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A genomewide survey of developmentally relevant genes in Ciona intestinalis

I. Genes for bHLH transcription factors

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Abstract

The basic helix-loop-helix (bHLH) proteins are transcription factors that play important roles in many biological processes, including the development of various animals. We identified 46 genes encoding bHLH proteins in the draft genome sequence of the basal chordate Ciona intestinalis. These 46 genes represent an almost complete set of bHLH genes in this animal. This number is comparable to 39 and 58 bHLH genes in those of Caenorhabditis elegans and Drosophila melanogaster but is much smaller than the 125 in the human genome. Genes that encode NeuroD, Beta3, Oligo, SCL, NSCL, SRC, Clock and Bmal were not found in the Ciona genome. We could also identify groucho and CBP orthologues in the Ciona genome. In addition, the comparison between the numbers of orthologous human and Ciona bHLH factors reveals the simplicity of the Ciona genome, in accordance with its phylogenetic position within chordates. The present analysis provides an insight into the basic set of bHLH genes that the last common ancestor of ascidians and vertebrates had, and will provide important background information for future studies using ascidians as a model system for vertebrate development.

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References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Atchely WR, Fitch WM (1997) A natural classification of the basic helix-loop helix class transcription factors. Proc Natl Acad Sci USA 94:5172–5176

    Article  Google Scholar 

  • Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam protein families database. Nucleic Acids Res 30:276–280

    Article  PubMed  CAS  Google Scholar 

  • Crews ST (1998) Control of cell lineage-specific development and transcription by bHLH-PAS proteins. Genes Dev 12:607–620

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J (1993) Phylogeny Inference Package (PHYLIP). University of Washington, Seattle

  • Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237–244

    Article  PubMed  CAS  Google Scholar 

  • Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245

    Article  PubMed  CAS  Google Scholar 

  • Ledent V, Vervoort M (2001) The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res 11:754–770

    Article  PubMed  CAS  Google Scholar 

  • Ledent V, Paquet O, Vervoort M (2002) Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol 3:RESEARCH0030

    Article  PubMed  Google Scholar 

  • Massari ME, Murre C (2000) Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol Cell Biol 20:429–440

    Article  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Meinertzhagen IA, Okamura Y (2001) The larval ascidian nervous system: the chordate brain from its small beginnings. Trends Neurosci 24:401–410

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • 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 (2002) A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33:153–154

    Article  PubMed  CAS  Google Scholar 

  • Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA 95:5857–5864

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This research was supported by Grants-in-Aid for Scientific Research from MEXT and JSPS, Japan, to Y.S. (14704070) and N.S. (12202001). K.S.I. was a Predoctoral Fellow of JSPS with a research grant (12003588). We thank Kazuko Hirayama, Chikako Imaizumi, Asako Fujimoto, and Hisayoshi Ishikawa for their technical support.

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Correspondence to Yutaka Satou.

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Edited by: D. Tautz

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Satou, Y., Imai, K.S., Levine, M. et al. A genomewide survey of developmentally relevant genes in Ciona intestinalis . Dev Genes Evol 213, 213–221 (2003). https://doi.org/10.1007/s00427-003-0319-7

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  • DOI: https://doi.org/10.1007/s00427-003-0319-7

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