Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis

Nature

Volumn 436, Issue 7052, 2005, Pages 861-865

  Gunsalus, Kristin C ^a   Ge, Hui ^b   Schetter, Aaron J ^a   Goldberg, Debra S ^b   Han, Jing Dong J ^b   Hao, Tong ^b   Berriz, Gabriel F ^b   Bertin, Nicolas ^b   Huang, Jerry ^a   Chuang, Ling Shiang ^a   Li, Ning ^b   Mani, Ramamurthy ^b   Hyman, Anthony A ^c   Sönnichsen, Birte ^d   Echeverri, Christophe J ^d   Roth, Frederick P ^b   Vidal, Marc ^b   Piano, Fabio ^a  

^a NEW YORK UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c MAX PLANCK INSTITUTE OF MOLECULAR CELL BIOLOGY AND GENETICS   (Germany)

^d Cenix BioScience GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CYTOLOGY; GENES; MOLECULAR BIOLOGY; PROTEINS; RNA;

EMBRYOGENESIS; EMBRYONIC RNA; MOLECULAR ASSEMBLIES; MOLECULAR MACHINES;

GENETIC ENGINEERING;

GREEN FLUORESCENT PROTEIN; RNA;

BIOLOGY;

ARTICLE; CAENORHABDITIS ELEGANS; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RNA INTERFERENCE; TRANSGENIC ANIMAL;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; CELL DIVISION; CELL POLARITY; EMBRYONIC DEVELOPMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MODELS, BIOLOGICAL; PHENOTYPE; PROTEIN BINDING; RECOMBINANT FUSION PROTEINS; RNA INTERFERENCE; SYSTEMS BIOLOGY;

CAENORHABDITIS ELEGANS;

EID: 23844494458     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03876     Document Type: Article

References (30)

1. Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294 (1998).
2. Vidal, M. A biological atlas of functional maps. Cell 104, 333-339 (2001).
3. Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004).
4. Kim, S. K. et al. A gene expression map for Caenorhabditis elegans. Science 293, 2087-2092 (2001).
5. Piano, F. et al. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr. Biol. 12, 1959-1964 (2002).
6. Sönnichsen, B. et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462-469 (2005).
7. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. & Eisenberg, D. A combined algorithm for genome-wide prediction of protein function. Nature 402, 83-86 (1999).
8. Ge, H., Liu, Z., Church, G. M. & Vidal, M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genet. 29, 482-486 (2001).
9. Jansen, R., Greenbaum, D. & Gerstein, M. Relating whole-genome expression data with protein-protein interactions. Genome Res. 12, 37-46 (2002).
10. Walhout, A. J. et al. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12, 1952-1958 (2002).
11. Lee, I., Date, S. V., Adai, A. T. & Marcotte, E. M. A probabilistic functional network of yeast genes. Science 306, 1555-1558 (2004).
12. Bader, J. S., Chaudhuri, A., Rothberg, J. M. & Chant, J. Gaining confidence in high-throughput protein interaction networks. Nature Biotechnol. 22, 78-85 (2004).
13. Jansen, R. et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302, 449-453 (2003).
14. Boulton, S. J. et al. Combined functional genomic maps of the C. elegans DNA damage response. Science 295, 127-131 (2002).
15. Begley, T. J., Rosenbach, A. S., Ideker, T. & Samson, L. D. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol. Cancer Res. 1, 103-112 (2002).
16. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25-29 (2000).
17. Bader, G. D. & Hogue, C. W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2 (2003).
18. Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736 (2003).
19. O'Connell, K. F. et al. The C. elegans zyg-1 gene encodes a regulator of centrosome duplication with distinct maternal and paternal roles in the embryo. Cell 105, 547-558 (2001).
20. Schumacher, J. M., Ashcroft, N., Donovan, P. J. & Golden, A. A highly conserved centrosomal kinase, AIR-1, is required for accurate cell cycle progression and segregation of developmental factors in Caenorhabditis elegans embryos. Development 125, 4391-4402 (1998).
21. Kirkham, M., Muller-Reichert, T., Oegema, K., Grill, S. & Hyman, A. A. SAS-4 is a C. elegans centriolar protein that controls centrosome size. Cell 112, 575-587 (2003).
22. Leidel, S. & Gönczy, P. SAS-4 is essential for centrosome duplication in C. elegans and is recruited to daughter centrioles once per cell cycle. Dev. Cell 4, 431-439 (2003).
23. Kitagawa, R., Law, E., Tang, L. & Rose, A. M. The Cdc20 homolog, FZY-1, and its interacting protein, IFY-1, are required for proper chromosome segregation in Caenorhabditis elegans. Curr. Biol. 12, 2118-2123 (2002).
24. Delattre, M. et al. Centriolar SAS-5 is required for centrosome duplication in C. elegans. Nature Cell Biol. 6, 656-664 (2004).
25. Dammermann, A. et al. Centriole assembly requires both centriolar and pericentriolar material proteins. Dev. Cell 7, 815-829 (2004).
26. Leidel, S., Delattre, M., Cerutti, L., Baumer, K. & Gönczy, P. SAS-6 defines a protein family required for centrosome duplication in C. elegans and in human cells. Nature Cell Biol. 7, 115-125 (2005).
27. Schneider, S. Q. & Bowerman, B. Cell polarity and the cytoskeleton in the Caenorhabditis elegans zygote. Annu. Rev. Genet. 37, 221-249 (2003).
28. Brajenovic, M., Joberty, G., Kuster, B., Bouwmeester, T. & Drewes, G. Comprehensive proteomic analysis of human Par protein complexes reveals an interconnected protein network. J. Biol. Chem. 279, 12804-12811 (2004).
29. Baas, A. F., Smit, L. & Clevers, H. LKB1 tumour suppressor protein: PARtaker in cell polarity. Trends Cell Biol. 14, 312-319 (2004).
30. Cheeseman, I. M. et al. A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev. 18, 2255-2268 (2004).