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.

The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the brachyury gene regulatory network

“…3A,B), consistent with previous work (Imai et al, 2004;Hotta et al, 2008); however, we observed that the expression of this gene became progressively restricted at later stages ( Fig. 3C-F).…”

“…In Xenopus, screens for Xbra transcriptional targets led to the identification of the paired-like homeobox genes Bix1 and Bix2-4 (Tada et al, 1998;Casey et al, 1999). Previously published work in Ciona has identified Ci-STAT5/6-b as a Ci-Bra target (Hotta et al, 2008), and with the present analysis we have uncovered the notochord expression of this gene.…”

“…Mammalian genomes contain seven STAT family genes while Drosophila has a single STAT ortholog, dSTAT, which most closely resembles the mammalian STAT5a/b genes (Yan et al, 1996). Two STAT genes have been found in Ciona, Ci-STAT-a and Ci-STAT-b (Imai et al, 2004), both related to vertebrate STAT5a/b and STAT6 (Hino et al, 2003); Ci-STAT-b has also been reported as Ci-STAT5/6-b (Hotta et al, 2003;Hotta et al, 2008).…”

“…In Ciona, Brachyury (Ci-Bra) is expressed exclusively in the notochord and its precursors beginning at the 64-cell stage, concurrent with notochord fate restriction (Corbo et al, 1997). The upstream regulatory cascade leading to Ci-Bra expression is well characterized Imai et al, 2006;Matsumoto et al, 2007), and at least 50 Ciona genes have been found to be controlled by Ci-Bra (Di Takahashi et al, 1999;Hotta et al, 2000;Oda-Ishii and Di Gregorio, 2007;Hotta et al, 2008;Kugler et al, 2008). A surprisingly low number of transcription factors was included within this first set of transcriptional targets; however, this number has been sharply increased by recent wholegenome studies of the in vivo occupancy of chromatin by Ci-Bra in early Ciona embryos (Kubo et al, 2010).…”

In silico and in vivo identification of the intermediate filament vimentin that is downregulated downstream of Brachyury during Xenopus embryogenesis

“…To identify the genes expressed downstream of Brachyury, several groups have conducted subtractive screens in the frog (X. laevis), ascidian (Ciona intestinalis), and sea urchin (Strongylocentrotus purpuratus) using Brachyury-misexpressing embryos and embryos in which Brachyury was either normally expressed or repressed (Hotta et al, 2008;Rast et al, 2002;Saka et al, 2000;Tada et al, 1998;. Several genes identified in these screens encoded proteins similar to those associated with cell shape modification and cell movements although these genes were not orthologs conserved among all 3 species.…”