Dissection of Genetic Pathways in C. elegans

Methods in Cell Biology

Volumn 106, Issue , 2011, Pages 113-157

  Wang, Zheng ^a   Sherwood, David R ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Genetic pathway; Germ line; Mutant; Programmed cell death; Screen; Transduction

Indexed keywords

EID: 82355181650     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-544172-8.00005-0     Document Type: Chapter

References (203)

1. Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
2. Ahringer, J. (2006). Reverse genetics. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.47.1, http://www.wormbook.org/.
3. Ahringer J. Turn to the worm!. Curr. Opin. Genet. Dev. 1997, 7:410-415.
4. Alfonso A., Grundahl K., Duerr J.S., Han H.P., Rand J.B. The Caenorhabditis elegans unc-17 gene: a putative vesicular acetylcholine transporter. Science 1993, 261:617-619.
5. Aroian R.V., Koga M., Mendel J.E., Ohshima Y., Sternberg P.W. The let-23 gene necessary for Caenorhabditis elegans vulval induction encodes a tyrosine kinase of the EGF receptor subfamily. Nature 1990, 348:693-699.
6. Ashman K., Moran M.F., Sicheri F., Pawson T., Tyers M. Cell signalling - the proteomics of it all. Sci. STKE 2001, 2001:pe33.
7. Avery L., Wasserman S. Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Trends Genet. 1992, 8:312-316.
8. Barr M.M., DeModena J., Braun D., Nguyen C.Q., Hall D.H., Sternberg P.W. The Caenorhabditis elegans autosomal dominant polycystic kidney disease gene homologs lov-1 and pkd-2 act in the same pathway. Curr. Biol. 2001, 11:1341-1346.
9. Barr M.M., Sternberg P.W. A polycystic kidney-disease gene homologue required for male mating behaviour in C. elegans. Nature 1999, 401:386-389.
10. Bateson W. Mendel's Principles of Heredity 1909, Cambridge University Press, Cambridge, UK.
11. Baugh L.R., Demodena J., Sternberg P.W. RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 2009, 324:92-94.
12. Bergamaschi D., Samuels Y., O'Neil N.J., Trigiante G., Crook T., Hsieh J.K., O'Connor D.J., Zhong S., Campargue I., Tomlinson M.L., et al. iASPP oncoprotein is a key inhibitor of p53 conserved from worm to human. Nat. Genet. 2003, 33:162-167.
13. Berset T., Hoier E.F., Battu G., Canevascini S., Hajnal A. Notch inhibition of RAS signaling through MAP kinase phosphatase LIP-1 during C. elegans vulval development. Science 2001, 291:1055-1058.
14. Boone C., Bussey H., Andrews B.J. Exploring genetic interactions and networks with yeast. Nat. Rev. Genet. 2007, 8:437-449.
15. Boulton S.J., Gartner A., Reboul J., Vaglio P., Dyson N., Hill D.E., Vidal M. Combined functional genomic maps of the C. elegans DNA damage response. Science 2002, 295:127-131.
16. Boutros M., Ahringer J. The art and design of genetic screens: RNA interference. Nat. Rev. Genet. 2008, 9:554-566.
17. Brenner S. The genetics of Caenorhabditis elegans. Genetics 1974, 77:71-94.
18. Budovskaya Y.V., Wu K., Southworth L.K., Jiang M., Tedesco P., Johnson T.E., Kim S.K. An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans. Cell 2008, 134:291-303.
19. Chalfie M., Tu Y., Euskirchen G., Ward W.W., Prasher D.C. Green fluorescent protein as a marker for gene expression. Science 1994, 263:802-805.
20. Chan S.S., Zheng H., Su M.W., Wilk R., Killeen M.T., Hedgecock E.M., Culotti J.G. UNC-40, a C. elegans homolog of DCC (Deleted in Colorectal Cancer), is required in motile cells responding to UNC-6 netrin cues. Cell 1996, 87:187-195.
21. Chang C., Hopper N.A., Sternberg P.W. Caenorhabditis elegans SOS-1 is necessary for multiple RAS-mediated developmental signals. EMBO J. 2000, 19:3283-3294.
22. Chang S., Johnston R.J., Frokjaer-Jensen C., Lockery S., Hobert O. MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 2004, 430:785-789.
23. Chang S., Johnston R.J., Hobert O. A transcriptional regulatory cascade that controls left/right asymmetry in chemosensory neurons of C. elegans. Genes Dev. 2003, 17:2123-2137.
24. Cheeseman I.M., Desai A. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. STKE 2005, 2005:pl1.
25. Cheeseman I.M., Niessen S., Anderson S., Hyndman F., Yates J.R., Oegema K., Desai A. A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev. 2004, 18:2255-2268.
26. Chen N., Greenwald I. The lateral signal for LIN-12/Notch in C. elegans vulval development comprises redundant secreted and transmembrane DSL proteins. Dev. Cell 2004, 6:183-192.
27. Chong H., Vikis H.G., Guan K.L. Mechanisms of regulating the Raf kinase family. Cell Signal. 2003, 15:463-469.
28. Clapham D.E. TRP channels as cellular sensors. Nature 2003, 426:517-524.
29. Clark S.G., Stern M.J., Horvitz H.R. C. elegans cell-signalling gene sem-5 encodes a protein with SH2 and SH3 domains. Nature 1992, 356:340-344.
30. Clarke A.R., Maandag E.R., van Roon M., van der Lugt N.M., van der Valk M., Hooper M.L., Berns A., te Riele H. Requirement for a functional Rb-1 gene in murine development. Nature 1992, 359:328-330.
31. Cordell H.J. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum. Mol. Genet. 2002, 11:2463-2468.
32. Culetto E., Sattelle D.B. A role for Caenorhabditis elegans in understanding the function and interactions of human disease genes. Hum. Mol. Genet. 2000, 9:869-877.
33. Cusick M.E., Klitgord N., Vidal M., Hill D.E. Interactome: gateway into systems biology. Hum. Mol. Genet. 2005, 14(Spec No. 2):R171-R181.
34. Dawson I.A., Roth S., Artavanis-Tsakonas S. The Drosophila cell cycle gene fizzy is required for normal degradation of cyclins A and B during mitosis and has homology to the CDC20 gene of Saccharomyces cerevisiae. J. Cell. Biol. 1995, 129:725-737.
35. Derry W.B., Putzke A.P., Rothman J.H. Caenorhabditis elegans p53: role in apoptosis, meiosis, and stress resistance. Science 2001, 294:591-595.
36. Dimitriadi M., Hart A.C. Neurodegenerative disorders: insights from the nematode Caenorhabditis elegans. Neurobiol. Dis. 2010, 40:4-11.
37. Doitsidou M., Flames N., Lee A.C., Boyanov A., Hobert O. Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans. Nat. Methods 2008, 5:869-872.
38. Dorfman M., Gomes J.E., O'Rourke S., Bowerman B. Using RNA interference to identify specific modifiers of a temperature-sensitive, embryonic-lethal mutation in the Caenorhabditis elegans ubiquitin-like Nedd8 protein modification pathway E1-activating gene rfl-1. Genetics 2009, 182:1035-1049.
39. Du W., Dyson N. The role of RBF in the introduction of G1 regulation during Drosophila embryogenesis. EMBO J. 1999, 18:916-925.
40. Dupuy D., Bertin N., Hidalgo C.A., Venkatesan K., Tu D., Lee D., Rosenberg J., Svrzikapa N., Blanc A., Carnec A., et al. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat. Biotechnol. 2007, 25:663-668.
41. Fay D.S., Keenan S., Han M. fzr-1 and lin-35/Rb function redundantly to control cell proliferation in C. elegans as revealed by a nonbiased synthetic screen. Genes Dev. 2002, 16:503-517.
42. Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature 1989, 340:245-246.
43. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
44. Fraser A.G., Kamath R.S., Zipperlen P., Martinez-Campos M., Sohrmann M., Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 2000, 408:325-330.
45. Friedman D.B., Johnson T.E. A mutation in the age-1 gene in Caenorhabditis elegans lengthens life and reduces hermaphrodite fertility. Genetics 1988, 118:75-86.
46. Fuhrman L.E., Goel A.K., Smith J., Shianna K.V., Aballay A. Nucleolar proteins suppress Caenorhabditis elegans innate immunity by inhibiting p53/CEP-1. PLoS Genet. 2009, 5:e1000657.
47. Gao M.X., Liao E.H., Yu B., Wang Y., Zhen M., Derry W.B. The SCF FSN-1 ubiquitin ligase controls germline apoptosis through CEP-1/p53 in C. elegans. Cell Death Differ. 2008, 15:1054-1062.
48. Ge H., Walhout A.J., Vidal M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet. 2003, 19:551-560.
49. Gengyo-Ando K., Mitani S. Characterization of mutations induced by ethyl methanesulfonate, UV, and trimethylpsoralen in the nematode Caenorhabditis elegans. Biochem. Biophys. Res. Commun. 2000, 269:64-69.
50. Gilleard J.S., McGhee J.D. Activation of hypodermal differentiation in the Caenorhabditis elegans embryo by GATA transcription factors ELT-1 and ELT-3. Mol. Cell. Biol. 2001, 21:2533-2544.
51. Gilleard J.S., Shafi Y., Barry J.D., McGhee J.D. ELT-3: a Caenorhabditis elegans GATA factor expressed in the embryonic epidermis during morphogenesis. Dev. Biol. 1999, 208:265-280.
52. Gilsdorf M., Horn T., Arziman Z., Pelz O., Kiner E., Boutros M. GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update. Nucleic Acids Res. 2010, 38:D448-D452.
53. Gitai Z., Yu T.W., Lundquist E.A., Tessier-Lavigne M., Bargmann C.I. The netrin receptor UNC-40/DCC stimulates axon attraction and outgrowth through enabled and, in parallel, Rac and UNC-115/AbLIM. Neuron 2003, 37:53-65.
54. Goldstein B., Hird S.N. Specification of the anteroposterior axis in Caenorhabditis elegans. Development 1996, 122:1467-1474.
55. Goodwin E.B., Ellis R.E. Turning clustering loops: sex determination in Caenorhabditis elegans. Curr. Biol. 2002, 12:R111-R120.
56. Grad Y., Aach J., Hayes G.D., Reinhart B.J., Church G.M., Ruvkun G., Kim J. Computational and experimental identification of C. elegans microRNAs. Mol. Cell 2003, 11:1253-1263.
57. Grant B., Hirsh D. Receptor-mediated endocytosis in the Caenorhabditis elegans oocyte. Mol. Biol. Cell 1999, 10:4311-4326.
58. Grant B., Zhang Y., Paupard M.C., Lin S.X., Hall D.H., Hirsh D. Evidence that RME-1, a conserved C. elegans EH-domain protein, functions in endocytic recycling. Nat. Cell Biol. 2001, 3:573-579.
59. Grant B.D., Wilkinson H.A. Functional genomic maps in Caenorhabditis elegans. Curr. Opin. Cell Biol. 2003, 15:206-212.
60. Greenwald I.S., Sternberg P.W., Horvitz H.R. The lin-12 locus specifies cell fates in Caenorhabditis elegans. Cell 1983, 34:435-444.
61. Guarente L. Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 1993, 9:362-366.
62. Gunsalus K.C., Ge H., Schetter A.J., Goldberg D.S., Han J.D., Hao T., Berriz G.F., Bertin N., Huang J., Chuang L.S., et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 2005, 436:861-865.
63. Gunsalus K.C., Yueh W.C., MacMenamin P., Piano F. RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res. 2004, 32:D406-D410.
64. Guthrie C.R., Schellenberg G.D., Kraemer B.C. SUT-2 potentiates tau-induced neurotoxicity in Caenorhabditis elegans. Hum. Mol. Genet. 2009, 18:1825-1838.
65. Hagedorn E.J., Yashiro H., Ziel J.W., Ihara S., Wang Z., Sherwood D.R. Integrin acts upstream of netrin signaling to regulate formation of the anchor cell's invasive membrane in C. elegans. Dev. Cell 2009, 17:187-198.
66. Hajdu-Cronin Y.M., Chen W.J., Patikoglou G., Koelle M.R., Sternberg P.W. Antagonism between G(o)alpha and G(q)alpha in Caenorhabditis elegans: the RGS protein EAT-16 is necessary for G(o)alpha signaling and regulates G(q)alpha activity. Genes Dev. 1999, 13:1780-1793.
67. Hajnal A., Whitfield C.W., Kim S.K. Inhibition of Caenorhabditis elegans vulval induction by gap-1 and by let-23 receptor tyrosine kinase. Genes Dev. 1997, 11:2715-2728.
68. Han M., Golden A., Han Y., Sternberg P.W. C. elegans lin-45 raf gene participates in let-60 ras-stimulated vulval differentiation. Nature 1993, 363:133-140.
69. Hao J.C., Yu T.W., Fujisawa K., Culotti J.G., Gengyo-Ando K., Mitani S., Moulder G., Barstead R., Tessier-Lavigne M., Bargmann C.I. C. elegans slit acts in midline, dorsal-ventral, and anterior-posterior guidance via the SAX-3/Robo receptor. Neuron 2001, 32:25-38.
70. Harris P.C., Torres V.E. Polycystic kidney disease. Annu. Rev. Med. 2009, 60:321-337.
71. Harris R., Sabatelli L.M., Seeger M.A. Guidance cues at the Drosophila CNS midline: identification and characterization of two Drosophila Netrin/UNC-6 homologs. Neuron 1996, 17:217-228.
72. Harris T.W., Antoshechkin I., Bieri T., Blasiar D., Chan J., Chen W.J., De La Cruz N., Davis P., Duesbury M., Fang R., et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010, 38:D463-D467.
73. Hartman J.L.t., Garvik B., Hartwell L. Principles for the buffering of genetic variation. Science 2001, 291:1001-1004.
74. Hedgecock E.M., Culotti J.G., Hall D.H. The unc-5, unc-6, and unc-40 genes guide circumferential migrations of pioneer axons and mesodermal cells on the epidermis in C. elegans. Neuron 1990, 4:61-85.
75. Hill R.J., Sternberg P.W. The gene lin-3 encodes an inductive signal for vulval development in C. elegans. Nature 1992, 358:470-476.
76. Hobert O. Architecture of a microRNA-controlled gene regulatory network that diversifies neuronal cell fates. Cold Spring Harb. Symp. Quant. Biol. 2006, 71:181-188.
77. Hodgkin, J. (2005). Genetic suppression. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.59.1, http://www.wormbook.org/.
78. Hodgkin J., Herman R.K. Changing styles in C. elegans genetics. Trends Genet. 1998, 14:352-357.
79. Hoeppner D.J., Spector M.S., Ratliff T.M., Kinchen J.M., Granat S., Lin S.C., Bhusri S.S., Conradt B., Herman M.A., Hengartner M.O. EOR-1 and EOR-2 are required for cell-specific apoptotic death in C. elegans. Dev. Biol. 2004, 274:125-138.
80. Hopper N.A., Lee J., Sternberg P.W. ARK-1 inhibits EGFR signaling in C. elegans. Mol. Cell 2000, 6:65-75.
81. Howell K., Arur S., Schedl T., Sundaram M.V. EOR-2 is an obligate binding partner of the BTB-zinc finger protein EOR-1 in Caenorhabditis elegans. Genetics 2010, 184:899-913.
82. Hsu V., Zobel C.L., Lambie E.J., Schedl T., Kornfeld K. Caenorhabditis elegans lin-45 raf is essential for larval viability, fertility and the induction of vulval cell fates. Genetics 2002, 160:481-492.
83. Huang L.S., Sternberg P.W. Genetic dissection of developmental pathways. Methods Cell Biol. 1995, 48:97-122.
84. Hudson M.L., Kinnunen T., Cinar H.N., Chisholm A.D. C. elegans Kallmann syndrome protein KAL-1 interacts with syndecan and glypican to regulate neuronal cell migrations. Dev. Biol. 2006, 294:352-365.
85. Hwang B.J., Meruelo A.D., Sternberg P.W. C. elegans EVI1 proto-oncogene, EGL-43, is necessary for Notch-mediated cell fate specification and regulates cell invasion. Development 2007, 134:669-679.
86. Igarashi P., Somlo S. Genetics and pathogenesis of polycystic kidney disease. J. Am. Soc. Nephrol. 2002, 13:2384-2398.
87. Ishii N., Wadsworth W.G., Stern B.D., Culotti J.G., Hedgecock E.M. UNC-6, a laminin-related protein, guides cell and pioneer axon migrations in C. elegans. Neuron 1992, 9:873-881.
88. Jacks T., Fazeli A., Schmitt E.M., Bronson R.T., Goodell M.A., Weinberg R.A. Effects of an Rb mutation in the mouse. Nature 1992, 359:295-300.
89. Jansen G., Hazendonk E., Thijssen K.L., Plasterk R.H. Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat. Genet. 1997, 17:119-121.
90. Jansen R., Greenbaum D., Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res. 2002, 12:37-46.
91. Jeong H., Mason S.P., Barabasi A.L., Oltvai Z.N. Lethality and centrality in protein networks. Nature 2001, 411:41-42.
92. Johnsen R.C., Baillie D.L. Genetic analysis of a major segment [LGV(left)] of the genome of Caenorhabditis elegans. Genetics 1991, 129:735-752.
93. Johnston R.J., Hobert O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 2003, 426:845-849.
94. Jorgensen E.M., Mango S.E. The art and design of genetic screens: caenorhabditis elegans. Nat. Rev. Genet. 2002, 3:356-369.
95. Kaletta T., Hengartner M.O. Finding function in novel targets: C. elegans as a model organism. Nat. Rev. Drug Discov. 2006, 5:387-398.
96. Kamath R.S., Fraser A.G., Dong Y., Poulin G., Durbin R., Gotta M., Kanapin A., Le Bot N., Moreno S., Sohrmann M., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003, 421:231-237.
97. Kemphues K. (2005). Essential Genes. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.57.1, http://www.wormbook.org/.
98. Kemphues K.J., Priess J.R., Morton D.G., Cheng N.S. Identification of genes required for cytoplasmic localization in early C. elegans embryos. Cell 1988, 52:311-320.
99. Kennedy T.E., Serafini T., de la Torre J.R., Tessier-Lavigne M. Netrins are diffusible chemotropic factors for commissural axons in the embryonic spinal cord. Cell 1994, 78:425-435.
100. Kim H., Rogers M.J., Richmond J.E., McIntire S.L. SNF-6 is an acetylcholine transporter interacting with the dystrophin complex in Caenorhabditis elegans. Nature 2004, 430:891-896.
101. Kim S.K. Http://C. elegans: mining the functional genomic landscape. Nat. Rev. Genet. 2001, 2:681-689.
102. Kimble J., Hirsh D. The postembryonic cell lineages of the hermaphrodite and male gonads in Caenorhabditis elegans. Dev. Biol. 1979, 70:396-417.
103. Kimura K.D., Tissenbaum H.A., Liu Y., Ruvkun G. daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Science 1997, 277:942-946.
104. Kirienko N.V., Mani K., Fay D.S. Cancer models in Caenorhabditis elegans. Dev. Dyn. 2010, 239:1413-1448.
105. Kornfeld K., Guan K.L., Horvitz H.R. The Caenorhabditis elegans gene mek-2 is required for vulval induction and encodes a protein similar to the protein kinase MEK. Genes Dev. 1995 a, 9:756-768.
106. Kornfeld K., Hom D.B., Horvitz H.R. The ksr-1 gene encodes a novel protein kinase involved in Ras-mediated signaling in C. elegans. Cell 1995 b, 83:903-913.
107. Lackner M.R., Kornfeld K., Miller L.M., Horvitz H.R., Kim S.K. A MAP kinase homolog, mpk-1, is involved in ras-mediated induction of vulval cell fates in Caenorhabditis elegans. Genes Dev. 1994, 8:160-173.
108. Lakso M., Vartiainen S., Moilanen A.M., Sirvio J., Thomas J.H., Nass R., Blakely R.D., Wong G. Dopaminergic neuronal loss and motor deficits in Caenorhabditis elegans overexpressing human alpha-synuclein. J. Neurochem. 2003, 86:165-172.
109. Lauderdale J.D., Davis N.M., Kuwada J.Y. Axon tracts correlate with netrin-1a expression in the zebrafish embryo. Mol. Cell. Neurosci. 1997, 9:293-313.
110. Lee J., Jongeward G.D., Sternberg P.W. unc-101, a gene required for many aspects of Caenorhabditis elegans development and behavior, encodes a clathrin-associated protein. Genes Dev. 1994, 8:60-73.
111. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
112. Lee V.M., Goedert M., Trojanowski J.Q. Neurodegenerative tauopathies. Annu. Rev. Neurosci. 2001, 24:1121-1159.
113. Lehner B., Tischler J., Fraser A.G. RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat. Protoc. 2006, 1:1617-1620.
114. Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., Vidalain P.O., Han J.D., Chesneau A., Hao T., et al. A map of the interactome network of the metazoan C. elegans. Science 2004, 303:540-543.
115. Liao E.H., Hung W., Abrams B., Zhen M. An SCF-like ubiquitin ligase complex that controls presynaptic differentiation. Nature 2004, 430:345-350.
116. Lin K., Hsin H., Libina N., Kenyon C. Regulation of the Caenorhabditis elegans longevity protein DAF-16 by insulin/IGF-1 and germline signaling. Nat. Genet. 2001, 28:139-145.
117. Liu L.X., Spoerke J.M., Mulligan E.L., Chen J., Reardon B., Westlund B., Sun L., Abel K., Armstrong B., Hardiman G., et al. High-throughput isolation of Caenorhabditis elegans deletion mutants. Genome Res. 1999, 9:859-867.
118. Lu X., Horvitz H.R. lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48. Cell 1998, 95:981-991.
119. Maiato H., DeLuca J., Salmon E.D., Earnshaw W.C. The dynamic kinetochore-microtubule interface. J. Cell Sci. 2004, 117:5461-5477.
120. Matus D.Q., Li X.Y., Durbin S., Agarwal D., Chi Q., Weiss S.J., Sherwood D.R. In vivo identification of regulators of cell invasion across basement membranes. Sci. Signal 2010, 3:ra35.
121. Mani R., St Onge R.P., Hartman J.L., Giaever G., Roth F.P. Defining genetic interaction. Proc. Natl Acad. Sci. U. S. A. 2008, 105:3461-3466.
122. Mello C., Fire A. DNA transformation. Methods Cell Biol. 1995, 48:451-482.
123. Metzstein M.M., Stanfield G.M., Horvitz H.R. Genetics of programmed cell death in C. elegans: past, present and future. Trends Genet. 1998, 14:410-416.
124. Miller D.M., Niemeyer C.J., Chitkara P. Dominant unc-37 mutations suppress the movement defect of a homeodomain mutation in unc-4, a neural specificity gene in Caenorhabditis elegans. Genetics 1993, 135:741-753.
125. Miller K.G., Emerson M.D., Rand J.B. Goalpha and diacylglycerol kinase negatively regulate the Gqalpha pathway in C. elegans. Neuron 1999, 24:323-333.
126. Mitchell K.J., Doyle J.L., Serafini T., Kennedy T.E., Tessier-Lavigne M., Goodman C.S., Dickson B.J. Genetic analysis of Netrin genes in Drosophila: Netrins guide CNS commissural axons and peripheral motor axons. Neuron 1996, 17:203-215.
127. Munro E., Nance J., Priess J.R. Cortical flows powered by asymmetrical contraction transport PAR proteins to establish and maintain anterior-posterior polarity in the early C. elegans embryo. Dev. Cell 2004, 7:413-424.
128. Murphy C.T., McCarroll S.A., Bargmann C.I., Fraser A., Kamath R.S., Ahringer J., Li H., Kenyon C. Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature 2003, 424:277-283.
129. Nakata K., Abrams B., Grill B., Goncharov A., Huang X., Chisholm A.D., Jin Y. Regulation of a DLK-1 and p38 MAP kinase pathway by the ubiquitin ligase RPM-1 is required for presynaptic development. Cell 2005, 120:407-420.
130. Nauli S.M., Alenghat F.J., Luo Y., Williams E., Vassilev P., Li X., Elia A.E., Lu W., Brown E.M., Quinn S.J., et al. Polycystins 1 and 2 mediate mechanosensation in the primary cilium of kidney cells. Nat. Genet. 2003, 33:129-137.
131. Nurrish S., Segalat L., Kaplan J.M. Serotonin inhibition of synaptic transmission: Galpha(0) decreases the abundance of UNC-13 at release sites. Neuron 1999, 24:231-242.
132. Oltvai Z.N., Barabasi A.L. Systems biology Life's complexity pyramid. Science 2002, 298:763-764.
133. Pazour G.J., San Agustin J.T., Follit J.A., Rosenbaum J.L., Witman G.B. Polycystin-2 localizes to kidney cilia and the ciliary level is elevated in orpk mice with polycystic kidney disease. Curr. Biol. 2002, 12:R378-R380.
134. Phillips P.C. Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat. Rev. Genet. 2008, 9:855-867.
135. Piano, F., Gunsalus, K. C., Hill, D. E., and Vidal, M. (2006). C. elegans network biology: a beginning. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.118.1, http://www.wormbook.org/.
136. Piano F., Schetter A.J., Morton D.G., Gunsalus K.C., Reinke V., Kim S.K., Kemphues K.J. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr. Biol. 2002, 12:1959-1964.
137. Pierce S.B., Costa M., Wisotzkey R., Devadhar S., Homburger S.A., Buchman A.R., Ferguson K.C., Heller J., Platt D.M., Pasquinelli A.A., et al. 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. 2001, 15:672-686.
138. Polanowska J., Martin J.S., Fisher R., Scopa T., Rae I., Boulton S.J. Tandem immunoaffinity purification of protein complexes from Caenorhabditis elegans. Biotechniques 2004, 36:778-780. 782.
139. Pollock D.D., Larkin J.C. Estimating the degree of saturation in mutant screens. Genetics 2004, 168:489-502.
140. Qiao L., Lissemore J.L., Shu P., Smardon A., Gelber M.B., Maine E.M. Enhancers of glp-1, a gene required for cell-signaling in Caenorhabditis elegans, define a set of genes required for germline development. Genetics 1995, 141:551-569.
141. Reboul J., Vaglio P., Rual J.F., Lamesch P., Martinez M., Armstrong C.M., Li S., Jacotot L., Bertin N., Janky R., et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 2003, 34:35-41.
142. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bettinger J.C., Rougvie A.E., Horvitz H.R., Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000, 403:901-906.
143. Rhee S.Y., Dickerson J., Xu D. Bioinformatics and its applications in plant biology. Annu. Rev. Plant Biol. 2006, 57:335-360.
144. Rhiner C., Gysi S., Frohli E., Hengartner M.O., Hajnal A. Syndecan regulates cell migration and axon guidance in C. elegans. Development 2005, 132:4621-4633.
145. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 1999, 17:1030-1032.
146. Rocheleau C.E., Howard R.M., Goldman A.P., Volk M.L., Girard L.J., Sundaram M.V. A lin-45 raf enhancer screen identifies EOR-1, EOR-2 and unusual alleles of Ras pathway genes in Caenorhabditis elegans. Genetics 2002, 161:121-131.
147. Rogers A., Antoshechkin I., Bieri T., Blasiar D., Bastiani C., Canaran P., Chan J., Chen W.J., Davis P., Fernandes J., et al. WormBase 2007. Nucleic Acids Res. 2008, 36:D612-D617.
148. Rual J.F., Ceron J., Koreth J., Hao T., Nicot A.S., Hirozane-Kishikawa T., Vandenhaute J., Orkin S.H., Hill D.E., van den Heuvel S., et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 2004, 14:2162-2168.
149. Rubin C., Gur G., Yarden Y. Negative regulation of receptor tyrosine kinases: unexpected links to c-Cbl and receptor ubiquitylation. Cell Res. 2005, 15:66-71.
150. Rubin G.M., Yandell M.D., Wortman J.R., Gabor Miklos G.L., Nelson C.R., Hariharan I.K., Fortini M.E., Li P.W., Apweiler R., Fleischmann W., et al. Comparative genomics of the eukaryotes. Science 2000, 287:2204-2215.
151. Rushforth A.M., Saari B., Anderson P. Site-selected insertion of the transposon Tc1 into a Caenorhabditis elegans myosin light chain gene. Mol. Cell. Biol. 1993, 13:902-910.
152. Sato M., Sato K., Liou W., Pant S., Harada A., Grant B.D. Regulation of endocytic recycling by C. elegans Rab35 and its regulator RME-4, a coated-pit protein. EMBO J. 2008, 27:1183-1196.
153. Savage C., Das P., Finelli A.L., Townsend S.R., Sun C.Y., Baird S.E., Padgett R.W. Caenorhabditis elegans genes sma-2, sma-3, and sma-4 define a conserved family of transforming growth factor beta pathway components. Proc. Natl Acad. Sci. U. S. A. 1996, 93:790-794.
154. Savage-Dunn C., Tokarz R., Wang H., Cohen S., Giannikas C., Padgett R.W. SMA-3 smad has specific and critical functions in DBL-1/SMA-6 TGFbeta-related signaling. Dev. Biol. 2000, 223:70-76.
155. Schumacher B., Hanazawa M., Lee M.H., Nayak S., Volkmann K., Hofmann E.R., Hengartner M., Schedl T., Gartner A. Translational repression of C. elegans p53 by GLD-1 regulates DNA damage-induced apoptosis. Cell 2005, 120:357-368.
156. Schwab M., Lutum A.S., Seufert W. Yeast Hct1 is a regulator of Clb2 cyclin proteolysis. Cell 1997, 90:683-693.
157. Schwabiuk M., Coudiere L., Merz D.C. SDN-1/syndecan regulates growth factor signaling in distal tip cell migrations in C. elegans. Dev. Biol. 2009, 334:235-242.
158. Sendoel A., Kohler I., Fellmann C., Lowe S.W., Hengartner M.O. HIF-1 antagonizes p53-mediated apoptosis through a secreted neuronal tyrosinase. Nature 2010, 465:577-583.
159. Serafini T., Kennedy T.E., Galko M.J., Mirzayan C., Jessell T.M., Tessier-Lavigne M. The netrins define a family of axon outgrowth-promoting proteins homologous to C. elegans UNC-6. Cell 1994, 78:409-424.
160. Shen K., Bargmann C.I. The immunoglobulin superfamily protein SYG-1 determines the location of specific synapses in C. elegans. Cell 2003, 112:619-630.
161. Sherwood D.R. Cell invasion through basement membranes: an anchor of understanding. Trends Cell Biol. 2006, 16:250-256.
162. Sherwood D.R., Butler J.A., Kramer J.M., Sternberg P.W. FOS-1 promotes basement-membrane removal during anchor-cell invasion in C. elegans. Cell 2005, 121:951-962.
163. Shim J., Sternberg P.W., Lee J. Distinct and redundant functions of mu1 medium chains of the AP-1 clathrin-associated protein complex in the nematode Caenorhabditis elegans. Mol. Biol. Cell 2000, 11:2743-2756.
164. Sigrist S., Jacobs H., Stratmann R., Lehner C.F. Exit from mitosis is regulated by Drosophila fizzy and the sequential destruction of cyclins A, B and B3. EMBO J. 1995, 14:4827-4838.
165. Simmer F., Moorman C., van der Linden A.M., Kuijk E., van den Berghe P.V., Kamath R.S., Fraser A.G., Ahringer J., Plasterk R.H. Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol. 2003, 1:E12.
166. Simon D.J., Madison J.M., Conery A.L., Thompson-Peer K.L., Soskis M., Ruvkun G.B., Kaplan J.M., Kim J.K. The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell 2008, 133:903-915.
167. Simonis N., Rual J.F., Carvunis A.R., Tasan M., Lemmens I., Hirozane-Kishikawa T., Hao T., Sahalie J.M., Venkatesan K., Gebreab F., et al. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat. Methods 2009, 6:47-54.
168. Singh N., Han M. sur-2, a novel gene, functions late in the let-60 ras-mediated signaling pathway during Caenorhabditis elegans vulval induction. Genes Dev. 1995, 9:2251-2265.
169. Sonnichsen B., Koski L.B., Walsh A., Marschall P., Neumann B., Brehm M., Alleaume A.M., Artelt J., Bettencourt P., Cassin E., et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 2005, 434:462-469.
170. Spilker A.C., Rabilotta A., Zbinden C., Labbe J.C., Gotta M. MAP kinase signaling antagonizes PAR-1 function during polarization of the early Caenorhabditis elegans embryo. Genetics 2009, 183:965-977.
171. Sternberg P.W. Developmental biology: a pattern of precision. Science 2004, 303:637-638.
172. Sternberg P.W., Golden A., Han M. Role of a raf proto-oncogene during Caenorhabditis elegans vulval development. Phil. Trans. R. Soc. Lond. B Biol. Sci. 1993, 340:259-265.
173. Sternberg P.W., Horvitz H.R. Pattern formation during vulval development in C. elegans. Cell 1986, 44:761-772.
174. Sternberg P.W., Horvitz H.R. The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans. Cell 1989, 58:679-693.
175. Sternberg P.W., Yoon C.H., Lee J., Jongeward G.D., Kayne P.S., Katz W.S., Lesa G., Liu J., Golden A., Huang L.S., et al. Molecular genetics of proto-oncogenes and candidate tumor suppressors in Caenorhabditis elegans. Cold Spring Harb. Symp. Quant. Biol. 1994, 59:155-163.
176. Styer K.L., Singh V., Macosko E., Steele S.E., Bargmann C.I., Aballay A. Innate immunity in Caenorhabditis elegans is regulated by neurons expressing NPR-1/GPCR. Science 2008, 322:460-464.
177. Sulston J.E., Horvitz H.R. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 1977, 56:110-156.
178. Sulston J.E., Schierenberg E., White J.G., Thomson J.N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 1983, 100:64-119.
179. Sundaram, M. V. (2006). RTK/Ras/MAPK signaling. WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.80.1, http://www.wormbook.org/.
180. Sundaram M., Han M. The C. elegans ksr-1 gene encodes a novel Raf-related kinase involved in Ras-mediated signal transduction. Cell 1995, 83:889-901.
181. Swaminathan G., Tsygankov A.Y. The Cbl family proteins: ring leaders in regulation of cell signaling. J. Cell Physiol. 2006, 209:21-43.
182. Tan P.B., Lackner M.R., Kim S.K. MAP kinase signaling specificity mediated by the LIN-1 Ets/LIN-31 WH transcription factor complex during C. elegans vulval induction. Cell 1998, 93:569-580.
183. Tavernarakis N., Wang S.L., Dorovkov M., Ryazanov A., Driscoll M. Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes. Nat. Genet. 2000, 24:180-183.
184. Tewari M., Hu P.J., Ahn J.S., Ayivi-Guedehoussou N., Vidalain P.O., Li S., Milstein S., Armstrong C.M., Boxem M., Butler M.D., et al. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol. Cell 2004, 13:469-482.
185. Thomas J.H., Birnby D.A., Vowels J.J. Evidence for parallel processing of sensory information controlling dauer formation in Caenorhabditis elegans. Genetics 1993, 134:1105-1117.
186. Velculescu V.E., Zhang L., Vogelstein B., Kinzler K.W. Serial analysis of gene expression. Science 1995, 270:484-487.
187. Wagner A. Robustness against mutations in genetic networks of yeast. Nat. Genet. 2000, 24:355-361.
188. Walhout A.J., Reboul J., Shtanko O., Bertin N., Vaglio P., Ge H., Lee H., Doucette-Stamm L., Gunsalus K.C., Schetter A.J., et al. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 2002, 12:1952-1958.
189. Walhout A.J., Sordella R., Lu X., Hartley J.L., Temple G.F., Brasch M.A., Thierry-Mieg N., Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 2000, 287:116-122.
190. Walthall W.W., Chalfie M. Cell-cell interactions in the guidance of late-developing neurons in Caenorhabditis elegans. Science 1988, 239:643-645.
191. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
192. Winnier A.R., Meir J.Y., Ross J.M., Tavernarakis N., Driscoll M., Ishihara T., Katsura I., Miller D.M. UNC-4/UNC-37-dependent repression of motor neuron-specific genes controls synaptic choice in Caenorhabditis elegans. Genes Dev. 1999, 13:2774-2786.
193. Wu J.W., Hu M., Chai J., Seoane J., Huse M., Li C., Rigotti D.J., Kyin S., Muir T.W., Fairman R., et al. Crystal structure of a phosphorylated Smad2. Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling. Mol. Cell 2001, 8:1277-1289.
194. Wu Y., Han M. Suppression of activated Let-60 ras protein defines a role of Caenorhabditis elegans Sur-1 MAP kinase in vulval differentiation. Genes Dev. 1994, 8:147-159.
195. Wu Y., Han M., Guan K.L. MEK-2, a Caenorhabditis elegans MAP kinase kinase, functions in Ras-mediated vulval induction and other developmental events. Genes Dev. 1995, 9:742-755.
196. Xiao Z.S., Quarles L.D. Role of the polycytin-primary cilia complex in bone development and mechanosensing. Ann. N. Y. Acad. Sci. 2010, 1192:410-421.
197. Yoder B.K., Hou X., Guay-Woodford L.M. The polycystic kidney disease proteins, polycystin-1, polycystin-2, polaris, and cystin, are co-localized in renal cilia. J. Am. Soc. Nephrol. 2002, 13:2508-2516.
198. Yoo A.S., Bais C., Greenwald I. Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development. Science 2004, 303:663-666.
199. Zallen J.A., Yi B.A., Bargmann C.I. The conserved immunoglobulin superfamily member SAX-3/Robo directs multiple aspects of axon guidance in C. elegans. Cell 1998, 92:217-227.
200. Zhen M., Huang X., Bamber B., Jin Y. Regulation of presynaptic terminal organization by C. elegans RPM-1, a putative guanine nucleotide exchanger with a RING-H2 finger domain. Neuron 2000, 26:331-343.
201. Zheng Y., Mellem J.E., Brockie P.J., Madsen D.M., Maricq A.V. SOL-1 is a CUB-domain protein required for GLR-1 glutamate receptor function in C. elegans. Nature 2004, 427:451-457.
202. Zhong W., Sternberg P.W. Genome-wide prediction of C. elegans genetic interactions. Science 2006, 311:1481-1484.
203. Ziel J.W., Hagedorn E.J., Audhya A., Sherwood D.R. UNC-6 (netrin) orients the invasive membrane of the anchor cell in C. elegans. Nat. Cell Biol. 2009, 11:183-189.