title: Brachyury-downstream gene sets in a chordate, Ciona intestinalis: integrating notochord specification, morphogenesis and chordate evolution.
abstract: 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: CionaNotochord 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, Nf kappaB and TGF-beta 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.
authors.affiliation: Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan. khotta@bio.keio.ac.jp
authors.forename: Kohji
authors.initials: K
authors.lastname: Hotta
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002454:Cell Differentiation; D002938:Ciona intestinalis / Q000196:embryology* / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D004625:Embryo, Nonmammalian / Q000166:cytology; D020224:Expressed Sequence Tags; D005326:Fetal Proteins / Q000235:genetics / Q000502:physiology*; D054262:Gastrulation / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D050437:Genes, Developmental; D009672:Notochord / Q000166:cytology* / Q000378:metabolism; D015398:Signal Transduction; D020825:T-Box Domain Proteins / Q000235:genetics / Q000502:physiology*; D000098908:Brachyury Protein
chemical_list: D005326:Fetal Proteins; D020825:T-Box Domain Proteins; D000098908:Brachyury Protein