Recent advances in understanding the molecular mechanisms regulating C. elegans transcription

Developmental Dynamics

Volumn 239, Issue 5, 2010, Pages 1388-1404

  Gaudet, Jeb ^a   McGhee, James D ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

C. elegans; Cell fate specification; Chromatin; Development; Transcription; Transcription factors

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

CAENORHABDITIS ELEGANS; CELL DIFFERENTIATION; CELL FATE; CELL MATURATION; CHROMATIN; GENE CONTROL; GENE TARGETING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MODIFICATION; REGULATOR GENE; REVIEW;

ANIMALS; CAENORHABDITIS ELEGANS; CELL LINEAGE; GENE EXPRESSION REGULATION; PROMOTER REGIONS, GENETIC; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

CAENORHABDITIS ELEGANS;

EID: 77951612492     PISSN: 10588388     EISSN: 10970177     Source Type: Journal    
DOI: 10.1002/dvdy.22246     Document Type: Review

References (145)

1. An JH, Blackwell TK. 2003. SKN-1 links C. elegans mesendodermal specification to a conserved oxidative stress response. Genes Dev 17:1882-1893.
2. An JH, Vranas K, Lucke M, Inoue H, Hisamoto N, Matsumoto K, Blackwell TK. 2005. Regulation of the Caenorhabditis elegans oxidative stress defense protein SKN-1 by glycogen synthase kinase-3. Proc Natl Acad Sci U S A 102:16275-16280.
3. Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J. 2009. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 19:1732-1741.
4. Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrancois P, Struhl K, Gerstein M, Snyder M. 2009. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A 106:14926-14931.
5. Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. 2009. Chromatin poises miRNA- and protein-coding genes for expression. Genome Res 19:1742-1751.
6. Barski A, Zhao K. 2009. Genomic location analysis by ChIP-Seq. J Cell Biochem 107:11-18.
7. 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.
8. Baugh LR, Demodena J, Sternberg PW. 2009. RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 324:92-94.
9. Bender LB, Cao R, Zhang Y, Strome S. 2004. The MES-2/MES-3/MES-6 complex and regulation of histone H3 methylation in C. elegans. Curr Biol 14:1639-1643. (Pubitemid 39239360)
10. Bertrand V, Hobert O. 2009. Linking asymmetric cell division to the terminal differentiation program of postmitotic neurons in C. elegans. Dev Cell 16:563-575.
11. Blackwell TK, Walker AK. 2006. Transcription mechanisms. WormBook:1-16.
12. Blumenthal T. 2005. Trans-splicing and operons. WormBook:1-9.
13. Broitman-Maduro G, Owraghi M, Hung WW, Kuntz S, Sternberg PW, Maduro MF. 2009. The NK-2 class homeodomain factor CEH-51 and the T-box factor TBX-35 have overlapping function in C. elegans mesoderm development. Development 136:2735-2746.
14. Bushey AM, Dorman ER, Corces VG. 2008. Chromatin insulators: regulatory mechanisms and epigenetic inheritance. Mol Cell 32:1-9.
15. Carroll SB. 2005. Endless forms most beautiful: the new science of evo-devo. New York: W. W. Norton and Co., Inc.
16. Casamassimi A, Napoli C. 2007. Mediator complexes and eukaryotic transcription regulation: an overview. Biochimie 89:1439-1446.
17. Cedar H, Bergman Y. 2009. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10:295-304.
18. Chen J, Li X, Greenwald I. 2004. sel-7, a positive regulator of lin-12 activity, encodes a novel nuclear protein in Caenorhabditis elegans. Genetics 166:151-160. (Pubitemid 38364710)
19. Clapier CR, Cairns BR. 2009. The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273-304.
20. Clayton JE, van den Heuvel SJ, Saito RM. 2008. Transcriptional control of cell-cycle quiescence during C. elegans development. Dev Biol 313:603-613.
21. Conradt B, Horvitz HR. 1999. The TRA-1A sex determination protein of C. elegans regulates sexually dimorphic cell deaths by repressing the egl-1 cell death activator gene [see comments]. Cell 98:317-327.
22. Cui M, Han M. 2007. Roles of chromatin factors in C. elegans development. WormBook:1-16.
23. Dantonel JC, Quintin S, Lakatos L, Labouesse M, Tora L. 2000. TBP-like factor is required for embryonic RNA polymerase II transcription in C. elegans. Mol Cell 6:715-722.
24. Dejardin J, Kingston RE. 2009. Purification of proteins associated with specific genomic Loci. Cell 136:175-186.
25. Dixon DK, Jones D, Candido EP. 1990. The differentially expressed 16-kD heat shock genes of Caenorhabditis elegans exhibit differential changes in chromatin structure during heat shock. DNA & Cell Biology 9:177-191. (Pubitemid 20149179)
26. Doitsidou M, Flames N, Lee AC, Boyanov A, Hobert O. 2008. Automated screening for mutants affecting dopaminergicneuron specification in C. elegans. Nat Methods 5:869-872.
27. Egan CR, Chung MA, Allen FL, Heschl MF, Van Buskirk CL, McGhee JD. 1995. A gut-to-pharynx/tail switch in embryonic expression of the Caenorhabditis elegans ges-1 gene centers on two GATA sequences. Developmental Biology 170:397-419.
28. Ercan S, Lieb JD. 2009. C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation. Chromosome Res 17:215-227.
29. Ercan S, Giresi PG, Whittle CM, Zhang X, Green RD, Lieb JD. 2007. X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nat Genet 39:403-408. (Pubitemid 46331818)
30. Fan X, Chou DM, Struhl K. 2006. Activator-specific recruitment of Mediator in vivo. Nat Struct Mol Biol 13:117-120.
31. Fay DS, Yochem J. 2007. The SynMuv genes of Caenorhabditis elegans in vulval development and beyond. Dev Biol 306:1-9. (Pubitemid 46809718)
32. Fire A, Alcazar R, Tan F. 2006. Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans. Genetics 173:1259-1273. (Pubitemid 44127633)
33. Flibotte S, Edgley ML, Maydan J, Taylor J, Zapf R, Waterston R, Moerman DG. 2009. Rapid high resolution single nucleotide polymorphism-comparative genome hybridization mapping in Caenorhabditis elegans. Genetics 181:33-37.
34. Fox RM, Watson JD, Von Stetina SE, McDermott J, Brodigan TM, Fukushige T, Krause M, Miller DM, 3rd. 2007. The embryonic muscle transcriptome of Caenorhabditis elegans. Genome Biol 8:R188.
35. Fuda NJ, Ardehali MB, Lis JT. 2009. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461:186-192.
36. Fukushige T, Brodigan TM, Schriefer LA, Waterston RH, Krause M. 2006. Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development. Genes Dev 20:3395-3406. (Pubitemid 44969158)
37. Gaudet J, Mango SE. 2002. Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295:821-825. (Pubitemid 34118356)
38. Ghai V, Gaudet J. 2008. The CSL transcription factor LAG-1 directly represses hlh-6 expression in C. elegans. Dev Biol 322:334-344.
39. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. 2007. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17:877-885. (Pubitemid 46919722)
40. Grant B, Zhang Y, Paupard MC, Lin SX, Hall DH, Hirsh D. 2001. Evidence that RME-1, a conserved C. elegans EH-domain protein, functions in endocytic recycling. Nat Cell Biol 3:573-579. (Pubitemid 32536854)
41. Gu SG, Fire A. 2009. Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning. Chromosoma.
42. Guven-Ozkan T, Nishi Y, Robertson SM, Lin R. 2008. Global transcriptional repression in C. elegans germline precursors by regulated sequestration of TAF-4. Cell 135:149-160.
43. Haenni S, Sharpe HE, Gravato Nobre M, Zechner K, Browne C, Hodgkin J, Furger A. 2009. Regulation of transcription termination in the nematode Caenorhabditis elegans. Nucleic Acids Res 37:6723-6736.
44. Hahn-Windgassen A, Van Gilst MR. 2009. The Caenorhabditis elegans HNF4alpha Homolog, NHR-31, mediates excretory tube growth and function through coordinate regulation of the vacuolar ATPase. PLoS Genet 5:e1000553.
45. Heger P, Marin B, Schierenberg E. 2009. Loss of the insulator protein CTCF during nematode evolution. BMC Mol Biol 10:84.
46. Henikoff S, Ahmad K. 2005. Assembly of variant histones into chromatin. Annu Rev Cell Dev Biol 21:133-153.
47. Hobert O. 2005. Specification of the nervous system. WormBook:1-19.
48. Hobert O. 2008. Regulatory logic of neuronal diversity: terminal selector genes and selector motifs. Proc Natl Acad Sci U S A 105:20067-20071.
49. Howard RM, Sundaram MV. 2002. C. elegans EOR-1/PLZF and EOR-2 positively regulate Ras and Wnt signaling and function redundantly with LIN-25 and the SUR-2 Mediator component. Genes Dev 16:1815-1827.
50. Inoue H, Hisamoto N, An JH, Oliveira RP, Nishida E, Blackwell TK, Matsumoto K. 2005. The C. elegans p38 MAPK pathway regulates nuclear localization of the transcription factor SKN-1 in oxidative stress response. Genes Dev 19:2278-2283.
51. Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G. 2009. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet 41:941-945.
52. Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. 2006. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res 16:1505-1516.
53. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. 2008. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 36:5221-5231.
54. Kalb JM, Lau KK, Goszczynski B, Fukushige T, Moons D, Okkema PG, McGhee JD. 1998. pha-4 is Ce-fkh-1, a fork head/HNF-3alpha,beta,gamma homolog that functions in organogenesis of the C. elegans pharynx. Development 125:2171-2180. (Pubitemid 28336379)
55. Kaltenbach L, Horner MA, Rothman JH, Mango SE. 2000. The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans embryogenesis. Mol Cell. 6:705-713.
56. Katz DJ, Edwards TM, Reinke V, Kelly WG. 2009. A C. elegans LSD1 demethylase contributes to germline immortality by reprogramming epigenetic memory. Cell 137:308-320.
57. Kauffman SA. 1987. Developmental logic and its evolution. Bioessays 6:82-87.
58. Kauffman SA. 1993. The origins of order. Self-organization and selection in evolution. Oxford University Press.
59. Kohara Y. 2001a. NEXTDB: the nematode expression pattern database. http://nematode.lab.nig.ac.jp/db2/index.php.
60. Kohara Y. 2001b. [Systematic analysis of gene expression of the C. elegans genome]. Tanpakushitsu Kakusan Koso 46:2425-2431.
61. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. 2009. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41:376-381.
62. Kornberg RD. 2007. The molecular basis of eukaryotic transcription. Proc Natl Acad Sci U S A 104:12955-12961.
63. Kornberg RD, Lorch Y. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285-294.
64. Kornberg RD, Thomas JO. 1974. Chromatin structure; oligomers of the histones. Science 184:865-868.
65. Kouzarides T. 2007. Chromatin modifications and their function. Cell 128:693-705.
66. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. 2009. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 37:D755-D761.
67. Kuntz SG, Schwarz EM, DeModena JA, De Buysscher T, Trout D, Shizuya H, Sternberg PW, Wold BJ. 2008. Multigenome DNA sequence conservation identifies Hox cis-regulatory elements. Genome Res 18:1955-1968.
68. Kwon JY, Park JM, Gim BS, Han SJ, Lee J, Kim YJ. 1999. Caenorhabditis elegans mediator complexes are required for developmental-specific transcriptional activation. Proc Natl Acad Sci U S A 96:14990-14995.
69. Kwon JY, Kim-Ha J, Lee BJ, Lee J. 2001. The MED-7 transcriptional mediator encoded by let-49 is required for gonad and germ cell development in Caenorhabditis elegans. FEBS Lett 508:305-308.
70. Lei H, Liu J, Fukushige T, Fire A, Krause M. 2009. Caudal-like PAL-1 directly activates the bodywall muscle module regulator hlh-1 in C. elegans to initiate the embryonic muscle gene regulatory network. Development 136:1241-1249.
71. Li B, Carey M, Workman JL. 2007. The role of chromatin during transcription. Cell 128:707-719.
72. Lin KT, Broitman-Maduro G, Hung WW, Cervantes S, Maduro MF. 2009. Knockdown of SKN-1 and the Wnt effector TCF/POP-1 reveals differences in endomesoderm specification in C. briggsae as compared with C. elegans. Dev Biol 325:296-306.
73. MacMorris M, Broverman S, Greenspoon S, Lea K, Madej C, Blumenthal T, Spieth J. 1992. Regulation of vitellogenin gene expression in transgenic Caenorhabditis elegans: short sequences required for activation of the vit-2 promoter. Mol Cell Biol 12:1652-1662.
74. Maduro MF. 2008. Structure and evolution of the C. elegans embryonic endomesoderm network. Biochim Biophys Acta 1789:250-260.
75. Mah AK, Armstrong KR, Chew DS, Chu JS, Tu DK, Johnsen RC, Chen N, Chamberlin HM, Baillie DL. 2007. Transcriptional regulation of AQP-8, a Caenorhabditis elegans aquaporin exclusively expressed in the excretory system, by the POU homeobox transcription factor CEH-6. J Biol Chem 282:28074-28086.
76. Mallo GV, Kurz CL, Couillault C, Pujol N, Granjeaud S, Kohara Y, Ewbank JJ. 2002. Inducible antibacterial defense system in C. elegans. Curr Biol 12:1209-1214.
77. Mango SE. 2007. The C. elegans pharynx: a model for organogenesis. WormBook: 1-26.
78. Mango SE. 2009. The molecular basis of organ formation: insights from the C. elegans foregut. Annu Rev Cell Dev Biol 25:597-628.
79. Marshall SD, McGhee JD. 2001. Coordination of ges-1 expression between the Caenorhabditis pharynx and intestine. Dev Biol 239:350-363.
80. McGhee JD. 2007. The C. elegans intestine (March 27, 2007) WormBook, eg. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1. 133.1, http://www.wormbook.org.
81. McGhee JD, Wood WI, Dolan M, Engel JD, Felsenfeld G. 1981. A 200 base pair region at the 50 end of the chicken adult beta-globin gene is accessible to nuclease digestion. Cell 27:45-55.
82. McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJ, Moerman DG, Robertson AG. 2007. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol 302:627-645.
83. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, Khattra J, Hirst M, Jones SJ, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, Kalb JM. 2009. ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol 327:551-565.
84. Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR. 2009. DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324:407-410.
85. Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM III, Baillie DL, Holt RA, Jones SJ, Marra MA, Moerman DG. 2009. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet 5:e1000537.
86. Meyer BJ. 2005. X-Chromosome dosage compensation. WormBook:1-14.
87. Moerman DG, Barstead RJ. 2008. Towards a mutation in every gene in Caenorhabditis elegans. Brief Funct Genomic Proteomic 7:195-204.
88. Moghal N, Sternberg PW. 2003. A component of the transcriptional mediator complex inhibits RAS-dependent vulval fate specification in C. elegans. Development 130:57-69. (Pubitemid 36113943)
89. Moilanen LH, Fukushige T, Freedman JH. 1999. Regulation of metallothionein gene transcription. Identification of upstream regulatory elements and transcription factors responsible for cell-specific expression of the metallothionein genes from Caenorhabditis elegans. J Biol Chem 274:29655-29665. (Pubitemid 29483332)
90. Morck C, Rauthan M, Wagberg F, Pilon M. 2004. pha-2 encodes the C. elegans ortholog of the homeodomain protein HEX and is required for the formation of the pharyngeal isthmus. Dev Biol 272:403-418. (Pubitemid 38992316)
91. Murray JI, Bao Z, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, Waterston RH. 2008. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat Methods 5:703-709.
92. Nelson CE, Hersh BM, Carroll SB. 2004. The regulatory content of intergenic DNA shapes genome architecture. Genome Biol 5:R25.
93. Neves A, English K, Priess JR. 2007. Notch-GATA synergy promotes endoderm- specific expression of ref-1 in C. elegans. Development 134:4459-4468.
94. Novick A, Weiner M. 1957. Enzyme induction as an all-or-none phenomenon. Proc Natl Acad Sci U S A 43:553-566.
95. O'Meara MM, Bigelow H, Flibotte S, Etchberger JF, Moerman DG, Hobert O. 2009. Cis-regulatory mutations in the Caenorhabditis elegans homeobox gene locus cog-1 affect neuronal development. Genetics 181:1679-1686.
96. Oh SW, Mukhopadhyay A, Dixit BL, Raha T, Green MR, Tissenbaum HA. 2006. Identification of direct DAF-16 targets controlling longevity, metabolism and diapause by chromatin immunoprecipitation. Nat Genet 38:251-257. (Pubitemid 43177243)
97. Okkema PG, Fire A. 1994. The Caenorhabditis elegans NK-2 class homeoprotein CEH-22 is involved in combinatorial activation of gene expression in pharyngeal muscle. Development 120:2175-2186. (Pubitemid 24232285)
98. Okkema PG, Krause M. 2005. Transcriptional regulation. WormBook:1-40.
99. Ooi SL, Priess JR, Henikoff S. 2006. Histone H3.3 variant dynamics in the germline of Caenorhabditis elegans. PLoS Genet 2:e97. (Pubitemid 43998841)
100. Ooi SL, Henikoff JG, Henikoff S. 2009. A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans. Nucleic Acids Res [Epub ahead of print].
101. Owraghi M, Broitman-Maduro G, Luu T, Roberson H, Maduro MF. 2009. Roles of the Wnt effector POP-1/TCF in the C. elegans endomesoderm specification gene network. Dev Biol.
102. Panne D. 2008. The enhanceosome. Curr Opin Struct Biol 18:236-242.
103. Pauli F, Liu Y, Kim YA, Chen PJ, Kim SK. 2006. Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans. Development 133:287-295. (Pubitemid 43210717)
104. Raharjo I, Gaudet J. 2007. Gland-specific expression of C. elegans hlh-6 requires the combinatorial action of three distinct promoter elements. Dev Biol 302:295-308. (Pubitemid 46096942)
105. Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ. 2005. A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol 6:R110. (Pubitemid 43871842)
106. Romney SJ, Thacker C, Leibold EA. 2008. An iron enhancer element in the FTN-1 gene directs iron-dependent expression in Caenorhabditis elegans intestine. J Biol Chem 283:716-725.
107. Roy PJ, Stuart JM, Lund J, Kim SK. 2002. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418:975-979. (Pubitemid 34976032)
108. Roy Chowdhuri S, Crum T, Woollard A, Aslam S, Okkema PG. 2006. The T-box factor TBX-2 and the SUMO conjugating enzyme UBC-9 are required for ABa-derived pharyngeal muscle in C. elegans. Dev Biol 295:664-677. (Pubitemid 43927702)
109. Schaner CE, Kelly WG. 2006. Germline chromatin. WormBook:1-14.
110. Schmitz C, Kinge P, Hutter H. 2007. Axon guidance genes identified in a largescale RNAi screen using the RNAihypersensitive Caenorhabditis elegans strain nre-1(hd20) lin-15b(hd126). Proc Natl Acad Sci U S A 104:834-839. (Pubitemid 46154697)
111. Segal E, Widom J. 2009. What controls nucleosome positions? Trends Genet 25:335-343.
112. Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. 2008. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451:535-540. (Pubitemid 351186263)
113. Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I. 2008. Comparing platforms for C. elegans mutant identification using highthroughput whole-genome sequencing. PLoS ONE 3:e4012.
114. Shi Y, Mello C. 1998. A CBP/p300 homolog specifies multiple differentiation pathways in Caenorhabditis elegans. Genes Dev 12:943-955. (Pubitemid 28204602)
115. Shim EY, Walker AK, Shi Y, Blackwell TK. 2002. CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo. Genes Dev 16:2135-2146.
116. Singh N, Han M. 1995. sur-2, a novel gene, functions late in the let-60 rasmediated signaling pathway during Caenorhabditis elegans vulval induction. Genes Dev 9:2251-2265.
117. Smit RB, Schnabel R, Gaudet J. 2008. The HLH-6 transcription factor regulates C. elegans pharyngeal gland development and function. PLoS Genet 4:e1000222.
118. Smith PA, Mango SE. 2006. Role of T-box gene tbx-2 for anterior foregut muscle development in C. elegans. Dev Biol 302:25-39.
119. Strome S. 2005. Specification of the germ line. WormBook:1-10.
120. Sulston JE, Schierenberg E, White JG, Thomson JN. 1983. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol 100:64-119.
121. Taubert S, Van Gilst MR, Hansen M, Yamamoto KR. 2006. A Mediator subunit, MDT-15, integrates regulation of fatty acid metabolism by NHR-49-dependent and -independent pathways in C. elegans. Genes Dev 20:1137-1149.
122. Taubert S, Hansen M, Van Gilst MR, Cooper SB, Yamamoto KR. 2008. The Mediator subunit MDT-15 confers metabolic adaptation to ingested material. PLoS Genet 4:e1000021. (Pubitemid 351328531)
123. Thatcher JD, Fernandez AP, Beaster-Jones L, Haun C, Okkema PG. 2001. The Caenorhabditis elegans peb-1 gene encodes a novel DNA-binding protein involved in morphogenesis of the pharynx, vulva, and hindgut. Dev Biol 229:480-493. (Pubitemid 32108707)
124. Uchida O, Nakano H, Koga M, Ohshima Y. 2003. The C. elegans che-1 gene encodes a zinc finger transcription factor required for specification of the ASE chemosensory neurons. Development 130:1215-1224. (Pubitemid 36410771)
125. Updike DL, Mango SE. 2006. Temporal regulation of foregut development by HTZ-1/H2A.Z and PHA-4/FoxA. PLoS Genet 2:e161.
126. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051-1063. (Pubitemid 351931156)
127. Von Stetina SE, Watson JD, Fox RM, Olszewski KL, Spencer WC, Roy PJ, Miller DM III. 2007. Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. Genome Biol 8:R135.
128. Wagmaister JA, Miley GR, Morris CA, Gleason JE, Miller LM, Kornfeld K, Eisenmann DM. 2006. Identification of cis-regulatory elements from the C. elegans Hox gene lin-39 required for embryonic expression and for regulation by the transcription factors LIN-1, LIN-31 and LIN-39. Dev Biol 297:550-565. (Pubitemid 44353469)
129. Walker AK, Blackwell TK. 2003. A broad but restricted requirement for TAF-5 (human TAFII100) for embryonic transcription in Caenorhabditis elegans. J Biol Chem 278:6181-6186.
130. Walker AK, Rothman JH, Shi Y, Blackwell TK. 2001. Distinct requirements for C.elegans TAF(II)s in early embryonic transcription. EMBO J 20:5269-5279. (Pubitemid 32910921)
131. Walker AK, Shi Y, Blackwell TK. 2004. An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription. J Biol Chem 279:15339-15347. (Pubitemid 38618932)
132. Wang JC, Walker A, Blackwell TK, Yamamoto KR. 2004. The Caenorhabditis elegans ortholog of TRAP240, CeTRAP240/let-19, selectively modulates gene expression and is essential for embryogenesis. J Biol Chem 279:29270-29277. (Pubitemid 38915803)
133. Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. 2009. Genomewide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138:1019-1031.
134. Wenick AS, Hobert O. 2004. Genomic cisregulatory architecture and trans-acting regulators of a single interneuronspecific gene battery in C. elegans. Dev Cell 6:757-770. (Pubitemid 38745411)
135. Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD. 2008. The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genet 4:e1000187.
136. Whittle CM, Lazakovitch E, Gronostajski RM, Lieb JD. 2009. DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I. Proc Natl Acad Sci U S A 106:12049-12054.
137. Xia D, Huang X, Zhang H. 2009. The temporally regulated transcription factor sel-7 controls developmental timing in C. elegans. Dev Biol 332:246-257.
138. Yanai I, Hunter CP. 2009. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Res.
139. Yang F, Vought BW, Satterlee JS, Walker AK, Jim Sun ZY, Watts JL, DeBeaumont R, Saito RM, Hyberts SG, Yang S, Macol C, Iyer L, Tjian R, van den Heuvel S, Hart AC, Wagner G, Naar AM. 2006. An ARC/mediator subunit required for SREBP control of cholesterol and lipid homeostasis. Nature 442:700-704.
140. Yi W, Zarkower D. 1999. Similarity of DNA binding and transcriptional regulation by Caenorhabditis elegans MAB-3 and Drosophila melanogaster DSX suggests conservation of sex determining mechanisms. Development 126:873-881.
141. Yoda A, Kouike H, Okano H, Sawa H. 2005. Components of the transcriptional Mediator complex are required for asymmetric cell division in C. elegans. Development 132:1885-1893.
142. Yuzyuk T, Fakhouri TH, Kiefer J, Mango SE. 2009. The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos. Dev Cell 16:699-710.
143. Zhao Z, Fang L, Chen N, Johnsen RC, Stein L, Baillie DL. 2005. Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans. J Biol Chem 280:38787-38794.
144. Zhu J, Hill RJ, Heid PJ, Fukuyama M, Sugimoto A, Priess JR, Rothman JH. 1997. end-1 encodes an apparent GATA factor that specifies the endoderm precursor in Caenorhabditis elegans embryos. Genes Dev 11:2883-2896.
145. Zhu X, Wiren M, Sinha I, Rasmussen NN, Linder T, Holmberg S, Ekwall K, Gustafsson CM. 2006. Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions. Mol Cell 22:169-178.