Evolutionary conservation of vertebrate notochord genes in the ascidian Ciona intestinalis

Genesis

Volumn 46, Issue 11, 2008, Pages 697-710

  Kugler, Jamie E ^a   Passamaneck, Yale J ^a   Feldman, Taya J ^a   Beh, Jeni ^b   Regnier, Todd W ^a   Di Gregorio, Anna ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b University of California Berkeley   (United States)

Author keywords

Ascidian; Brachyury; Chordate; Ciona; Evolution; Notochord

Indexed keywords

CARBONATE DEHYDRATASE III; COFILIN; ENTACTIN; FIBRONECTIN; FURIN; G PROTEIN COUPLED RECEPTOR; LAMININ ALPHA4; MESODERM INDUCTION EARLY RESPONSE 1; PROTEIN P48; SCLEROPROTEIN; SEMAPHORIN 3A; T BOX TRANSCRIPTION FACTOR; THROMBOSPONDIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; X BOX BINDING PROTEIN 1;

ARTICLE; ASCIDIACEA; CHORDATA; CIONA INTESTINALIS; CONTROLLED STUDY; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC CONSERVATION; NONHUMAN; NOTOCHORD; PREDICTION; PRIORITY JOURNAL; REGULATORY MECHANISM; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; VERTEBRATE;

ANIMALS; CIONA INTESTINALIS; EVOLUTION, MOLECULAR; FETAL PROTEINS; GENE EXPRESSION; NOTOCHORD; T-BOX DOMAIN PROTEINS; TRANSCRIPTION, GENETIC;

ASCIDIA; CHORDATA; CIONA; CIONA INTESTINALIS; VERTEBRATA;

EID: 63349112380     PISSN: 1526954X     EISSN: 1526968X     Source Type: Journal    
DOI: 10.1002/dvg.20403     Document Type: Article

References (55)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
2. Camón J, Degollada E, Verdú J. 1990. Ultrastructural aspects of the production of extracellular matrix components by the chick embryonic notochord in vitro. Acta Anat (Basel) 137:114-123.
3. Cantera R, Lüer K, Rusten TE, Barrio R, Kafatos FC, Technau GM. 2002. Mutations in spalt cause a severe but reversible neurodegenerative phenotype in the embryonic central nervous system of Drosophila melanogaster. Development 129:5577-5586.
4. Cleaver O, Krieg PA. 2001. Notochord patterning of the endoderm. Dev Biol 234:1-12.
5. Cloney RA. 1990. Urochordata: Ascidiacea. In: Adiyodi KG, Adiyodi RG, editors. Reproductive Biology of Invertebrates. New Delhi: Oxford and IBH. pp 391-451.
6. Corbo JC, Levine M, Zeller RW. 1997. Characterization of a notochordspecific enhancer from the Brachyury promoter region of the ascidian Ciona intestinalis. Development 124:589-602.
7. Coutinho P, Parsons MJ, Thomas KA, Hirst EM, Saúde L, Campos I, Williams PH, Stemple DL. 2004. Differential requirements for COPI transport during vertebrate early development. Dev Cell 7:547-558.
8. Di Gregorio A, Corbo JC, Levine M. 2001. The regulation of forkhead/ HNF-3β expression in the Ciona embryo. Dev Biol 229:31-43.
9. Di Gregorio A, Harland RM, Levine M, Casey ES. 2002. Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle. Dev Biol 244:385-395.
10. Di Gregorio A, Levine M. 1999. Regulation of Ci-tropomyosin-like, a Brachyury target gene in the ascidian, Ciona intestinalis. Development 126:5599-5609.
11. Di Gregorio A, Spagnuolo A, Ristoratore F, Pischetola M, Aniello F, Branno M, Cariello L, Di Lauro R. 1995. Cloning of ascidian homeobox genes provides evidence for a primordial chordate cluster. Gene 156:253-257.
12. Fekany K, Yamanaka Y, Leung T, Sirotkin HI, Topczewski J, Gates MA, Hibi M, Renucci A, Stemple D, Radbill A, Schier AF, Driever W, Hirano T, Talbot WS, Solnica-Krezel L. 1999. The zebrafish bozozok locus encodes Dharma, a homeodomain protein essential for induction of gastrula organizer and dorsoanterior embryonic structures. Development 126:1427-1438.
13. Fujiwara S, Maeda Y, Shin-I T, Kohara Y, Takatori N, Satou Y, Satoh N. 2002. Gene expression profiles in Ciona intestinalis cleavagestage embryos. Mech Dev 112:115-127.
14. Gansner JM, Mendelsohn BA, Hultman KA, Johnson SL, Gitlin JD. 2007. Essential role of lysyl oxidases in notochord development. Dev Biol 307:202-213.
15. Guo Y, Pischon N, Palamakumbura AH, Trackman PC. 2007. Intracellular distribution of the lysyl oxidase propeptide in osteoblastic cells. Am J Physiol Cell Physiol 292:C2095-C2102.
16. Hornstra IK, Birge S, Starcher B, Bailey AJ, Mecham RP, Shapiro SD. 2003. Lysyl oxidase is required for vascular and diaphragmatic development in mice. J Biol Chem 278:14387-14393.
17. Hotta K, Takahashi H, Asakura T, Saitoh B, Takatori N, Satou Y, Satoh N. 2000. Characterization of Brachyury-downstream notochord genes in the Ciona intestinalis embryo. Dev Biol 224:69-80.
18. Hotta K, Takahashi H, Erives A, Levine M, Satoh N. 1999. Temporal expression patterns of 39 Brachyury-downstream genes associated with notochord formation in the Ciona intestinalis embryo. Dev Growth Differ 41:657-664.
19. Hotta K, Takahashi H, Satoh N, Gojobori T. 2008. Brachyury-downstream gene sets in a chordate, Ciona intestinalis: Integrating notochord specification, morphogenesis and chordate evolution. Evol Dev 10:37-51.
20. Hotta K, Yamada S, Ueno N, Satoh N, Takahashi H. 2007. Brachyury-downstream notochord genes and convergent extension in Ciona intestinalis embryos. Dev Growth Differ 49:373-382.
21. Hughes AL, Friedman R. 2005. Loss of ancestral genes in the genomic evolution of Ciona intestinalis. Evol Dev 7:196-200.
22. Ikuta T, Yoshida N, Satoh N, Saiga H. 2004. Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development. Proc Natl Acad Sci USA 101:15118-15123.
23. Imai KS. 2003. Isolation and characterization of β-catenin downstream genes in early embryos of the ascidian Ciona savignyi. Differentiation 71:346-360.
24. Imai KS, Hino K, Yagi K, Satoh N, Satou Y. 2004. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: Towards a comprehensive understanding of gene networks. Development 131:4047-4058.
25. Imai KS, Levine M, Satoh N, Satou Y. 2006. Regulatory blueprint for a chordate embryo. Science 312:1183-1187.
26. Jansen MK, Csiszar K. 2007. Intracellular localization of the matrix enzyme lysyl oxidase in polarized epithelial cells. Matrix Biol 26:136-139.
27. Jaynes JB, O'Farrell PH. 1991. Active repression of transcription by the engrailed homeodomain protein. EMBO J 10:1427-1433.
28. Jiang D, Munro EM, Smith WC. 2005. Ascidian prickle regulates both mediolateral and anterior-posterior cell polarity of notochord cells. Curr Biol 15:79-85.
29. Jiang D, Smith WC. 2007. Ascidian notochord morphogenesis. Dev Dyn 236:1748-1757.
30. Kusakabe T, Yoshida R, Kawakami I, Kusakabe R, Mochizuki Y, Yamada L, Shin-i T, Kohara Y, Satoh N, Tsuda M, Satou Y. 2002. Gene expression profiles in tadpole larvae of Ciona intestinalis. Dev Biol 242:188-203.
31. Miwata K, Chiba T, Horii R, Yamada L, Kubo A, Miyamura D, Satoh N, Satou Y. 2006. Systematic analysis of embryonic expression profiles of zinc finger genes in Ciona intestinalis. Dev Biol 292:546-554.
32. Miyamoto DM, Crowther RJ. 1985. Formation of the notochord in living ascidian embryos. Embryol Exp Morphol 86:1-17.
33. Nakatani Y, Moody R, Smith WC. 1999. Mutations affecting tail and notochord development in the ascidian Ciona savignyi. Development 126:3293-3301.
34. Oda-Ishii I, Di Gregorio A. 2007. Lineage-independent mosaic expression and regulation of the Ciona multidom gene in the ancestral notochord. Dev Dyn 236:1806-1819.
35. Odani N, Pfaff SL, Nakamura H, Funahashi J. 2007. Cloning and developmental expression of a chick G-protein-coupled receptor SCGPR1. Gene Expr Patterns 7:375-380.
36. Ott T, Kaestner KH, Monaghan AP, Schütz G. 1996. The mouse homolog of the region specific homeotic gene spalt of Drosophila is expressed in the developing nervous system and in mesodermderived structures. Mech Dev 56:117-128.
37. Parsons MJ, Pollard SM, Saúde L, Feldman B, Coutinho P, Hirst EM, Stemple DL. 2002. Zebrafish mutants identify an essential role for laminins in notochord formation. Development 129:3137-3146.
38. Passamaneck YJ, Di Gregorio A. 2005. Ciona intestinalis: Chordate development made simple. Dev Dyn 233:1-19.
39. Placzek M, Jessell TM, Dodd J. 1993. Induction of floor plate differentiation by contact-dependent, homeogenetic signals. Development 117:205-218.
40. Satoh N. 1994. Developmental Biology of Ascidians. New York: Cambridge University Press.
41. Satou Y, Takatori N, Fujiwara S, Nishikata T, Saiga H, Kusakabe T, Shin-i T, Kohara Y, Satoh N. 2002. Ciona intestinalis cDNA projects: Expressed sequence tag analyses and gene expression profiles during embryogenesis. Gene 287:83-96.
42. Satou Y, Takatori N, Yamada L, Mochizuki Y, Hamaguchi M, Ishikawa H, Chiba S, Imai K, Kano S, Murakami SD, Nakayama A, Nishino A, Sasakura Y, Satoh G, Shimotori T, Shin-I T, Shoguchi E, Suzuki MM, Takada N, Utsumi N, Yoshida N, Saiga H, Kohara Y, Satoh N. 2001. Gene expression profiles in Ciona intestinalis tailbud embryos. Development 128:2893-2904.
43. Schulte-Merker S, van Eeden FJ, Halpern ME, Kimmel CB, Nüsslein-Volhard C. 1994. no tail (ntl) is the zebrafish homologue of the mouse T (Brachyury) gene. Development 120:1009-1015.
44. Scott A, Stemple DL. 2005. Zebrafish notochordal basement membrane: Signaling and structure. Curr Top Dev Biol 65:229-253.
45. Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D. 2004. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 431:67-71.
46. Spagnuolo A, Ristoratore F, Di Gregorio A, Aniello F, Branno M, Di Lauro R. 2003. Unusual number and genomic organization of Hox genes in the tunicate Ciona intestinalis. Gene 309:71-79.
47. Stemple DL. 2005. Structure and function of the notochord: An essential organ for chordate development. Development 132:2503-2512.
48. Suzuki F. 1996. Roles of cartilage matrix proteins, chondromodulin-I and -II, in endochondral bone formation: A review. Connect Tissue Res 35:303-307.
49. Swalla BJ, Smith AB. 2008. Deciphering deuterostome phylogeny: Molecular, morphological and palaeontological perspectives. Philos Trans R Soc Lond B Biol Sci 363:1557-1568.
50. Takahashi H, Hotta K, Erives A, Di Gregorio A, Zeller RW, Levine M, Satoh N. 1999. Brachyury downstream notochord differentiation in the ascidian embryo. Genes Dev 13:1519-1523.
51. Veeman MT, Nakatani Y, Hendrickson C, Ericson V, Lin C, Smith WC. 2008. chongmague reveals an essential role for laminin-mediated boundary formation in chordate convergence and extension movements. Development 135:33-41.
52. Whittaker JR. 1977. Segregation during cleavage of a factor determining endodermal alkaline phosphatase development in ascidian embryos. J Exp Zool 202:139-153.
53. Wilson V, Manson L, Skarnes WC, Beddington RS. 1995. The T gene is necessary for normal mesodermal morphogenetic cell movements during gastrulation. Development 121:877-886.
54. Yeh LC, Tsai AD, Lee JC. 2005. Cartilage-derived morphogenetic proteins induce osteogenic gene expression in the C2C12 mesenchymal cell line. J Cell Biochem 95:173-188.
55. Zorn AM, Krieg PA. 1997. The KH domain protein encoded by quaking functions as a dimer and is essential for notochord development in Xenopus embryos. Genes Dev 11:2176-2190.