Toward a global picture of development: Lessons from genome-scale analysis in Caenorhabditis elegans embryonic development

Developmental Dynamics

Volumn 235, Issue 8, 2006, Pages 2009-2017

  Ge, Hui ^a   Player, Christopher M ^a   Zou, Lihua ^b,c  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b HARVARD UNIVERSITY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Computational analysis; Genomics; High throughput approaches

Indexed keywords

GREEN FLUORESCENT PROTEIN; JANUS KINASE; SMALL INTERFERING RNA; STAT PROTEIN; TRANSCRIPTOME; WNT PROTEIN; WNT1 PROTEIN;

CAENORHABDITIS ELEGANS; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME SEGREGATION; DNA MICROARRAY; EMBRYO DEVELOPMENT; GENE FUNCTION; GENOME ANALYSIS; GENOMICS; HIGH THROUGHPUT SCREENING; KNOCKOUT GENE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; REPORTER GENE; REVIEW; RNA INTERFERENCE; SYSTEMATIC REVIEW; TWO HYBRID SYSTEM; WILD TYPE;

ANIMALS; CAENORHABDITIS ELEGANS; CELL LINEAGE; EMBRYO, NONMAMMALIAN; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME;

CAENORHABDITIS ELEGANS; INVERTEBRATA;

EID: 33746947356     PISSN: 10588388     EISSN: 10970177     Source Type: Journal    
DOI: 10.1002/dvdy.20865     Document Type: Review

References (37)

1. Baeg G-H, Zhou R, Perrimon N. 2005. Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila. Genes Dev 19:1861-1870.
2. Baugh LR, Hill AA, Slonim DK, Brown EL, Hunter CP. 2003. Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. Development 130:889-900.
3. Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, Hunter CP. 2005a. The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Development 132:1843-1854.
4. Baugh LR, Wen J, Hill A, Slonim D, Brown E, Hunter C. 2005b. Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions. Genome Biology 6:R45.
5. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA. 2005. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122:947-956.
6. DasGupta R, Kaykas A, Moon RT, Perrimon N. 2005. Functional genomic analysis of the Wnt-wingless signaling pathway. Science 308:826-833.
7. Deplancke B, Dupuy D, Vidal M, Walhout AJ. 2004. A gateway-compatible yeast one-hybrid system. Genome Res 14:2093-2101.
8. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J. 2000. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408:325-330.
9. Gaudet J, Mango SE. 2002. Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295: 821-825.
10. Ge H, Walhout AJ, Vidal M. 2003. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet 19:551-560.
11. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL Jr, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. 2003. A protein interaction map of Drosophila melanogaster. Science 302:1727-1736.
12. Gonczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlu N, Bork P, Hyman AA. 2000. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408:331-336.
13. Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han J-DJ, Hao T, Berriz GF, Bertin N, Huang J, Chuang L-S, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F. 2005. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436:861-865.
14. Hannon GJ. 2002. RNA interference. Nature 418:244-251.
15. Hannon GJ, Rossi JJ. 2004. Unlocking the potential of the human genome with RNA interference. Nature 431:371-378.
16. Hartman JL IV, Garvik B, Hartwell L. 2001. Principles for the buffering of genetic variation. Science 291:1001-1004.
17. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. 1999. From molecular to modular cell biology. Nature 402:C47-C52.
18. Hope IA. 2001. Broadcast interference - functional genomics. Trends Genet 17:297-299.
19. 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.
20. Kim SK, Lund J, Kiraly M, Duke K, Jiang M, Stuart JM, Eizinger A, Wylie BN, Davidson GS. 2001. A gene expression map for Caenorhabditis elegans. Science 293:2087-2092.
21. Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain P-O, Han J-DJ, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual J-F, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, van den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M. 2004. A Map of the Interactome Network of the Metazoan C. elegans. Science 303:540-543.
22. Lockhart DJ, Winzeler EA. 2000. Genomics, gene expression and DNA arrays. Nature 405:827-836.
23. Lum L, Yao S, Mozer B, Rovescalli A, Von Kessler D, Nirenberg M, Beachy PA. 2003. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299:2039-2045.
24. Maeda I, Kohara Y, Yamamoto M, Sugimoto A. 2001. Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr Biol 11:171-176.
25. Muller P, Kuttenkeuler D, Gesellchen V, Zeidler MP, Boutros M. 2005. Identification of JAK/STAT signalling components by genome-wide RNA interference. Nature 436:871-875.
26. Piano F, Schetter AJ, Morton DG, Gunsalus KC, Reinke V, Kim SK, Kemphues KJ. 2002. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol 12:1959-1964.
27. Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M. 2001. Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J Mol Biol 314:1053-1066.
28. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJM, Davis EB, Scherer S, Ward S, Kim SK. 2000. A global profile of germline gene expression in C. elegans. Mol Cell 6:605-616.
29. Rives AW, Galitski T. 2003. Modular organization of cellular networks. Proc Natl Acad Sci U S A 100:1128-1133.
30. Schneuwly S, Klemenz R, Gehring WJ. 1987. Redesigning the body plan of Drosophila by ectopic expression of the homoeotic gene Antennapedia. Nature 325:816-818.
31. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. 2003. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34:166-176.
32. Simmer F, Moorman C, van der Linden AM, Kuijk E, van den Berghe PVE, Kamath RS, Fraser AG, Ahringer J, Plasterk RHA. 2003. Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol 1:e12.
33. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Roder M, Finell J, Hantsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gonczy P, Coulson A, Hyman AA, Echeverri CJ. 2005. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434:462-469.
34. Sulston JE, Schierenberg E, White JG, Thomson JN. 1983. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol 100:64-119.
35. Walhout AJ, Vidal M. 2001. Protein interaction maps for model organisms. Nat Rev Mol Cell Biol 2:55-62.
36. Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. 2000. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287:116-122.
37. Wang J, Kim SK. 2003. Global analysis of dauer gene expression in Caenorhabditis elegans. Development 130:1621-1634.