Systems Biology Approaches To Unravel The Mechanisms Underlying The Evolution Of The Transcription Factor Brachyury

Bilaterians share a conserved molecular toolkit depicted in Gene Regulatory Networks (GRNs) that controls embryonic development and morphogenesis. Modifications of this toolkit can lead to the evolution of new cell types and new body plans. This work investigates the role of transcription factor (TF) Brachyury in the embryonic development of two sea urchin species – Strongylocentrotus purpuratus and Paracentrotus lividus. In non-vertebrate and vertebrate chordates, Brachyury acts as an activator of mesodermal genes. However, in protostomes, Brachyury activates endodermal and ectodermal genes, suggesting its ancestral function. Sea urchin, due to its phylogenetic position as a non-vertebrate deuterostome, the thorough characterization of its GRNs, and the expression of Brachyury in ectodermal and endodermal domains, served as a model system for this study. The goal of this study is to identify direct and indirect Brachyury targets and untangle the similarities and differences in Brachyury's role and function in the early development of two sea urchin species by combining gene perturbation and high-throughput sequencing technologies. The knock-down of Brachyury, followed by differential transcriptomics, allowed the investigation of its putative targets. Moreover, the use of available Brachyury ChIP-seq data to identify Brachyury direct interactions and ATAC-seq to discover open chromatin regions has led to the extension of a known GRN around Brachyury in S. purpuratus. This work showed that Brachyury acts mostly as an ectodermal and endodermal activator in both sea urchin species. Some mesodermal genes detected after the perturbation were commonly affected in both species, although it appears that Brachyury can directly repress mesodermal fate in endodermal veg2 cell lineage in S. purpuratus. The self-regulatory feedback loop of Brachyury seems to be conserved. Moreover, the analysis of the obtained data suggested the direction for further work.