The notochord is an embryonic structure of mesodermal origin that functions as a signaling center and structural support for the surrounding embryonic tissues. The functions of evolutionarily conserved notochord transcription factors (TFs) and of the cis-regulatory modules (CRMs/enhancers) that coordinate expression of their effectors during notochord development are still largely uncharacterized. Our lab uses an invertebrate chordate, Ciona robusta, to unravel the notochord gene regulatory network and to characterize structure and function of notochord CRMs. The TF Brachyury is a main evolutionarily conserved regulator of notochord development. Despite being expressed specifically and continuously in the notochord throughout all the stages of its development, Ciona Brachyury (Ci-Bra) is somehow able to regulate the staggered deployment of early-, middle- and late-onset notochord genes, and to coordinate the transcription of genes involved in sequential steps of notochord morphogenesis. Through the systematic characterization of Ci-Bra-downstream notochord CRMs, we have formulated a mechanistic hypothesis to explain how temporal information is encoded within Ci-Bra-downstream notochord CRMs. We are testing this hypothesis in light of recently published ATAC-Seq chromatin profiles, with the help of bioinformatic tools. The regulatory role of Brachyury during notochord evolution is remarkably conserved among species that diverged over 500 millions of years ago. Thus, studying the cis-regulatory strategies employed by Ci-Bra will inform research on notochord formation in more complex chordates.