Comparative developmental expression profiling of two C. elegans isolates

PLoS ONE

Volumn 3, Issue 12, 2008, Pages

  Capra, Emily J ^a   Skrovanek, Sonja M ^a   Kruglyak, Leonid ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; COMPARATIVE STUDY; CONTROLLED STUDY; DEVELOPMENTAL STAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENETIC LINKAGE; GENETIC VARIABILITY; INNATE IMMUNITY; MICROARRAY ANALYSIS; NONHUMAN; PARASITE DEVELOPMENT; PARASITE ISOLATION; PROTEIN MOTIF; ANIMAL; DNA MICROARRAY; GENETIC POLYMORPHISM; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY;

CAENORHABDITIS ELEGANS;

ANIMALS; CAENORHABDITIS ELEGANS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENETIC VARIATION; IMMUNITY, INNATE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC;

EID: 58149339911     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0004055     Document Type: Article

References (77)

1. Tan MP, Smith EN, Broach JR, Floudas CA (2008) Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures. BMC Bioinformatics 9: 268.
2. Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7: 55-65.
3. (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
4. Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC (2008) Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Res 36: e12.
5. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, et al. (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434: 462-469.
6. Parry DH, Xu J, Ruvkun G (2007) A whole-genome RNAi Screen for C. elegans miRNA pathway genes. Curr Biol 17: 2013-2022.
7. Hamilton B, Dong Y, Shindo M, LiuW, Odell I, et al. (2005) A systematic RNAi screen for longevity genes in C. elegans. Genes Dev 19: 1544-1555.
8. Kirienko NV, Fay DS (2007) Transcriptome profiling of the C. elegans Rb ortholog reveals diverse developmental roles. Dev Biol 305: 674-684.
9. Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, et al. (2005) The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Development 132: 1843-1854.
10. Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, et al. (2001) Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci U S A 98: 218-223.
11. Gaudet J, Mango SE (2002) Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295: 821-825.
12. Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, Brown EL (2000) Genomic analysis of gene expression in C. elegans. Science 290: 809-812.
13. Thoemke K, Yi W, Ross JM, Kim S, Reinke V, et al. (2005) Genome-wide analysis of sex-enriched gene expression during C. elegans larval development. Dev Biol 284: 500-508.
14. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, et al. (2000) A global profile of germline gene expression in C. elegans. Mol Cell 6: 605-616.
15. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, et al. (2002) Gene expression during the life cycle of Drosophila melanogaster. Science 297: 2270-2275.
16. Bar-Joseph Z (2004) Analyzing time series gene expression data. Bioinformatics 20: 2493-2503.
17. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
18. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, et al. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406: 90-94.
19. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
20. Brenner S (1974) The genetics of Caenorhabditis elegans. Genetics 77: 71-94.
21. Koch R, van Luenen HG, van der Horst M, Thijssen KL, Plasterk RH (2000) Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Genome Res 10: 1690-1696.
22. Wicks SR, Yeh RT, Gish WR, Waterston RH, Plasterk RH (2001) Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet 28: 160-164.
23. Swan KA, Curtis DE, McKusick KB, Voinov AV, Mapa FA, et al. (2002) High-throughput gene mapping in Caenorhabditis elegans. Genome Res 12: 1100-1105.
24. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK (2006) A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 38: 75-81.
25. Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 38: 82-85.
26. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, et al. (2006) Common deletion polymorphisms in the human genome. Nat Genet 38: 86-92.
27. Maydan JS, Flibotte S, Edgley ML, Lau J, Selzer RR, et al. (2007) Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Res 17: 337-347.
28. Cutter AD, Ward S (2005) Sexual and temporal dynamics of molecular evolution in C. elegans development. Mol Biol Evol 22: 178-188.
29. Wong D, Bazopoulou D, Pujol N, Tavernarakis N, Ewbank JJ (2007) Genome-wide investigation reveals pathogen-specific and shared signatures in the response of Caenorhabditis elegans to infection. Genome Biol 8: R194.
30. Thomas JH (2006) Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Res 16: 1017-1030.
31. Troemel ER, Chu SW, Reinke V, Lee SS, Ausubel FM, et al. (2006) p38 MAPK regulates expression of immune response genes and contributes to longevity in C. elegans. PLoS Genet 2: e183.
32. Shapira M, Hamlin BJ, Rong J, Chen K, Ronen M, et al. (2006) A conserved role for a GATA transcription factor in regulating epithelial innate immune responses. Proc Natl Acad Sci U S A 103: 14086-14091.
33. Ernst J, Bar-Joseph Z (2006) STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7: 191.
34. (2002-2006) WormAtlas. In: Altun ZFaH DH, ed.
35. Rose LS, Kemphues KJ (1998) Early patterning of the C. elegans embryo. Annu Rev Genet 32: 521-545.
36. Steven R, Zhang L, Culotti J, Pawson T (2005) The UNC-73/Trio RhoGEF-2 domain is required in separate isoforms for the regulation of pharynx pumping and normal neurotransmission in C. elegans. Genes Dev 19: 2016-2029.
37. Avery L (1993) The genetics of feeding in Caenorhabditis elegans. Genetics 133: 897-917.
38. Elemento O, Slonim N, Tavazoie S (2007) A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28: 337-350.
39. Sluder AE, Maina CV (2001) Nuclear receptors in nematodes: themes and variations. Trends Genet 17: 206-213.
40. Robinson-Rechavi M, Maina CV, Gissendanner CR, Laudet V, Sluder A (2005) Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes. J Mol Evol 60: 577-586.
41. Mangelsdorf DJ, Evans RM (1995) The RXR heterodimers and orphan receptors. Cell 83: 841-850.
42. Mangelsdorf DJ, Thummel C, Beato M, Herrlich P, Schutz G, et al. (1995) The nuclear receptor superfamily: the second decade. Cell 83: 835-839.
43. King-Jones K, Thummel CS (2005) Nuclear receptors-a perspective from Drosophila. Nat Rev Genet 6: 311-323.
44. Brozova E, Simeckova K, Kostrouch Z, Rall JE, Kostrouchova M (2006) NHR-40, a Caenorhabditis elegans supplementary nuclear receptor, regulates embryonic and early larval development. Mech Dev 123: 689-701.
45. Simeckova K, Brozova E, Vohanka J, Pohludka M, Kostrouch Z, et al. (2007) Supplementary nuclear receptor NHR-60 is required for normal embryonic and early larval development of Caenorhabditis elegans. Folia Biol (Praha) 53: 85-96.
46. McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, et al. (2007) The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol 302: 627-645.
47. Gissendanner CR, Crossgrove K, Kraus KA, Maina CV, Sluder AE (2004) Expression and function of conserved nuclear receptor genes in Caenorhabditis elegans. Dev Biol 266: 399-416.
48. Helin K (1998) Regulation of cell proliferation by the E2F transcription factors. Curr Opin Genet Dev 8: 28-35.
49. Bracken AP, Ciro M, Cocito A, Helin K (2004) E2F target genes: unraveling the biology. Trends Biochem Sci 29: 409-417.
50. Hateboer G, Wobst A, Petersen BO, Le Cam L, Vigo E, et al. (1998) Cell cycle-regulated expression of mammalian CDC6 is dependent on E2F. Mol Cell Biol 18: 6679-6697.
51. Reddien PW, Andersen EC, Huang MC, Horvitz HR (2007) DPL-1 DP, LIN-35 Rb and EFL-1 E2F act with the MCD-1 zinc-finger protein to promote programmed cell death in Caenorhabditis elegans. Genetics 175: 1719-1733.
52. Page BD, Guedes S, Waring D, Priess JR (2001) The C. elegans E2F- and DP-related proteins are required for embryonic asymmetry and negatively regulate Ras/MAPK signaling. Mol Cell 7: 451-460.
53. Fukushige T, Hendzel MJ, Bazett-Jones DP, McGhee JD (1999) Direct visualization of the elt-2 gut-specific GATA factor binding to a target promoter inside the living Caenorhabditis elegans embryo. Proc Natl Acad Sci U S A 96: 11883-11888.
54. Fay DS, Qiu X, Large E, Smith CP, Mango S, et al. (2004) The coordinate regulation of pharyngeal development in C. elegans by lin-35/Rb, pha-1, and ubc-18. Dev Biol 271: 11-25.
55. Hwang BJ, Meruelo AD, Sternberg PW (2007) C. elegans EVI1 proto-oncogene, EGL-43, is necessary for Notch-mediated cell fate specification and regulates cell invasion. Development 134: 669-679.
56. Tonkin LA, Saccomanno L, Morse DP, Brodigan T, Krause M, et al. (2002) RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J 21: 6025-6035.
57. Abbott AL, Alvarez-Saavedra E, Miska EA, Lau NC, Bartel DP, et al. (2005) The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9: 403-414.
58. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008.
59. Eckmann CR, Kraemer B, Wickens M, Kimble J (2002) GLD-3, a bicaudal-C homolog that inhibits FBF to control germline sex determination in C. elegans. Dev Cell 3: 697-710.
60. Karashima T, Sugimoto A, Yamamoto M (2000) Caenorhabditis elegans homologue of the human azoospermia factor DAZ is required for oogenesis but not for spermatogenesis. Development 127: 1069-1079.
61. Lee MH, Schedl T (2006) RNA-binding proteins. WormBook. pp 1-13.
62. Loria PM, Duke A, Rand JB, Hobert O (2003) Two neuronal, nuclear-localized RNA binding proteins involved in synaptic transmission. Curr Biol 13: 1317-1323.
63. Schubert CM, Lin R, de Vries CJ, Plasterk RH, Priess JR (2000) MEX-5 and MEX-6 function to establish soma/germline asymmetry in early C. elegans embryos. Mol Cell 5: 671-682.
64. Nepveu A (2001) Role of the multifunctional CDP/Cut/Cux homeodomain transcription factor in regulating differentiation, cell growth and development. Gene 270: 1-15.
65. Von Stetina SE, Watson JD, Fox RM, Olszewski KL, Spencer WC, et al. (2007) Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. Genome Biol 8: R135.
66. Nicholas HR, Hodgkin J (2004) Responses to infection and possible recognition strategies in the innate immune system of Caenorhabditis elegans. Mol Immunol 41: 479-493.
67. Alegado RA, Campbell MC, Chen WC, Slutz SS, Tan MW (2003) Characterization of mediators of microbial virulence and innate immunity using the Caenorhabditis elegans host-pathogen model. Cell Microbiol 5: 435-444.
68. Schulenburg H, Kurz CL, Ewbank JJ (2004) Evolution of the innate immune system: the worm perspective. Immunol Rev 198: 36-58.
69. Ding SW (2005) MicroRNA function in animal development. FEBS Let 579: 5911-5922.
70. Stiernagle T (2006) Maintenance of C. elegans. WormBook. pp 1-11.
71. Byerly L, Cassada RC, Russell RL (1976) The life cycle of the nematode Caenorhabditis elegans. I. Wild-type growth and reproduction. Dev Biol 51: 23-33.
72. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, et al. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics 17: 520-525.
73. Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378.
74. Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
75. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
76. Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, et al. (2008) WormBase 2007. Nucleic Acids Res 36: D612-617.
77. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.