Deep homology of a <i>brachyury</i> cis-regulatory syntax and the evolutionary origin of the notochord.

Abstract

Expression of <i>brachyury</i> 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 <i>brachyury</i> genes. SFZE was also identified in potential <i>brachyury</i> enhancers in various non-chordate animals and even in <i>Capsaspora</i>, 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 <i>brachyury</i>, likely predating the origin of animals. The emergence of notochordal <i>brachyury</i> 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.