Deep homology of a brachyury cis-regulatory syntax and the evolutionary origin of the notochord
2025-07-25
Expression of brachyury in the notochord is regarded as a chordate novelty and links to the origin of the notochord, yet the evolution of this regulatory control remains unclear. Here, we uncovered a regulatory syntax (named SFZE) consisting of binding sites for four transcription factors in notochord enhancers of chordate brachyury genes. SFZE was also identified in potential brachyury enhancers in various non-chordate animals and even in Capsaspora , a unicellular relative to animals. These non-chordate SFZE-containing enhancers exhibited activity in the zebrafish notochord. Furthermore, the SFZE syntax in a non-chordate confers endoderm activity. Our results indicate the ancient association of SFZE with brachyury , likely predating the origin of animals. The emergence of notochordal brachyury expression could be attributed to co-option of upstream signals acting on the conserved SFZE syntax, which facilitates the origin of the notochord from rudimentary endodermal cells.