Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline

Current Biology

Volumn 12, Issue 22, 2002, Pages 1952-1958

  Walhout, Albertha J M ^a   Reboul, Jérôme ^a   Shtanko, Olena ^a   Bertin, Nicolas ^a   Vaglio, Philippe ^a   Ge, Hui ^a   Lee, Hongmei ^b   Doucette Stamm, Lynn ^b   Gunsalus, Kristin C ^c,d   Schetter, Aaron J ^d   Morton, Diane G ^d   Kemphues, Kenneth J ^d   Reinke, Valerie ^e   Kim, Stuart K ^f   Piano, Fabio ^c,d   Vidal, Marc ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b GENOME THERAPEUTICS CORPORATION   (United States)

^c NEW YORK UNIVERSITY   (United States)

^d Department of Molecular Biology and Genetics   (United States)

^e YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE MAPPING; GENETIC TRANSCRIPTION; GERM LINE; PROTEIN EXPRESSION; PROTEIN INTERACTION; RNA INTERFERENCE; TRANSCRIPTOME; TWO HYBRID SYSTEM; ANIMAL; ARTICLE; CAENORHABDITIS ELEGANS; CHROMOSOME MAP; GENETIC PROCEDURES; GENETICS; GENOME; OPEN READING FRAME;

CAENORHABDITIS ELEGANS;

CAENORHABDITIS ELEGANS PROTEIN; PROTEOME;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CHROMOSOME MAPPING; GENETIC TECHNIQUES; GENOME; OPEN READING FRAMES; PROTEOME; TRANSCRIPTION, GENETIC;

EID: 0037137446     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-9822(02)01279-4     Document Type: Article

References (34)

1. Lockhart, D.J., and Winzeler, E.A. (2000). Genomics, gene expression and DNA arrays. Nature 405, 827-835.
2. Pandey, A., and Mann, M. (2000). Proteomics to study genes and genomes. Nature 405, 837-846.
3. Walhout, A.J.M., and Vidal, M. (2001). Protein interaction maps for model organisms. Nat. Rev. Mol. Cell. Biol. 2, 55-62.
4. Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O., and Eisenberg, D. (1999). A combined algorithm for genome-wide prediction of protein function. Nature 402, 83-86.
5. Vidal, M. (2001). A biological atlas of functional maps. Cell 104, 333-339.
6. Ge, H., Liu, Z., Church, G., and Vidal, M. (2001). Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29, 482-486.
7. Grigoriev, A. (2001). A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acid Res. 29, 3513-3519.
8. Jansen, R., Greenbaum, D., and Gerstein, M. (2002). Relating whole-genome expression data with protein-protein interactions. Genome Res. 12, 37-46.
9. Kemmeren, P., van Berkum, N.L., Vilo, J., Bijma, T., Donders, R., Brazma, A., and Holstege, F.C.P. (2002). Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell 9, 1133-1143.
10. Reinke, V., Smith, H.E., Nance, J., Wang, J., Van Doren, C., Begley, R., Jones, S.J.M., Davis, E.B., Scherer, S., Ward, S., et al. (2000). A global profile of germline gene expression in C. elegans. Mol. Cell 6, 605-616.
11. Kim, S.K., Lund, J., Kiraly, M., Duke, K., Jiang, M., Stuart, J.M., Eizinger, A., Wylie, B.N., and Davidson, G.S. (2001). A gene expression map for Caenorhabditis elegans. Science 293, 2087-2092.
12. Hartley, J.L., Temple, G.F., and Brasch, M.A. (2000). DNA cloning using in vitro site-specific recombination. Genome Res. 10, 1788-1795.
13. Walhout, A.J.M., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N., and Vidal, M. (2000). Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287, 116-122.
14. Walhout, A.J.M., Temple, G.F., Brasch, M.A., Hartley, J.L., Lotson, M.A., van den Heuvel, S., and Vidal, M. (2000). GATEWAY recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328, 575-592.
15. Reboul, J., Vaglio, P., Tzellas, N., Thierry-Mieg, N., Moore, T., Jackson, C., Shin-i, T., Kohara, Y., Thierry-Mieg, D., Thierry-Mieg, J., et al. (2001). Open-reading frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat. Genet. 27, 1-5.
16. Fields, S., and Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature 340, 245-246.
17. Vidal, M. (1997). The reverse two-hybrid system. In The Yeast Two-Hybrid System, P. Bartels and S. Fields, eds. (New York: Oxford University Press), pp. 109-147.
18. Walhout, A.J.M., and Vidal, M. (2001). High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24, 297-306.
19. Davy, A., Bello, P., Thierry-Mieg, N., Vaglio, P., Hitti, J., Doucette-Stamm, L., Thierry-Mieg, D., Reboul, J., Boulton, S., Walhout, A.J., et al. (2001). A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep. 2, 821-828.
20. Boulton, S.J., Gartner, A., Reboul, J., Vaglio, P., Dyson, N., Hill, D.E., and Vidal, M. (2002). Combined functional genomic maps of the C. elegans DNA damage response. Science 295, 127-131.
21. Constanzo, M.C., Hogan, J.D., Cusick, M.E., Davis, B.P., Fancher, A.M., Hodges, P.E., Kondu, P., Lengieza, C., Lew-Smith, J.E., Lingner, C., et al. (2000). The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28, 73-76.
22. Matthews, L.R., Vaglio, P., Reboul, J., Ge, H., Davis, B.P., Garrels, J., Vincent, S., and Vidal, M. (2001). Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 11, 2120-2126.
23. Church, D.L., Guan, K.L., and Lambie, E.J. (1995). Three genes of the MAP kinase cascade, mek-2, mpk-1/sur-1 and let-60 ras, are required for meiotic cell cycle progression in Caenorhabditis elegans. Development 121, 2525-2535.
24. Walhout, A.J.M., Boulton, S.J., and Vidal, M. (2000). Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17, 88-94.
25. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.
26. Aravind, L., and Koonin, E.V. (1998). The HORMA domain: A common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. Trends Biochem. Sci. 23, 284-286.
27. Zetka, M.C., Kawasaki, I., Strome, S., and Muller, F. (1999). Synapsis and chiasma formation in Caenorhabditis elegans require HIM-3, a meiotic chromosome core component that functions in chromosome segregation. Genes Dev. 13, 2258-2270.
28. Wickens, M., Bernstein, D.S., Kimble, J., and Parker, R. (2002). A PUF family portrait: 3'UTR regulation as a way of life. Trends Genet. 18, 150-157.
29. Nakahata, S., Katsu, Y., Mita, K., Inoue, K., Nagahama, Y., and Yamashita, M. (2001). Biochemical indentification of Xenopus pumilio as a sequence-specific cyclin B1 mRNA-binding protein that physically interacts with a nanos homolog, Xcat-2, and a cytoplasmic polyadenylation element-binding protein. J. Biol. Chem. 276, 20945-20953.
30. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., Fitzhugh, W., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
31. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A, et al. (2001). The sequence of the human genome. Science 291, 1304-1351.
32. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498.
33. Schwikowski, B., Uetz, P., and Fields, S. (2000). A network of protein-protein interactions in yeast. Nat. Genet. 18, 1257-1261.
34. Piano, F., Schetter, A.J., Morton, D.G., Gunsalus, K.C., Reinke, V., Kim, S.K., and Kemphues, K.J. (2002). Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr. Biol. 12, 1959-1964.