Systematic analysis of embryonic expression profiles of zinc finger genes in Ciona intestinalis

Developmental Biology

Volumn 292, Issue 2, 2006, Pages 546-554

  Miwata, Kyoko ^a   Chiba, Takuto ^a   Horii, Reiko ^a   Yamada, Lixy ^a   Kubo, Atsushi ^a   Miyamura, Daisuke ^a   Satoh, Nori ^a   Satou, Yutaka ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Ascidian; Ciona intestinalis; Expression profile; Zinc finger

Indexed keywords

NUCLEIC ACID; TRANSCRIPTION FACTOR; ZINC FINGER PROTEIN;

ARTICLE; ASCIDIACEA; BINDING AFFINITY; CIONA INTESTINALIS; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION PROFILING; GENE STRUCTURE; GENETIC ANALYSIS; GENOME; LARVA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; ZINC FINGER GENE;

ANIMALIA; ASCIDIA; CIONA INTESTINALIS;

EID: 33645939940     PISSN: 00121606     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ydbio.2006.01.024     Document Type: Article

References (33)

1. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., et al. The genome sequence of Drosophila melanogaster. Science 287 (2000) 2185-2195
2. Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29 (2001) 37-40
3. Arbeitman M.N., Furlong E.E., Imam F., Johnson E., Null B.H., Baker B.S., Krasnow M.A., Scott M.P., Davis R.W., and White K.P. Gene expression during the life cycle of Drosophila melanogaster. Science 297 (2002) 2270-2275
4. Bradley J.R., and Pober J.S. Tumor necrosis factor receptor-associated factors (TRAFs). Oncogene 20 (2001) 6482-6491
5. Clarke N.D., and Berg J.M. Zinc fingers in Caenorhabditis elegans: finding families and probing pathways. Science 282 (1998) 2018-2022
6. Conklin E.G. The organization and cell lineage of the ascidian egg. J. Acad. Natl. Sci. (Philadelphia) 13 (1905) 1-119
7. Corbo J.C., Erives A., Di Gregorio A., Chang A., and Levine M. Dorsoventral patterning of the vertebrate neural tube is conserved in a protochordate. Development 124 (1997) 2335-2344
8. Corbo J.C., Di Gregorio A., and Levine M. The ascidian as a model organism in developmental and evolutionary biology. Cell 106 (2001) 535-538
9. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., Minokawa T., Amore G., Hinman V., Arenas-Mena C., Otim O., Brown C.T., Livi C.B., Lee P.Y., Revilla R., Rust A.G., Pan Z., Schilstra M.J., Clarke P.J., Arnone M.I., Rowen L., Cameron R.A., McClay D.R., Hood L., and Bolouri H. A genomic regulatory network for development. Science 295 (2002) 1669-1678
10. 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 298 (2002) 2157-2167
11. Di Gregorio A., and Levine M. Ascidian embryogenesis and the origins of the chordate body plan. Curr. Opin. Genet. Dev. 8 (1998) 457-463
12. Imai K.S., Hino K., Yagi K., Satoh N., and Satou Y. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks. Development 131 (2004) 4047-4058
13. Ravasi T., Huber T., Zavolan M., Forrest A., Gaasterland T., Grimmond S., and Hume D.A. Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome. Res. 13 (2003) 1430-1442
14. Ruvkun G., and Hobert O. The taxonomy of developmental control in Caenorhabditis elegans. Science 282 (1998) 2033-2041
15. Sasakura Y., Ogasawara M., and Makabe K.W. Two pathways of maternal RNA localization at the posterior-vegetal cytoplasm in early ascidian embryos. Dev. Biol. 220 (2000) 365-378
16. Satoh N. The ascidian tadpole larva: comparative molecular development and genomics. Nat. Rev., Genet. 4 (2003) 285-295
17. Satou Y. Posterior end mark 3 (pem-3), an ascidian maternally expressed gene with localized mRNA encodes a protein with Caenorhabditis elegans MEX-3-like KH domains. Dev. Biol. 212 (1999) 337-350
18. Satoh N., and Jeffery W.R. Chasing tails in ascidians: developmental insights into the origin and evolution of chordates. Trends. Genet. 11 (1995) 354-359
19. Satou Y., and Satoh N. Posterior end mark 2 (pem-2), pem-4, pem-5, and pem-6: maternal genes with localized mRNA in the ascidian embryo. Dev. Biol. 192 (1997) 467-481
20. Satou Y., and Satoh N. Developmental gene activities in ascidian embryos. Curr. Opin. Genet. Dev. 9 (1999) 542-547
21. Satou Y., and Satoh N. Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis. Dev. Genes Evol. 215 (2005) 580-596
22. Satou Y., Takatori N., Fujiwara S., Nishikata T., Saiga H., Kusakabe T., Shin-i T., Kohara Y., and Satoh N. Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis. Gene 287 (2002) 83-96
23. Satou Y., Yagi K., Imai K.S., Yamada L., Nishida H., and Satoh N. macho-1-related genes in Ciona embryos. Dev. Genes Evol. 212 (2002) 87-92
24. Satou Y., Imai K.S., Levine M., Kohara Y., Rokhsar D., and Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis: I. Genes for bHLH transcription factors. Dev. Genes Evol. 213 (2003) 213-221
25. Satou Y., Kawashima T., Shoguchi E., Nakayama A., and Satoh N. An integrated database of the ascidian, Ciona intestinalis: towards functional genomics. Zool. Sci. 22 (2005) 837-843
26. Takatori N., Hotta K., Mochizuki Y., Satoh G., Mitani Y., Satoh N., Satou Y., and Takahashi H. T-box genes in the ascidian Ciona intestinalis: characterization of cDNAs and spatial expression. Dev. Dyn. 230 (2004) 743-753
27. Torok M., and Etkin L.D. Two B or not two B? Overview of the rapidly expanding B-box family of proteins. Differentiation 67 (2001) 63-71
28. 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., and Satou Y. A genomewide survey of developmentally relevant genes in Ciona intestinalis: II. Genes for homeobox transcription factors. Dev. Genes Evol. 213 (2003) 222-234
29. Yagi K., Satou Y., Mazet F., Shimeld S.M., Degnan B., Rokhsar D., Levine M., Kohara Y., and Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis: III. Genes for Fox, ETS, nuclear receptors and NFkappaB. Dev. Genes Evol. 213 (2003) 235-244
30. Yamada L., Kobayashi K., Degnan B., Satoh N., and 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. 213 (2003) 245-253
31. Yamada L., Kobayashi K., Satou Y., and Satoh N. Microarray analysis of localization of maternal transcripts in eggs and early embryos of the ascidian, Ciona intestinalis. Dev. Biol. 284 (2005) 536-550
32. Yoshida S., Marikawa Y., and Satoh N. Posterior end mark, a novel maternal gene encoding a localized factor in the ascidian embryo. Development 122 (1996) 2005-2012
33. Zdobnov E.M., and Apweiler R. InterProScan-An integration platform for the signature-recognition methods in InterPro. Bioinformatics 17 (2001) 847-848