of the human genome', Science, Vol. 291, pp. 1304-1351. (Pubitemid 32173090)
3. Harris, S. (2001), 'Transgenic knockouts as part of high-throughput, evidence-based target selection and validation strategies', Drug Discov. Today, Vol. 6, pp. 628-636. (Pubitemid 32567621)
4. Kim, S. K., Lund, J., Kiraly, M. et al. (2001), 'A gene expression map for Caenorhabditis elegans', Science, Vol. 293, pp. 2087-2092. (Pubitemid 32848057)
5. Wassmann, K. and Benezra, R. (2001), 'Mitotic checkpoints: from yeast to cancer', Curr. Opin. Genet. Dev., Vol. 11, pp. 83-90. (Pubitemid 32119283)
6. McEwen, D. G. and Peifer, M. (2000), 'Wnt signaling: moving in a new direction', Curr. Biol, Vol. 10, R562-564. (Pubitemid 30647612)
7. Tan, P. B. and Kim, S. K. (1999), 'Signaling specificity: the RTK/RAS/MAP kinase pathway in metazoans', Trends Genet., Vol. 15, pp. 145-149. (Pubitemid 29155436)
8. Wigge, P. A. and Weigel, D. (2001), 'Arabidopsis genome: life without notch', Curr. Biol., Vol. 11, pp. R112-114. (Pubitemid 32152097)
9. Derynck, R., Zhang, Y. and Feng, X. H. (1998), 'Smads: transcriptional activators of TGF-beta responses', Cell, Vol. 95, pp. 737-740. (Pubitemid 29014453)
10. Pierce, S. B., Costa, M., Wisotzkey, R. et al. (2001), 'Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family', Genes Dev., Vol. 15, pp. 672-686. (Pubitemid 32244897)
11. Duffy, J. B. and Perrimon, N. (1996), 'Recent advances in understanding signal transduction pathways in worms and flies', Curr. Opin. Cell Biol., Vol 8, pp. 231-238. (Pubitemid 26109097)
12. Anderson, G. L., Boyd, W. A. and Williams, P. L. (2001), 'Assessment of sublethal endpoints for toxicity testing with the nematode Caenorhabditis elegans'. Environ. Toxicol. Chem., Vol. 20, pp. 833-838. (Pubitemid 32861513)
13. Williams, P. L., Anderson, G. L., Johnstone, J. L., Nunn, A. D., Tweedle, M. F. and Wedeking, P. (2000), 'Caenorhabditis elegans as an alternative animal species', J, Toxicol. Environ. Health A, Vol. 61, pp. 641-647.
14. Ball, C. A. and Cherry, J. M. (2001), 'Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms', Curr. Opin. Chem. Biol., Vol. 5, pp. 86-89. (Pubitemid 32144965)
15. Chervitz, S. A., Aravind, L., Sherlock, G. et al. (1998), 'Comparison of the complete protein sets of worm and yeast: orthology and divergence', Science, Vol. 282, pp. 2022-2028. (Pubitemid 29001253)
16. Riddle, R. D., Ensini, M., Nelson, C, Tsuchida, T., Jessell, T. M. and Tabin C. (1995), 'Induction of the LIM homeobox gene Lmx1 by WNT7a establishes dorsoventral pattern in the vertebrate limb', Cell, Vol. 83, pp. 631-640.
17. Li, X. and Greenwald, I. (1997), 'HOP-1, a Caenorhabditis elegans presenilin, appears to be functionally redundant with SEL-12 presenilin and to facilitate LIN-12 and GLP-1 signaling'. Proc. Natl. Acad. Sci. USA, Vol. 94, pp. 12204-12209. (Pubitemid 27467867)
18. Westlund, B., Parry, D., Clover, R., Basson, M. and Johnson, C. D. (1999), 'Reverse genetic analysis of Caenorhabditis elegans presenilins reveals redundant but unequal roles for sel-12 and hop-1 in Notch-pathway signaling', Proc. Natl. Acad. Sci. USA, Vol. 96, pp. 2497-2502. (Pubitemid 29117944)
19. Kumar, A., Cheung, K. H., Ross-Macdonald, P., Coelho, P. S., Miller, P. and Snyder, M. (2000), 'TRIPLES: a database of gene function in Saccharomyces cerevisiae'. Nucleic Acids Res., Vol. 28, pp. 81-84. (Pubitemid 30047720)
20. Lucau-Danila, A., Wysocki, R., Roganti, T. and Foury, F. (2000), 'Systematic disruption of 456 ORFs in the yeast Saccharomyces cerevisiae', Yeast, Vol 16, pp. 547-552. (Pubitemid 30201019)
21. Fraser, A. G., Kamath, R. S., Zipperlen, P., Martinez-Campos, M., Sohrmann, M. and Ahringer, J. (2000), 'Functional genomic analysis of C. elegans chromosome I by systematic RNA interference', Nature, Vol. 408, pp. 325-330.
22. Gonczy, P., Echeverri, G., Oegema, K. et al. (2000), 'Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III', Nature, Vol. 408, pp. 331-336.
23. Piano, F., Schetter, A. J., Mangone, M., Stein, L. and Kemphues, K.J. (2000), 'RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans', Curr. Biol., Vol. 10, pp. 1619-1622.' (Pubitemid 32062668)
24. Maeda, I., Kohara, Y., Yamamoto, M. and Sugimoto, A. (2001), 'Large-scale analysis of gene function in Caenorhabditis elegans by high throughput RNAi', Curr. Biol., Vol. 11, pp. 171-176. (Pubitemid 32152101)
25. Link, C. D. (1995), 'Expression of human beta-amyloid peptide in transgenic Caenorhabditis elegans', Proc. Natl. Acad. Sci. USA, Vol. 92, pp. 9368-9372.
26. Fossgreen, A., Bruckner, B., Czech, C, Masters, C. L., Beyreuther, K. and Paro, R. (1998), 'Transgenic Drosophila expressing human amyloid precursor protein show gamma-secretase activity and a blistered-wing phenotype', Proc. Natl. Acad. Sci. USA, Vol. 95, pp. 13703-13708. (Pubitemid 28523036)
27. Feany, M. B. (2000), 'Studying human neurodegenerative diseases in flies and worms', J. Neuropathol. Exp. Neurol., Vol. 59, pp. 847-856.
28. Feany, M. B. and Bender, W. W. A. (2000), 'Drosophila model of Parkinson's disease', Nature, Vol. 404, pp. 394-398.
29. Faber, P. W., Alter, J. R., MacDonald, M. E. and Hart, A. C. (1999), 'Polyglutamine-mediated dysfunction and apoptotic death of a Caenorhabditis elegans sensory neuron', Proc. Natl. Acad. Sci. USA, Vol. 96, pp. 179-184. (Pubitemid 29036073)
30. Kazemi-Esfarjani, P. and Benzer, S. (2000), 'Genetic suppression of polyglutamine toxicity in Drosophila', Science, Vol. 287, pp. 1837-1840. (Pubitemid 30143971)
31. Feany, M. B. and Bender, W. W. (2000), 'A Drosophila model of Parkinson's disease', Nature, Vol. 404, pp. 394-398. (Pubitemid 30164341)
32. Wittmann, C. W., Wszolek, M. F., Shulman, J. M. et al. (2001), 'Tauopathy in Drosophila: neurodegeneration without neurofibrillary tangles', Science, Vol. 293, pp. 711-714. (Pubitemid 32728676)
33. Grishok, A., Pasquinelli, A. E., Conte, D. et al. (2001), 'Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing', Cell, Vol. 106, pp. 23-34. (Pubitemid 32709955)
34. Ekker, S. C. (2000), 'Morphants: a new systematic vertebrate functional genomics approach', Yeast, Vol. 17, pp. 302-306. (Pubitemid 32051423)
35. Tavernarakis, N., Wang, S. L., Dorovkov, M, Ryazanov, A. and Driscoll, M. (2000), 'Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes', Nat. Genet., Vol. 24, pp. 180-183. (Pubitemid 30094721)
36. Wicks, S. R., de Vries, C. J., van Luenen, H. G. and Plasterk, R. H. (2000), 'CHE-3, a cytosolic dynein heavy chain, is required for sensory cilia structure and function in Caenorhabditis elegans', Dev. Biol., Vol. 221, pp. 295-307. (Pubitemid 30322512)
37. Jansen, G., Hazendonk, E., Thyssen, K. L. and Plasterk, R. H. A. (1997), 'Reverse genetics by chemical mutagenesis in Caenorhabditis elegans', Nat. Genet., Vol. 17, pp. 119-121. (Pubitemid 27377545)
38. Rong, Y. S. and Golic, K. G. (2001), 'A targeted gene knockout in Drosophila', Genetics, Vol. 157, pp. 1307-1312. (Pubitemid 32225023)
39. Erkman, L, McEvilly, R.J., Luo, L. et al. (1996), 'Role of transcription factors Brn-3.1 and Brn-3.2 in auditory and visual system development', Nature, Vol. 381, pp. 603-606. (Pubitemid 26177475)
40. Xiang, M., Gan, L., Li, D. et al. (1997), 'Essential role of POU-domain factor Brn-3c in auditory and vestibular hair cell development', Proc. Natl. Acad. Sci. USA, Vol. 94, pp. 9445-9450. (Pubitemid 27357849)
41. Vahava, O., Morell, R., Lynch, E. D. et al. (1998), 'Mutation in transcription factor POU4F3 associated with inherited progressive hearing loss in humans', Science, Vol. 279, pp. 1950-1954. (Pubitemid 28168652)
42. Nicolson, T., Rusch, A., Friedrich, R. W., Granato, M., Ruppersberg, J. P. and Nusslein-Volhard, C. (1998), 'Genetic analysis of vertebrate sensory hair cell mechanosensation: the zebrafish circler mutants', Neuron, Vol. 20, pp. 271-283. (Pubitemid 28125071)
43. Chalfie, M., Sulston, J. E., White, J. G., Southgate, E., Thomson, J. N. and Brenner, S. (1985), 'The neural circuit for touch sensitivity in Caenorhabditis elegans', J. Neurosci., Vol. 5, pp. 956-964. (Pubitemid 15123043)
44. Rohrig, S., Rockelein, I., Donhauser, R. and Baumeister, R. (2000), 'Protein interaction surface of the POU transcription factor UNC-86 selectively used in touch neurons', Embo J., Vol. 19, pp. 3694-3703. (Pubitemid 30462127)
45. Baumeister, R., Liu, Y. and Ruvkun, G. (1996), 'Lineage-specific regulators couple cell lineage asymmetry to the transcription of the Caenorhabditis elegans POU gene unc-86 during neurogenesis', Genes Dev., Vol. 10, pp. 1395-1410. (Pubitemid 26260718)
46. Baumeister, R. and Haass, C. (1998), 'Prensenilin proteins and their role in development and Notch signalling', in Haass, C., Ed., 'The Molecular Biology of Alzheimer's Disease', Harwood Academic Publishers, Chur, pp. 219-234.
47. Haass, C. and de Strooper, B. (1999), 'The presenilins in Alzheimer's disease-proteolysis holds the key', Science, Vol. 286, pp. 916-919.
48. Wittenburg, N., Eimer, S., Lakowski, B., Rohrig, S., Rudolph, C. and Baumeister, R. (2000), 'Presenilin is required for proper morphology and function of neurons in C. elegans'. Nature, Vol. 406, pp. 306-309. (Pubitemid 30604408)
49. Levitan, D. and Greenwald, I. (1995), 'Facilitation of lin- 12-mediated signalling by sel- 12, a Caenorhabditis elegans S182 Alzheimer's disease gene', Nature, Vol. 377, pp. 351-354.
50. Guo, Y., Livne-Bar, I., Zhou, L. and Boulianne, G. L. (1999), 'Drosophila presenilin is required for neuronal differentiation and affects Notch subcellular localization and signaling', J. Neurosci., Vol. 19, pp. 8435-8442. (Pubitemid 30226762)
51. Levitan, D., Doyle, T. G., Brousseau, D. et al. (1996), 'Assessment of normal and mutant human presenilin function in Caenorhabditis elegans', Proc. Natl. Acad. Sci. USA, Vol. 93, pp. 14940-14944. (Pubitemid 26419074)
52. Baumeister, R., Leimer, U., Zweckbronner, I., Jakubek, C., Grunberg, J. and Haass, C. (1997), 'Human presenilin-1, but not familial Alzheimer's disease (FAD) mutants, facilitate Caenorhabditis elegans Notch signalling independently of proteolytic processing', Genes Fund., Vol. 1, pp. 149-159.
53. Han, M. and Sternberg, P. W. (1991), 'Analysis of dominant-negative mutations of the Caenorhabditis elegans let-60 ns gene', Genes Dev., Vol. 5, pp. 2188-2198. (Pubitemid 21905909)
54. Kornfeld, K. (1997), 'Vulval development in Caenorhabditis elegans', Trends Genet., Vol. 13, pp. 55-61. (Pubitemid 27061073)
55. Wilkinson, H. A. and Greenwald, I. (1995), 'Spatial and temporal patterns of lin- 12 expression during C. elegans hermaphrodite development', Genetics, Vol. 141, pp. 513-526.
56. Hengartner, M. O. and Horvitz, H. R. (1994), 'C. elegans cell survival gene ced-9 encodes a functional homolog of the mammalian proto-oncogene bcl-2'. Cell, Vol. 76, pp. 665-676. (Pubitemid 24070651)
57. Gaumer, S., Guenal, I., Brun, S., Theodore, L. and Mignotte, B. (2000), 'Bcl-2 and Bax mammalian regulators of apoptosis are functional in Drosophila', Cell Death Differ., Vol. 7, pp. 804-814.
58. Larsson, K., Bohl, F., Sjostrom, I. et al. (1998), 'The Saccharomyces cerevisiae SOP1 and SOP2 genes, which act in cation homeostasis, can be functionally substituted by the Drosophila lethal(2)giant larvae tumor suppressor gene', J. Biol. Chetn., Vol. 273, pp. 33610-33618. (Pubitemid 29005748)
59. Hunter, C. P. and Kenyon, C. (1995), 'Specification of anteroposterior cell fates in Caenorhabditis elegans by Drosophila Hox proteins', Nature, Vol. 377, pp. 229-232.
60. Furlong, E. E., Profitt, D. and Scott, M. P. (2001), 'Automated sorting of live transgenic embryos', Nat. Biotechnol., Vol. 19, pp. 153-156. (Pubitemid 32144444)
61. Foury, F. (1997), 'Human genetic diseases: a cross-talk between man and yeast', Gene, Vol. 195, pp. 1-10. (Pubitemid 27336954)
62. Lawrence, P. A. and Morata, G. (1994), 'Homeobox genes: their function in Drosophila segmentation and pattern formation', Cell, Vol. 78, pp. 181-189. (Pubitemid 24241087)
63. Glaser, T., Jepeal, L., Edwards, J. G., Young, S. R., Favor, J. and Maas, R. L. (1994), 'PAX6 gene dosage effect in a family with congenital cataracts, aniridia, anophthalmia and central nervous system defects', Nat. Genet., Vol. 7, pp. 463-471. (Pubitemid 24308331)
64. Gehring, W.J. and Ikeo, K. (1999), 'Pax 6: mastering eye morphogenesis and eye evolution', Trends Genet., Vol. 15, pp. 371-377. (Pubitemid 29417592)
65. Giugia, J., Gieseler, K., Arpagaus, M. and Segalat, L. (1999), 'Mutations in the dystrophin-like dys- 1 gene of Caenorhabditis elegans result in reduced acetylcholinesterase activity', FEBS Lett., Vol. 463, pp. 270-272. (Pubitemid 30001932)
66. Chamberlain, J. S. and Benian, G. M. (2000), 'Muscular dystrophy: the worm turns to genetic disease', Curr. Biol., Vol. 10, pp. R795-797.
67. Capell, A., Steiner, H., Romig, H. et al. (2000), 'Presenilin- 1 differentially facilitates endoproteolysis of the beta-amyloid precursor protein and notch', Nat. Cell Biol, Vol. 2, pp. 205-211.
68. Brand, A. H. and Perrimon, N. (1993), 'Targeted gene expression as a means of altering cell fates and generating dominant phenotypes', Development, Vol. 118, pp. 401-415. (Pubitemid 23214028)
69. Tissenbaum, H. A. and Ruvkun, G. (1998), 'An insulin-like signaling pathway affects both longevity and reproduction in Caenorhabditis elegans', Genetics, Vol. 148, pp. 703-717. (Pubitemid 28087620)
70. Wong, P. C., Zheng, H., Chen, H. et al. (1997), 'Presenilinl is required for Notchl and D111 expression in the paraxial mesoderm', Nature, Vol. 387, pp. 288-292. (Pubitemid 27220764)
71. Shen, J., Bronson, R. T., Chen, D. F., Xia, W., Selkoe, D.J. and Tonegawa, S. (1997), 'Skeletal and CNS defects in presenilin-1-deficient mice', Cell, Vol. 89, pp. 629-639. (Pubitemid 27511773)
72. The C. elegans Knockout Consortium (1998), 'Genome sequence of the nematode C. elegansa platform for investigating biology', Science, Vol. 282, pp. 2012-2018.
73. Dodd, A., Curtis, P. M., Williams, L. C. and Love, D. R. (2000), 'Zebrafish: bridging the gap between development and disease', Hunt. Mol. Genet., Vol. 9, pp. 2443-2449.
74. Koster, R. W. and Fraser, S. E. (2001), 'Tracing transgene expression in living zebrafish embryos', Dev. Biol., Vol. 233, pp. 329-346. (Pubitemid 32467680)
75. Kennedy, B. N., Vihtelic, T. S., Checkley, L., Vaughan, K. T. and Hyde, D. R. (2001), 'Isolation of a zebrafish rod opsin promoter to generate a transgenic zebrafish line expressing enhanced green fluorescent protein in rod photoreceptors', J. Biol. Chem., Vol. 276, pp. 14037-14043.
76. Snell, G. D. (1981), 'Studies in histocompatibility', Science, Vol. 213, pp. 172-178. (Pubitemid 11060563)
77. Kistner, A., Gossen, M., Zimmermann, F. et al. (1996), 'Doxycycline-mediated quantitative and tissue-specific control of gene expression in transgenic mice', Proc. Natl. Acad. Sci. USA, Vol. 93, pp. 10933-10938. (Pubitemid 26333095)
78. Hrabe de Angelis, M. H., Flaswinkel, H., Fuchs, H. et al. (2000), 'Genome-wide, large-scale production of mutant mice by ENU mutagenesis', Nat. Genei., Vol. 25, pp. 444-447. (Pubitemid 32983440)
79. Li, X. and Greenwald, I. (1996), 'Membrane topology of the C. elegans SEL-12 presenilin', Neuron, Vol. 17, pp. 1015-1021. (Pubitemid 26424027)
80. Brockhaus, M., Grunberg, J., Rohrig, S. et al. (1998), 'Caspase-mediated cleavage is not required for the activity of presenilins in amyloidogenesis and NOTCH signaling', Neuroreport, Vol. 9, pp. 1481-1486. (Pubitemid 28264274)
81. Steiner, H., Kostka, M., Romig, H. et al. (2000), 'Glycine 384 is required for presenilin- 1 function and is conserved in bacterial polytopic aspartyl proteases', Nat. Cell Biol, Vol 2, pp. 848-851.
82. Link, E. M., Hardiman, G., Sluder, A. E., Johnson, C. D. and Liu, L. X. (2000), 'Therapeutic target discovery using Caenorhabditis elegans', Pharmacogenomics, Vol. 1, pp. 203-217.