Development Genes and Evolution

, Volume 213, Issue 5–6, pp 314–318 | Cite as

Large scale EST analyses in Ciona intestinalis

Its application as Northern blot analyses
  • Yutaka Satou
  • Takeshi Kawashima
  • Yuji Kohara
  • Nori Satoh
Technical Note

Abstract

We have conducted large-scale EST analyses of transcripts expressed in the basal chordate Ciona intestinalis. The cDNA libraries examined were from fertilized eggs, cleaving embryos, gastrulae/neurulae, tailbud embryos, larvae and whole young adults, and the gonad (ovary and testis), endostyle, neural complex, heart, and blood cells of the adult. Because the libraries were not normalized or amplified, the occurrence of cDNA clones or EST counts in each library may reflect the quantity of transcripts of the corresponding genes. Thus, comparison of the EST counts of a certain gene at the six developmental stages may reflect the temporal expression pattern of the gene, while the comparison of EST counts in different tissues of the adult may reflect the spatial expression pattern of the gene. Here we present evidence that this is the case, and that the EST count can therefore be used like "Northern blot analysis" of Ciona genes.

Keywords

Ciona intestinalis Gene expression pattern Large scale EST analyses Northern blot analyses 

Notes

Acknowledgements

We wish to thank our laboratory members for their help in EST analyses. This work was supported by Grants-in-Aid from the MEXT of Japan to Y.S. (14704070), Y.K. (12201001) and N.S. (12202001). T.K. was a postdoctoral fellow of JSPS with a research grant (13060049).

References

  1. Chiba S, Satou Y, Nishikata T, Satoh N (1998) Isolation and characterization of cDNA clones for epidermis-specific and muscle-specific genes in Ciona savignyi embryos. Zool Sci 15:239–246CrossRefGoogle Scholar
  2. Chiba S, Awazu S, Itoh M, Chin-Bow ST, Satoh N, Satou Y, Hastings KEM (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. IX. Genes for muscle structural proteins. Dev Genes Evol DOI 10.1007/s00427-003-0324-xGoogle Scholar
  3. Corbo JC, Levine M, Zeller RW (1997) Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development 124:589–602PubMedGoogle Scholar
  4. Dehal P, Satou Y, Campbell RK et al (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298:2157–2167PubMedCrossRefGoogle Scholar
  5. Etani K, Nishikata T (2002) Novel G-protein-coupled receptor gene expressed specifically in the entire neural tube of the ascidian Ciona intestinalis. Dev Genes Evol 212:447–451PubMedCrossRefGoogle Scholar
  6. Fujimura M, Takamura K (2000) Characterization of an ascidian DEAD-box gene, Ci-DEAD1: specific expression in the germ cells and its mRNA localization in the posterior-most blastomeres in early embryos. Dev Genes Evol 210:64–72PubMedCrossRefGoogle Scholar
  7. Fujiwara S, Corbo JC, Levine M (1998) The Snail repressor establishes a muscle/notochord boundary in the Ciona embryo. Development 125:2511–2520PubMedGoogle Scholar
  8. Fujiwara S, Maeda Y, Shin-i T, Kohara Y, Takatori N, Satou Y, Satoh N (2002) Gene expression profiles in Ciona intestinalis cleavage-stage embryos. Mech Dev 112:115–127PubMedCrossRefGoogle Scholar
  9. 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 224:69–80PubMedCrossRefGoogle Scholar
  10. Hudson C, Lemaire P (2001) Induction of anterior neural fates in the ascidian Ciona intestinalis. Mech Dev 2:189–203CrossRefGoogle Scholar
  11. Imai K, Takada N, Satoh N, Satou Y (2000) β-catenin mediates the specification of endoderm cells in ascidian embryos. Development 14:3009–3020Google Scholar
  12. Imai KS, Satoh N, Satou Y (2002a) Early embryonic expression of FGF4/6/9 gene and its role in the induction of mesenchyme and notochord in Ciona savignyi embryos. Development 129:1729–1738PubMedGoogle Scholar
  13. Imai KS, Satoh N, Satou Y (2002b) Region specific gene expressions in the central nervous system of the ascidian embryo. Gene Exp Patt 3–4:319–321Google Scholar
  14. Inaba K, Padma P, Satouh Y, Shin-i T, Kohara Y, Satoh N, Satou Y (2002) EST analysis of gene expression in testis of the ascidian Ciona intestinalis. Mol Reprod Dev 62:431–445PubMedCrossRefGoogle Scholar
  15. 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 242:188–203PubMedCrossRefGoogle Scholar
  16. 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 the evolution of chordate muscle gene regulation. Development 9:1711–1721Google Scholar
  17. Nakayama A, Satou Y, Satoh N (2002) Further characterization of genes expressed during Ciona intestinalis metamorphosis. Differentiation 70:429–437CrossRefGoogle Scholar
  18. Nishida H, Sawada K (2001) macho-1 encodes a localized mRNA in ascidian eggs that specifies muscle fate during embryogenesis. Nature 409:724–729PubMedCrossRefGoogle Scholar
  19. Nishikata T, Yamada L, Mochizuki Y, Satou Y, Shin-i T, Kohara Y, Satoh N (2001) Profiles of maternally expressed genes in fertilized eggs of Ciona intestinalis. Dev Biol 238:315–331PubMedCrossRefGoogle Scholar
  20. Ogasawara M, Sasaki A, Metoki H, Shin-i T, Kohara Y, Satoh N, Satou Y (2002) Gene expression profiles in young adult Ciona intestinalis. Dev Genes Evol 212:173–185PubMedCrossRefGoogle Scholar
  21. 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 128:2893–2904PubMedGoogle Scholar
  22. 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 (2002a) A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33:153–154PubMedCrossRefGoogle Scholar
  23. Satou Y, Takatori N, Fujiwara S, Nishikata T, Saiga H, Kusakabe T, Shin-i T, Kohara Y, Satoh N (2002b) Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis. Gene 287:83–96PubMedCrossRefGoogle Scholar
  24. Satou Y, Yagi K, Imai KS, Yamada L, Nishida H, Satoh N (2002c) macho-1-related genes in Ciona embryos. Dev Genes Evol 212:87–92PubMedCrossRefGoogle Scholar
  25. Satou Y, Imai KS, Levine M, Kohara Y, Rokhsar D, Satoh N (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev Genes Evol DOI 10.1007/s00427-003-0319-7Google Scholar
  26. 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 DOI 10.1007/s00427-003-0321-0Google Scholar
  27. 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 DOI 10.1007/s00427-003-0322-zGoogle Scholar
  28. 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 DOI 10.1007/s00427-003-0316-xGoogle Scholar
  29. Yoshida S, Marikawa Y, Satoh N (1996) posterior end mark, a novel maternal gene encoding a localized factor in the ascidian embryo. Development 122:2005–2012PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • Yutaka Satou
    • 1
  • Takeshi Kawashima
    • 2
  • Yuji Kohara
    • 3
  • Nori Satoh
    • 1
  1. 1.Department of Zoology, Graduate School of ScienceKyoto UniversityKyoto 606–8502Japan
  2. 2.Bioinformatics Center, Institute for Chemical ResearchKyoto UniversityKyoto 611–0011Japan
  3. 3.Center for Genetic Resource InformationsNational Institute of GeneticsShizuoka 411-8540Japan

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