# Control of precisely timed gene expression during notochord development by Brachyury > **NIH NIH R01** · NEW YORK UNIVERSITY · 2024 · $322,000 ## Abstract PROJECT SUMMARY/ABSTRACT Precise temporal regulation of stage-specific gene expression is fundamental for the proper development of all organisms. Different molecular mechanisms that ensure the regionalized activation of gene expression, such as activator gradients or localized transcriptional repressors, have been elucidated in remarkable detail; however, the structural features of cis-regulatory sequences that enable transcription factors to achieve the timely deployment of their downstream genes remain mostly unclear. The evolutionarily conserved transcription factor Brachyury provides an example of a regulator that controls the spatial and temporal expression of a large number of genes, many of which are required for the development of the notochord. The notochord is the main feature shared by all chordate embryos, from tunicates to humans. During the early embryogenesis of all chordates, the notochord provides support and patterning signals to the developing body and is indispensable for patterning neural tube, endoderm, paraxial mesoderm, and the structures that they will form. In the tunicate Ciona, an invertebrate chordate, Brachyury is exclusively expressed in notochord cells, where it controls the expression of hundreds of genes. Even though Ciona Brachyury (Ci-Bra) is steadily transcribed and transported to the nuclei of the notochord cells throughout development, the genes downstream of Ci-Bra exhibit a distinctive, temporally staggered onset. In an effort to identify the cis-regulatory strategies responsible for the precise temporal regulation of notochord gene expression by Ci-Bra, we have characterized several cis-regulatory regions (aka enhancers) that control the notochord expression of Ci-Bra- downstream genes characterized by different temporal onsets. These studies have led us to formulate a working hypothesis that explains how Brachyury controls its early-, middle- and late-onset target genes. This hypothesis will be tested through the following experimental approaches: the elucidation of the cis-regulatory principles underlying the sequential activation of early-onset and middle-onset notochord genes directly controlled by Ci-Bra (Aim 1); the functional analysis of two transcription factors that activate expression of late- onset notochord genes (Aim 2); the exploration of the role of transcriptional repressors in notochord development (Aim 3). These studies will shed light on the modalities employed by a pivotal transcription factor to set the temporal context for developmental processes of widespread relevance, such as convergent extension and extracellular matrix secretion, and will provide the mechanistic framework that is needed to diagnose and prevent malformations and tumorigenesis associated with the multifaceted transcription factor Brachyury. ## Key facts - **NIH application ID:** 10803557 - **Project number:** 1R01GM149841-01A1 - **Recipient organization:** NEW YORK UNIVERSITY - **Principal Investigator:** ANNA DI GREGORIO - **Activity code:** R01 (R01, R21, SBIR, etc.) - **Funding institute:** NIH - **Fiscal year:** 2024 - **Award amount:** $322,000 - **Award type:** 1 - **Project period:** 2024-07-05 → 2028-05-31 ## Primary source NIH RePORTER: https://reporter.nih.gov/project-details/10803557 ## Citation > US National Institutes of Health, RePORTER application 10803557, Control of precisely timed gene expression during notochord development by Brachyury (1R01GM149841-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10803557. Licensed CC0. --- *[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*