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

Abstract

The notochord is the distinctive characteristic of chordates; however, the knowledge of the complement of transcription factors governing the development of this structure is still incomplete. Here we present the expression patterns of seven transcription factor genes detected in the notochord of the ascidian Ciona intestinalis at various stages of embryonic development. Four of these transcription factors, Fos-a, NFAT5, AFF and Klf15, have not been directly associated with the notochord in previous studies, while the others, including Spalt-like-a, Lmx-like and STAT5/6-b, display evolutionarily conserved expression in this structure as well as in other domains. We examined the hierarchical relationships between these genes and the transcription factor Brachyury, which is necessary for notochord development in all chordates. We found that Ciona Brachyury regulates the expression of most, although not all, of these genes. These results shed light on the genetic regulatory program underlying notochord formation in Ciona and possibly other chordates.

Functional Brachyury Binding Sites Establish a Temporal Read-out of Gene Expression in the Ciona Notochord

“…The expression patterns of numerous notochord genes that are likely controlled by Ci-Bra have been described in previous studies [11],[22],[23],[25],[31]. In this study we used whole-mount in situ hybridization (WMISH) to precisely determine the onset of notochord gene expression for a subset of bona fide Ci-Bra target genes for which this information was missing or incomplete (Figures 1A–1O and S1).…”

“…Therefore it seems conceivable that these minimal CRMs might be controlled by Ci-Bra indirectly through transcriptional intermediaries. We have previously shown that transcription factors of different families are expressed in the Ciona notochord following the onset of Ci-Bra expression, and that the expression of several of these genes is controlled by Ci-Bra [25],[31]; these reports, along with the results of genome-wide screens [13],[42],[58] provide a number of candidate activators for these CRMs.…”

NFAT5 Has a Job in the Brain

“…The expression of NFAT5 in fetal brains has been confirmed not only in humans [25], but also in many other species [11, 27]. One study using quantitative PCR analysis found that the mRNA of NFAT5 was detected in both fetal and adult human brains, and it was expressed approximately 10-fold higher in fetal brains.…”

Cis-Regulatory Timers for Developmental Gene Expression

“…Consistent with this finding, chromatin immunoprecipitation (ChIP) assays showed direct binding of the endogenous Bra protein to early- and middle-onset CRMs but not to the late-onset CRM in tailbud embryos. Thus, it appears that Bra controls late-onset gene expression indirectly by a “relay” mechanism in which early- and/or middle-onset transcription regulators, such as those recently identified by the Di Gregorio team [16],[17], activate late-onset gene transcription (Figure 1). …”

“…As in C. elegans post-mitotic neurons and male tail tip differentiation [25],[26], it is possible that a single terminal selector gene, Ci-Bra , controls most aspects of notochord differentiation in ascidians. However, additional transcription regulators, such as FoxA and Tbx2/3, govern late notochord gene expression and probably also contribute to regulating early- and middle-onset gene expression [16],[17],[27]. These additional transcription regulators, acting downstream of and/or in parallel to Bra, suggest that coherent feed-forward loops, whereby Bra activates a downstream factor that then cooperates with Bra to activate further downstream targets, and maybe also other gene regulatory network motifs [28], control the onset of notochord gene expression.…”