Transcriptional Enhancers in Ascidian Development

Current Topics in Developmental Biology

Volumn 98, Issue , 2012, Pages 147-172

  Wang, Wei ^a   Christiaen, Lionel ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

Chromatin; Cis regulatory module; Gene Regulatory Network; Genomic; Muscle; Operon; SL trans splicing; Transgenic; Tunicates

Indexed keywords

EID: 84863014826     PISSN: 00702153     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-386499-4.00006-9     Document Type: Chapter

References (131)

1. Ahn S.H., Kim M., Buratowski S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing. Mol. Cell 2004, 13(1):67-76.
2. Anno C., Satou A., Fujiwara S. Transcriptional regulation of ZicL in the Ciona intestinalis embryo. Dev. Genes Evol. 2006, 216(10):597-605.
3. Arnone M.I., Davidson E.H. The hardwiring of development: Organization and function of genomic regulatory systems. Development 1997, 124(10):1851-1864.
4. Auger H., Lamy C., Haeussler M., Khoueiry P., Lemaire P., Joly J.S. Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5. Dev. Biol. 2009, 329(2):364-373.
5. Awazu S., Sasaki A., Matsuoka T., Satoh N., Sasakura Y. An enhancer trap in the ascidian Ciona intestinalis identifies enhancers of its Musashi orthologous gene. Dev. Biol. 2004, 275(2):459-472.
6. Awazu S., Matsuoka T., Inaba K., Satoh N., Sasakura Y. High-throughput enhancer trap by remobilization of transposon Minos in Ciona intestinalis. Genesis 2007, 45(5):307-317.
7. Beh J., Shi W., Levine M., Davidson B., Christiaen L. FoxF is essential for FGF-induced migration of heart progenitor cells in the ascidian Ciona intestinalis. Development 2007, 134(18):3297-3305.
8. Belteki G., Gertsenstein M., Ow D.W., Nagy A. Site-specific cassette exchange and germline transmission with mouse ES cells expressing phiC31 integrase. Nat. Biotechnol. 2003, 21(3):321-324.
9. Berger S.L. The complex language of chromatin regulation during transcription. Nature 2007, 447(7143):407-412.
10. Bertrand V., Hudson C., Caillol D., Popovici C., Lemaire P. Neural tissue in ascidian embryos is induced by FGF9/16/20, acting via a combination of maternal GATA and Ets transcription factors. Cell 2003, 115(5):615-627.
11. Boffelli D., Weer C.V., Weng L., Lewis K.D., Shoukry M.I., Pachter L., Keys D.N., Rubin E.M. Intraspecies sequence comparisons for annotating genomes. Genome Res. 2004, 14(12):2406-2411.
12. Brookes E., Pombo A. Modifications of RNA polymerase II are pivotal in regulating gene expression states. EMBO Rep. 2009, 10(11):1213-1219.
13. Brown C.D., Johnson D.S., Sidow A. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 2007, 317(5844):1557-1560.
14. Byrd J., Lambert C.C. Mechanism of the block to hybridization and selfing between the sympatric ascidians Ciona intestinalis and Ciona savignyi. Mol. Reprod. Dev. 2000, 56(4):541.
15. Chiba S., Jiang D., Satoh N., Smith W.C. Brachyury null mutant-induced defects in juvenile ascidian endodermal organs. Development 2009, 136(1):35-39.
16. Christiaen L., Bourrat F., Joly J.S. A modular cis-regulatory system controls isoform-specific pitx expression in ascidian stomodaeum. Dev. Biol. 2005, 277(2):557-566.
17. Christiaen L., Davidson B., Kawashima T., Powell W., Nolla H., Vranizan K., Levine M. The transcription/migration interface in heart precursors of Ciona intestinalis. Science 2008, 320(5881):1349-1352.
18. Christiaen L., Stolfi A., Davidson B., Levine M. Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp. Dev. Biol. 2009, 328(2):552-560.
19. Christiaen L., Wagner E., Shi W., Levine M. Electroporation of transgenic DNAs in the sea squirt Ciona. Cold Spring Harb. Protoc. 2009, 2009(12). pdb.prot5345.
20. Corbo J.C., Levine M., Zeller R.W. Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development 1997, 124(3):589-602.
21. Corbo J.C., Di Gregorio A., Levine M. The ascidian as a model organism in developmental and evolutionary biology. Cell 2001, 106(5):535-538.
22. Davidson E. The Regulatory Genome 2006, Academic Press, St. Louis.
23. Davidson E.H. Network design principles from the sea urchin embryo. Curr. Opin. Genet. Dev. 2009, 19(6):535-540.
24. Davidson B., Levine M. Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis. Proc. Natl. Acad. Sci. USA 2003, 100(20):11469-11473.
25. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., Minokawa T., Amore G., Hinman V., Arenas-Mena C., et al. A genomic regulatory network for development. Science 2002, 295(5560):1669-1678.
26. Davidson B., Shi W., Levine M. Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis. Development 2005, 132(21):4811-4818.
27. Davidson B., Shi W., Beh J., Christiaen L., Levine M. FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis. Genes Dev. 2006, 20(19):2728-2738.
28. Dehal P., Satou Y., Campbell R.K., Chapman J., Degnan B., De Tomaso A., Davidson B., Di Gregorio A., Gelpke M., Goodstein D.M., et al. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 2002, 298(5601):2157-2167.
29. Delsuc F., Brinkmann H., Chourrout D., Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006, 439(7079):965-968.
30. Deno T., Nishida H., Satoh N. Autonomous muscle cell differentiation in partial ascidian embryos according to the newly verified cell lineages. Dev. Biol. 1984, 104(2):322-328.
31. Deschet K., Nakatani Y., Smith W.C. Generation of Ci-Brachyury-GFP stable transgenic lines in the ascidian Ciona savignyi. Genesis 2003, 35(4):248-259.
32. Di Gregorio A., Levine M. Regulation of Ci-tropomyosin-like, a Brachyury target gene in the ascidian, Ciona intestinalis. Development 1999, 126(24):5599-5609.
33. Flames N., Hobert O. Gene regulatory logic of dopamine neuron differentiation. Nature 2009, 458(7240):885-889.
34. Frazer K.A., Pachter L., Poliakov A., Rubin E.M., Dubchak I. VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 2004, 32(Web Server issue):W273-W279.
35. Fujioka M., Emi-Sarker Y., Yusibova G.L., Goto T., Jaynes J.B. Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients. Development 1999, 126(11):2527-2538.
36. Ganot P., Kallesoe T., Reinhardt R., Chourrout D., Thompson E.M. Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Mol. Cell. Biol. 2004, 24(17):7795-7805.
37. Geyer P.K., Vitalini M.W., Wallrath L.L. Nuclear organization: Taking a position on gene expression. Curr. Opin. Cell Biol. 2011, 23(3):354-359.
38. Ghosh D., Seydoux G. Inhibition of transcription by the Caenorhabditis elegans germline protein PIE-1: Genetic evidence for distinct mechanisms targeting initiation and elongation. Genetics 2008, 178(1):235-243.
39. Groth A.C., Fish M., Nusse R., Calos M.P. Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics 2004, 166(4):1775-1782.
40. Haeussler M., Joly J.S. When needles look like hay: How to find tissue-specific enhancers in model organism genomes. Dev. Biol. 2011, 350(2):239-254.
41. Haeussler M., Jaszczyszyn Y., Christiaen L., Joly J.S. A cis-regulatory signature for chordate anterior neuroectodermal genes. PLoS Genet. 2010, 6(4):e1000912.
42. Hanyu-Nakamura K., Sonobe-Nojima H., Tanigawa A., Lasko P., Nakamura A. Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells. Nature 2008, 451(7179):730-733.
43. Harafuji N., Keys D.N., Levine M. Genome-wide identification of tissue-specific enhancers in the Ciona tadpole. Proc. Natl. Acad. Sci. USA 2002, 99(10):6802-6805.
44. Hastings K.E. SL trans-splicing: Easy come or easy go?. Trends Genet. 2005, 21(4):240-247.
45. Hikosaka A., Kusakabe T., Satoh N. Short upstream sequences associated with the muscle-specific expression of an actin gene in ascidian embryos. Dev. Biol. 1994, 166(2):763-769.
46. Hill M.M., Broman K.W., Stupka E., Smith W.C., Jiang D., Sidow A. The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res. 2008, 18(8):1369-1379.
47. Hino K., Satou Y., Yagi K., Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. VI. Genes for Wnt, TGFbeta, Hedgehog and JAK/STAT signaling pathways. Dev. Genes Evol. 2003, 213(5-6):264-272.
48. Hirano T., Nishida H. Developmental fates of larval tissues after metamorphosis in ascidian Halocynthia roretzi. I. Origin of mesodermal tissues of the juvenile. Dev. Biol. 1997, 192(2):199-210.
49. Hozumi A., Kawai N., Yoshida R., Ogura Y., Ohta N., Satake H., Satoh N., Sasakura Y. Efficient transposition of a single Minos transposon copy in the genome of the ascidian Ciona intestinalis with a transgenic line expressing transposase in eggs. Dev. Dyn. 2010, 239(4):1076-1088.
50. Hudson C., Lemaire P. Induction of anterior neural fates in the ascidian Ciona intestinalis. Mech. Dev. 2001, 100(2):189-203.
51. Imai K.S., Satou Y., Satoh N. Multiple functions of a Zic-like gene in the differentiation of notochord, central nervous system and muscle in Ciona savignyi embryos. Development 2002, 129(11):2723-2732.
52. Imai K.S., Hino K., Yagi K., Satoh N., Satou Y. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: Towards a comprehensive understanding of gene networks. Development 2004, 131(16):4047-4058.
53. Imai K.S., Levine M., Satoh N., Satou Y. Regulatory blueprint for a chordate embryo. Science 2006, 312(5777):1183-1187.
54. Imai K.S., Stolfi A., Levine M., Satou Y. Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system. Development 2009, 136(2):285-293.
55. Johnson D.S., Davidson B., Brown C.D., Smith W.C., Sidow A. Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. Genome Res. 2004, 14(12):2448-2456.
56. Johnson D.S., Zhou Q., Yagi K., Satoh N., Wong W., Sidow A. De novo discovery of a tissue-specific gene regulatory module in a chordate. Genome Res. 2005, 15(10):1315-1324.
57. Keys D.N., Lee B.I., Di Gregorio A., Harafuji N., Detter J.C., Wang M., Kahsai O., Ahn S., Zhang C., Doyle S.A., et al. A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proc. Natl. Acad. Sci. USA 2005, 102(3):679-683.
58. Khare P., Mortimer S.I., Cleto C.L., Okamura K., Suzuki Y., Kusakabe T., Nakai K., Meedel T.H., Hastings K.E. Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene. Nucleic Acids Res. 2011, 39(7):2638-2648.
59. Khoueiry P., Rothbacher U., Ohtsuka Y., Daian F., Frangulian E., Roure A., Dubchak I., Lemaire P. A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr. Biol. 2010, 20(9):792-802.
60. Kubo A., Suzuki N., Yuan X.Y., Nakai K., Satoh N., Imai K.S., Satou Y. Genomic cis-regulatory networks in the early Ciona intestinalis embryo. Development 2010, 137(10):1613-1623.
61. Kugler J.E., Gazdoiu S., Oda-Ishii I., Passamaneck Y.J., Erives A.J., Di Gregorio A. Temporal regulation of the muscle gene cascade by Macho1 and Tbx6 transcription factors in Ciona intestinalis. J. Cell Sci. 2010, 123(Pt 14):2453-2463.
62. Kumano G., Takatori N., Negishi T., Takada T., Nishida H. A maternal factor unique to ascidians silences the germline via binding to P-TEFb and RNAP II regulation. Curr. Biol. 2011, 21(15):1308-1313.
63. Kusakabe T., Hikosaka A., Satoh N. Coexpression and promoter function in two muscle actin gene complexes of different structural organization in the ascidian Halocynthia roretzi. Dev. Biol. 1995, 169(2):461-472.
64. Kusakabe T., Yoshida R., Kawakami I., Kusakabe R., Mochizuki Y., Yamada L., Shin-i T., Kohara Y., Satoh N., Tsuda M., et al. Gene expression profiles in tadpole larvae of Ciona intestinalis. Dev. Biol. 2002, 242(2):188-203.
65. Kusakabe T., Yoshida R., Ikeda Y., Tsuda M. Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona. Dev. Biol. 2004, 276(2):563-580.
66. Lamy C., Rothbacher U., Caillol D., Lemaire P. Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5. Development 2006, 133(15):2835-2844.
67. Levine M. Transcriptional enhancers in animal development and evolution. Curr. Biol. 2010, 20(17):R754-R763.
68. Levine M., Davidson E.H. Gene regulatory networks for development. Proc. Natl. Acad. Sci. USA 2005, 102(14):4936-4942.
69. Longabaugh W.J., Davidson E.H., Bolouri H. Computational representation of developmental genetic regulatory networks. Dev. Biol. 2005, 283(1):1-16.
70. Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., et al. The sequence and analysis of duplication-rich human chromosome 16. Nature 2004, 432(7020):988-994.
71. Matsumoto J., Dewar K., Wasserscheid J., Wiley G.B., Macmil S.L., Roe B.A., Zeller R.W., Satou Y., Hastings K.E. High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates. Genome Res. 2010, 20(5):636-645.
72. Matsuoka T., Awazu S., Satoh N., Sasakura Y. Minos transposon causes germline transgenesis of the ascidian Ciona savignyi. Dev. Growth Differ. 2004, 46(3):249-255.
73. Matsuoka T., Awazu S., Shoguchi E., Satoh N., Sasakura Y. Germline transgenesis of the ascidian Ciona intestinalis by electroporation. Genesis 2005, 41(2):67-72.
74. Meedel T.H., Whittaker J.R. Lineage segregation and developmental autonomy in expression of functional muscle acetylcholinesterase mRNA in the ascidian embryo. Dev. Biol. 1984, 105(2):479-487.
75. Meedel T.H., Chang P., Yasuo H. Muscle development in Ciona intestinalis requires the b-HLH myogenic regulatory factor gene Ci-MRF. Dev. Biol. 2007, 302(1):333-344.
76. Miwata K., Chiba T., Horii R., Yamada L., Kubo A., Miyamura D., Satoh N., Satou Y. Systematic analysis of embryonic expression profiles of zinc finger genes in Ciona intestinalis. Dev. Biol. 2006, 292(2):546-554.
77. Nishida H. Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. III. Up to the tissue restricted stage. Dev. Biol. 1987, 121(2):526-541.
78. Nishida H., Satoh N. Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. I. Up to the eight-cell stage. Dev. Biol. 1983, 99(2):382-394.
79. Nishida H., Satoh N. Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. II. The 16- and 32-cell stages. Dev. Biol. 1985, 110(2):440-454.
80. Nishida H., Sawada K. macho-1 encodes a localized mRNA in ascidian eggs that specifies muscle fate during embryogenesis. Nature 2001, 409(6821):724-729.
81. Oda-Ishii I., Bertrand V., Matsuo I., Lemaire P., Saiga H. Making very similar embryos with divergent genomes: Conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis. Development 2005, 132(7):1663-1674.
82. Pennacchio L.A., Ahituv N., Moses A.M., Prabhakar S., Nobrega M.A., Shoukry M., Minovitsky S., Dubchak I., Holt A., Lewis K.D., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444(7118):499-502.
83. Reese M.G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 2001, 26(1):51-56.
84. Sardet C., Dru P., Prodon F. Maternal determinants and mRNAs in the cortex of ascidian oocytes, zygotes and embryos. Biol. Cell 2005, 97(1):35-49.
85. Sasakura Y., Awazu S., Chiba S., Satoh N. Germ-line transgenesis of the Tc1/mariner superfamily transposon Minos in Ciona intestinalis. Proc. Natl. Acad. Sci. USA 2003, 100(13):7726-7730.
86. Sasakura Y., Konno A., Mizuno K., Satoh N., Inaba K. Enhancer detection in the ascidian Ciona intestinalis with transposase-expressing lines of Minos. Dev. Dyn. 2008, 237(1):39-50.
87. Sasakura Y., Suzuki M.M., Hozumi A., Inaba K., Satoh N. Maternal factor-mediated epigenetic gene silencing in the ascidian Ciona intestinalis. Mol. Genet. Genomics 2010, 283(1):99-110.
88. Satoh N. Developmental Biology of Ascidians 1994, Cambridge University Press, England.
89. Satou Y., Imai K.S., Satoh N. Early embryonic expression of a LIM-homeobox gene Cs-lhx3 is downstream of beta-catenin and responsible for the endoderm differentiation in Ciona savignyi embryos. Development 2001, 128(18):3559-3570.
90. Satou Y., Takatori N., Yamada L., Mochizuki Y., Hamaguchi M., Ishikawa H., Chiba S., Imai K., Kano S., Murakami S.D., et al. Gene expression profiles in Ciona intestinalis tailbud embryos. Development 2001, 128(15):2893-2904.
91. Satou Y., Takatori N., Fujiwara S., Nishikata T., Saiga H., Kusakabe T., Shin-i T., Kohara Y., Satoh N. Ciona intestinalis cDNA projects: Expressed sequence tag analyses and gene expression profiles during embryogenesis. Gene 2002, 287(1-2):83-96.
92. Satou Y., Yagi K., Imai K.S., Yamada L., Nishida H., Satoh N. macho-1-related genes in Ciona embryos. Dev. Genes Evol. 2002, 212(2):87-92.
93. Satou Y., Yamada L., Mochizuki Y., Takatori N., Kawashima T., Sasaki A., Hamaguchi M., Awazu S., Yagi K., Sasakura Y., et al. A cDNA resource from the basal chordate Ciona intestinalis. Genesis 2002, 33(4):153-154.
94. Satou Y., Imai K.S., Levine M., Kohara Y., Rokhsar D., Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev. Genes Evol. 2003, 213(5-6):213-221.
95. Satou Y., Sasakura Y., Yamada L., Imai K.S., Satoh N., Degnan B. A genomewide survey of developmentally relevant genes in Ciona intestinalis. V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway. Dev. Genes Evol. 2003, 213(5-6):254-263.
96. Satou Y., Imai K.S., Satoh N. The ascidian Mesp gene specifies heart precursor cells. Development 2004, 131(11):2533-2541.
97. Satou Y., Kawashima T., Shoguchi E., Nakayama A., Satoh N. An integrated database of the ascidian, Ciona intestinalis: Towards functional genomics. Zoolog. Sci. 2005, 22(8):837-843.
98. Satou Y., Hamaguchi M., Takeuchi K., Hastings K.E., Satoh N. Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis. Nucleic Acids Res. 2006, 34(11):3378-3388.
99. Satou Y., Mineta K., Ogasawara M., Sasakura Y., Shoguchi E., Ueno K., Yamada L., Matsumoto J., Wasserscheid J., Dewar K., et al. Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: New insight into intron and operon populations. Genome Biol. 2008, 9(10):R152.
100. Sawada K., Fukushima Y., Nishida H. Macho-1 functions as transcriptional activator for muscle formation in embryos of the ascidian Halocynthia roretzi. Gene Expr. Patterns 2005, 5(3):429-437.
101. Seydoux G., Dunn M.A. Transcriptionally repressed germ cells lack a subpopulation of phosphorylated RNA polymerase II in early embryos of Caenorhabditis elegans and Drosophila melanogaster. Development 1997, 124(11):2191-2201.
102. Shirae-Kurabayashi M., Matsuda K., Nakamura A. Ci-Pem-1 localizes to the nucleus and represses somatic gene transcription in the germline of Ciona intestinalis embryos. Development 2011, 138(14):2871-2881.
103. Sierro N., Kusakabe T., Park K.J., Yamashita R., Kinoshita K., Nakai K. DBTGR: A database of tunicate promoters and their regulatory elements. Nucleic Acids Res. 2006, 34(Database issue):D552-D555.
104. Simmen M.W., Leitgeb S., Charlton J., Jones S.J., Harris B.R., Clark V.H., Bird A. Nonmethylated transposable elements and methylated genes in a chordate genome. Science 1999, 283(5405):1164-1167.
105. Small K.S., Brudno M., Hill M.M., Sidow A. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol. 2007, 8(3):R41.
106. Spada F., Koch J., Sadoni N., Mitchell N., Ganot P., De Boni U., Zink D., Thompson E.M. Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura. Biol. Cell 2007, 99(5):273-287.
107. Squarzoni P., Parveen F., Zanetti L., Ristoratore F., Spagnuolo A. FGF/MAPK/Ets signaling renders pigment cell precursors competent to respond to Wnt signal by directly controlling Ci-Tcf transcription. Development 2011, 138(7):1421-1432.
108. Stathopoulos A., Levine M. Genomic regulatory networks and animal development. Dev. Cell 2005, 9(4):449-462.
109. Stolfi A., Gainous T.B., Young J.J., Mori A., Levine M., Christiaen L. Early chordate origins of the vertebrate second heart field. Science 2010, 329(5991):565-568.
110. Suzuki M.M., Kerr A.R., De Sousa D., Bird A. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res. 2007, 17(5):625-631.
111. Tagle D.A., Koop B.F., Goodman M., Slightom J.L., Hess D.L., Jones R.T. Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 1988, 203(2):439-455.
112. Takahashi H., Hotta K., Erives A., Di Gregorio A., Zeller R.W., Levine M., Satoh N. Brachyury downstream notochord differentiation in the ascidian embryo. Genes Dev. 1999, 13(12):1519-1523.
113. Takatori N., Hotta K., Mochizuki Y., Satoh G., Mitani Y., Satoh N., Satou Y., Takahashi H. T-box genes in the ascidian Ciona intestinalis: Characterization of cDNAs and spatial expression. Dev. Dyn. 2004, 230(4):743-753.
114. Tassy O., Dauga D., Daian F., Sobral D., Robin F., Khoueiry P., Salgado D., Fox V., Caillol D., Schiappa R., et al. The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program. Genome Res. 2010, 20(10):1459-1468.
115. Tweedie S., Charlton J., Clark V., Bird A. Methylation of genomes and genes at the invertebrate-vertebrate boundary. Mol. Cell. Biol. 1997, 17(3):1469-1475.
116. Vandenberghe A.E., Meedel T.H., Hastings K.E. mRNA 5'-leader trans-splicing in the chordates. Genes Dev. 2001, 15(3):294-303.
117. Vinson J.P., Jaffe D.B., O'Neill K., Karlsson E.K., Stange-Thomann N., Anderson S., Mesirov J.P., Satoh N., Satou Y., Nusbaum C., et al. Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi. Genome Res. 2005, 15(8):1127-1135.
118. Wada S., Katsuyama Y., Sato Y., Itoh C., Saiga H. Hroth an orthodenticle-related homeobox gene of the ascidian, Halocynthia roretzi: Its expression and putative roles in the axis formation during embryogenesis. Mech. Dev. 1996, 60(1):59-71.
119. Wada S., Tokuoka M., Shoguchi E., Kobayashi K., Di Gregorio A., Spagnuolo A., Branno M., Kohara Y., Rokhsar D., Levine M., et al. A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors. Dev. Genes Evol. 2003, 213(5-6):222-234.
120. Wang Y., Leung F.C. GC content increased at CpG flanking positions of fish genes compared with sea squirt orthologs as a mechanism for reducing impact of DNA methylation. PLoS One 2008, 3(11):e3612.
121. Wenick A.S., Hobert O. Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. Dev. Cell 2004, 6(6):757-770.
122. Yagi K., Satou Y., Mazet F., Shimeld S.M., Degnan B., Rokhsar D., Levine M., Kohara Y., Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFkappaB. Dev. Genes Evol. 2003, 213(5-6):235-244.
123. Yagi K., Satoh N., Satou Y. Identification of downstream genes of the ascidian muscle determinant gene Ci-macho1. Dev. Biol. 2004, 274(2):478-489.
124. Yagi K., Satou Y., Satoh N. A zinc finger transcription factor, ZicL, is a direct activator of Brachyury in the notochord specification of Ciona intestinalis. Development 2004, 131(6):1279-1288.
125. Yagi K., Takatori N., Satou Y., Satoh N. Ci-Tbx6b and Ci-Tbx6c are key mediators of the maternal effect gene Ci-macho1 in muscle cell differentiation in Ciona intestinalis embryos. Dev. Biol. 2005, 282(2):535-549.
126. Yamada L., Kobayashi K., Degnan B., Satoh N., Satou Y. A genomewide survey of developmentally relevant genes in Ciona intestinalis. IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail. Dev. Genes Evol. 2003, 213(5-6):245-253.
127. Yasuo H., Satoh N. Function of vertebrate T gene. Nature 1993, 364(6438):582-583.
128. Yeats B., Matsumoto J., Mortimer S.I., Shoguchi E., Satoh N., Hastings K.E. SL RNA genes of the ascidian tunicates Ciona intestinalis and Ciona savignyi. Zoolog. Sci. 2010, 27(2):171-180.
129. Yuasa H.J., Kawamura K., Yamamoto H., Takagi T. The structural organization of ascidian Halocynthia roretzi troponin I genes. J. Biochem. 2002, 132(1):135-141.
130. Zeller R.W. Computational analysis of Ciona intestinalis operons. Integr. Comp. Biol. 2010, 50(1):75-85.
131. Zinzen R.P., Girardot C., Gagneur J., Braun M., Furlong E.E. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 2009, 462(7269):65-70.