Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis

Development Genes and Evolution

Volumn 215, Issue 11, 2005, Pages 580-596

  Satou, Yutaka ^a   Satoh, Nori ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Ciona intestinalis; Genome; Transcription factor

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTION FACTOR;

ARTICLE; CIONA INTESTINALIS; CONTROLLED STUDY; DNA SEQUENCE; FUNCTIONAL GENOMICS; GENE STRUCTURE; GENETIC RESOURCE; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RELIABILITY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; UNINDEXED SEQUENCE;

ANIMALS; CIONA INTESTINALIS; EXPRESSED SEQUENCE TAGS; GENOMICS; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

ASCIDIA; CIONA INTESTINALIS;

EID: 28044451519     PISSN: 0949944X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00427-005-0016-9     Document Type: Article

References (42)

1. Aniello F, Locascio A, Villani MG, Di Gregorio A, Fucci L, Branno M (1999) Identification and developmental expression of Ci-msxb: A novel homologue of Drosophila msh gene in Ciona intestinalis. Mech Dev 88:123-126 10.1016/S0925-4773(99)00178-1
2. Boorman CJ, Shimeld SM (2002) Pitx homeobox genes in Ciona and amphioxus show left-right asymmetry is a conserved chordate character and define the ascidian adenohypophysis. Evol Dev 4:354-365 10.1046/ j.1525-142X.2002.02021.x
3. Candiani S, Pennati R, Oliveri D, Locascio A, Branno M, Castagnola P, Pestarino M, De Bernardi F (2005) Ci-POU-IV expression identifies PNS neurons in embryos and larvae of the ascidian Ciona intestinalis. Dev Genes Evol 215:41-45 10.1007/s00427-004-0444-y
4. Caracciolo A, Di Gregorio A, Aniello F, Di Lauro R, Branno M (2000) Identification and developmental expression of three Distal-less homeobox containing genes in the ascidian Ciona intestinalis. Mech Dev 99:173-176 10.1016/S0925-4773(00)00474-3
5. Carosa E, Fanelli A, Ulisse S, Di Lauro R, Rall JE, Jannini EA (1998) Ciona intestinalis nuclear receptor 1: A member of steroid/thyroid hormone receptor family. Proc Natl Acad Sci U S A 95:11152-11157 10.1073/ pnas.95.19.11152
6. Corbo JC, Levine M, Zeller RW (1997a) Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development 124:589-602 9043074
7. Corbo JC, Erives A, Di Gregorio A, Chang A, Levine M (1997b) Dorsoventral patterning of the vertebrate neural tube is conserved in a protochordate. Development 124:2335-2344 9199360
8. Corbo JC, Fujiwara S, Levine M, Di Gregorio A (1998) Suppressor of hairless activates brachyury expression in the Ciona embryo. Dev Biol 203:358-368 10.1006/dbio.1998.9067
9. Corrado M, Aniello F, Fucci L, Branno M (2001) Ci-IPF1, the pancreatic homeodomain transcription factor, is expressed in neural cells of Ciona intestinalis larva. Mech Dev 102:271-274 10.1016/S0925-4773(01)00311-2
10. Dehal P, Satou Y, Campbell RK et al (2002) The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298:2157-2167 10.1126/science.1080049
11. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-185 9521921
12. Gionti M, Ristoratore F, Di Gregorio A, Aniello F, Branno M, Di Lauro R (1998) Cihox5, a new Ciona intestinalis Hox-related gene, is involved in regionalization of the spinal cord. Dev Genes Evol 207:515-523 10.1007/s004270050142
13. Giuliano P, Marino R, Pinto MR, De Santis R (1998) Identification and developmental expression of Ci-isl, a homologue of vertebrate islet genes, in the ascidian Ciona intestinalis. Mech Dev 78:199-202 10.1016/ S0925-4773(98)00143-9
14. Gordon D, Abajian C, Green P (1998) Consed: A graphical tool for sequence finishing. Genome Res 8:195-202 9521923
15. Hino K, Satou Y, Yagi K, Satoh N (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. VI. Genes for Wnt, TGFβ, Hedgehog and JAK/STAT signaling pathways. Dev Genes Evol 213:264-272 10.1007/s00427-003-0318-8
16. Hudson C, Lemaire P (2001) Induction of anterior neural fates in the ascidian Ciona intestinalis. Mech Dev 100:189-203 10.1016/ S0925-4773(00)00528-1
17. Imai K, Takada N, Satoh N, Satou Y (2000) β-catenin mediates the specification of endoderm cells in ascidian embryos. Development 127:3009-3020 10862739
18. Imai KS, Satoh N, Satou Y (2002) Region specific gene expressions in the central nervous system of the ascidian embryo. Mech Dev 119(Suppl 1):S275-S277 10.1016/S0925-4773(03)00128-X
19. 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 10.1242/dev.01270
20. Kawai N, Takahashi H, Nishida H, Yokosawa H (2005) Regulation of NF-κB/Rel by IκB is essential for ascidian notochord formation. Dev Biol 277:80-91 10.1016/j.ydbio.2004.09.007
21. Kent WJ (2002) BLAT - the BLAST-like alignment tool. Genome Res 12:656-664 11932250
22. Kusakabe T, Yoshida R, Ikeda Y, Tsuda M (2004) Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona. Dev Biol 276:563-580 10.1016/j.ydbio.2004.09.037
23. Leveugle M, Prat K, Popovici C, Birnbaum D, Coulier F (2004) Phylogenetic analysis of Ciona intestinalis gene superfamilies supports the hypothesis of successive gene expansions. J Mol Evol 58:168-181 10.1007/s00239-003-2538-y
24. Meedel TH, Farmer SC, Lee JJ (1997) The single MyoD family gene of Ciona intestinalis encodes two differentially expressed proteins: Implications for the evolution of chordate muscle gene regulation. Development 124:1711-1721 9165119
25. Meedel TH, Lee JJ, Whittaker JR (2002) Muscle development and lineage-specific expression of CiMDF, the MyoD-family gene of Ciona intestinalis. Dev Biol 241:238-246 10.1006/dbio.2001.0511
26. Ogasawara M, Wada H, Peters H, Satoh N (1999) Developmental expression of Pax1/9 genes in urochordate and hemichordate gills: Insight into function and evolution of the pharyngeal epithelium. Development 126:2539-2550 10226012
27. Ristoratore F, Spagnuolo A, Aniello F, Branno M, Fabbrini F, Di Lauro R (1999) Expression and functional analysis of Cititf1, an ascidian NK-2 class gene, suggest its role in endoderm development. Development 126:5149-5159 10529431
28. Satoh N (2003) The ascidian tadpole larva: Comparative molecular development and genomics. Nat Rev Genet 4:285-295 10.1038/nrg1042
29. Satou Y, Imai KS, Satoh N (2001) Action of morpholinos in Ciona embryos. Genesis 30:103-106 10.1002/gene.1040
30. Satou Y, Imai KS, Satoh N (2002a) Fgf genes in the basal chordate Ciona intestinalis. Dev Genes Evol 212:432-438 10.1007/s00427-002-0266-8
31. Satou Y, Yamada L, Mochizuki Y, Takatori N, Kawashima T, Sasaki A, Hamaguchi M, Awazu S, Yagi K, Sasakura Y, Nakayama A, Ishikawa H, Inaba K, Satoh N (2002b) A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33:153-154 10.1002/gene.10119
32. Satou Y, Yagi K, Imai KS, Yamada L, Nishida H, Satoh N (2002c) macho-1 -related genes in Ciona embryos. Dev Genes Evol 212:87-92 10.1007/ s00427-002-0218-3
33. Satou Y, Imai KS, Levine M, Kohara Y, Rokhsar D, Satoh N (2003a) A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev Genes Evol 213:213-221 10.1007/s00427-003-0319-7
34. Satou Y, Sasakura Y, Yamada L, Imai KS, Satoh N, Degnan B (2003b) A genomewide survey of developmentally relevant genes in Ciona intestinalis. V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway. Dev Genes Evol 213:254-263 10.1007/s00427-003-0317-9
35. 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 10.1016/S0378-1119(03)00488-8
36. Takahashi T, Holland PW (2004) Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development. Development 131:3285-3294 10.1242/dev.01201
37. Takatori N, Satou Y, Satoh N (2002) Expression of hedgehog genes in Ciona intestinalis embryos. Mech Dev 116:235-238 10.1016/ S0925-4773(02)00150-8
38. Takatori N, Hotta K, Mochizuki Y, Satoh G, Mitani Y, Satoh N, Satou Y, Takahashi H (2004) T-box genes in the ascidian Ciona intestinalis: characterization of cDNAs and spatial expression. Dev Dyn 230:743-753 10.1002/dvdy.20082
39. Tokuoka M, Imai KS, Satou Y, Satoh N (2004) Three distinct lineages of mesenchymal cells in Ciona intestinalis embryos demonstrated by specific gene expression. Dev Biol 274:211-224 10.1016/j.ydbio.2004.07.007
40. Wada S, Tokuoka M, Shoguchi E, Kobayashi K, Di Gregorio A, Spagnuolo A, Branno M, Kohara Y, Rokhsar D, Levine M, Saiga H, Satoh N, Satou Y (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors. Dev Genes Evol 213:222-234 10.1007/s00427-003-0321-0
41. Yagi K, Satou Y, Mazet F, Shimeld SM, Degnan B, Rokhsar D, Levine M, Kohara Y, Satoh N (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFκB. Dev Genes Evol 213:235-244 10.1007/s00427-003-0322-z
42. Yamada L, Kobayashi K, Degnan B, Satoh N, Satou Y (2003) 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 213:245-253 10.1007/s00427-003-0316-x