Brachyury-downstream gene sets in a chordate, Ciona intestinalis: Integrating notochord specification, morphogenesis and chordate evolution

Kohji Hotta, Hiroki Takahashi, Nori Satoh, Takashi Gojobori

Research output: Contribution to journalArticle

46 Citations (Scopus)


In vertebrates, Brachyury, a T-box transcription factor gene, seems to have a dual role in the differentiation of axial midline mesoderm cells into notochord and gastrulation cell movements regulated by non-canonical Wnt/planar cell polarity (Wnt/PCP) signaling. To understand the function of Brachyury-downstream genes in chordate embryos, from a series of our survey on differential expression, including subtractive hybridization, dot-blot assays, EST sequences and the expression patterns in whole-mount in situ hybridization at embryonic stages, we developed a knowledge database called "CINOBI: Ciona Notochord and Brachyury-downstream gene Index" to create comprehensive catalogues of Brachyury-downstream gene sets in Ciona intestinalis. Combining genome and large-scale cDNA data, we were able to characterize 450 non-redundant Brachyury-downstream genes: Twenty-four genes were newly annotated as notochord-expressed genes. Several genes are components of signaling pathways such as Wnt/PCP, NfκB and TGF-β signaling. We propose that Brachyury is linked to these pathways regulating the expression of each component, and such a regulatory mechanism might be conserved among chordates.

Original languageEnglish
Pages (from-to)37-51
Number of pages15
JournalEvolution and Development
Issue number1
Publication statusPublished - 2008 Jan 1


ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Developmental Biology

Cite this