Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network

Abstract

Gene regulatory networks coordinate the formation of organs and structures that compose the evolving body plans of different organisms. We are using a simple chordate model, the Ciona embryo, to investigate the essential gene regulatory network that orchestrates morphogenesis of the notochord, a structure necessary for the proper development of all chordate embryos. Although numerous transcription factors expressed in the notochord have been identified in different chordates, several of them remain to be positioned within a regulatory framework. Here we focus on Xbp1, a transcription factor expressed during notochord formation in Ciona and other chordates. Through the identification of Xbp1-downstream notochord genes in Ciona, we found evidence of the early co-option of genes involved in the unfolded protein response to the notochord developmental program. We report the regulatory interplay between Xbp1 and Brachyury, and by extending these results to Xenopus, we show that Brachyury and Xbp1 form a cross-regulatory subcircuit of the notochord gene regulatory network that has been consolidated during chordate evolution.

Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona

“…In fact, morpholino-oligonucleotide mediated inactivation of Foxa.a leads to the down-regulation of Ci-Bra 23 , the Foxa.a locus is bound by Ci-Bra in early embryos 54 . In addition to this central cross-regulatory interaction, which is conserved across chordates 33 , 104 , our group has recently reported the positive feedback of Xbp1, another Ci-Bra-downstream notochord TF, on Ci-Bra itself, and we have verified the conservation of this subcircuit of the notochord GRN in Xenopus 36 . Interestingly, even though Lmx1-r had surfaced as one of the potential transcriptional targets of Xbp1 36 , the main activator of the Lmx1-r notochord CRM is Foxa.a, an additional indication that Ci-Bra would only play a minor indirect role, if any, in the transcriptional regulation of this TF.…”

“…The Ciona notochord GRN coordinates evolutionarily conserved morphogenetic milestones, including cell movements, intercalation, extracellular matrix secretion, cell-shape changes and tail elongation. In Ciona , we have uncovered the regulatory connection between Brachyury, which in Ciona is notochord-specific 28 (hereinafter abbreviated as Ci-Bra) and two other notochord TFs, Tbx2/3 and Xbp1, which act as Ci-Bra intermediaries 35 , 36 . We have also presented evidence that the positive feedback between Brachyury and Xbp1, which we first uncovered in Ciona , is conserved in Xenopus embryos 36 .…”

“…In Ciona , we have uncovered the regulatory connection between Brachyury, which in Ciona is notochord-specific 28 (hereinafter abbreviated as Ci-Bra) and two other notochord TFs, Tbx2/3 and Xbp1, which act as Ci-Bra intermediaries 35 , 36 . We have also presented evidence that the positive feedback between Brachyury and Xbp1, which we first uncovered in Ciona , is conserved in Xenopus embryos 36 . To further illuminate the regulatory connections that make up the notochord GRN, we selected for the present study ten TFs expressed in the Ciona notochord during widely different developmental windows.…”

Searching for marine embryos, finding my path

“…In collaboration with Profs. Licia Selleri, Chitra Dahia, and Jean-Pierre Saint-Jeannet, we have shown the conservation of the notochord expression of zebrafish, Xenopus, mouse, and human orthologs of Ciona notochord genes (Capellini et al, 2008;Raghavan et al, 2023) and we have found evidence that the regulatory relationship that we identified using Ciona between Brachyury and another transcription factor, Xbp1, is maintained in the notochord of Xenopus (Wu et al, 2022).…”