The cell type-specific expression of key transcription factors is central to development. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three Brachyury-controlling notochord enhancers T3, C, and I in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, deletion of all three enhancers in mouse abolishes Brachyury/T expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. Sequence and functional conservation of Brachyury-driving notochord enhancers with the brachyury/tbxtb loci from diverse lineages of fishes dates their origin to the last common ancestor of jawed vertebrates. Our data define the enhancers for Brachyury/T/TBXTB notochord expression as ancient mechanism in axis development.

Biological Sciences Graduate Program University of California San Diego La Jolla CA USA

Cluster of Excellence Physics of Life Technische Universität Dresden Dresden Germany

Comparative Biochemistry Program University of California Berkeley CA 94720 USA

Department for BioMedical Research University of Bern Bern Switzerland

Department of Anatomy University of California San Francisco San Francisco CA USA

Department of Cardiology Berne University Hospital Berne Switzerland

Department of Integrative Biology and Ecology Evolution and Behavior Program Michigan State University East Lansing MI USA

Department of Medicine Health Sciences University of California San Diego La Jolla CA USA

Department of Molecular Biology Biological Sciences University of California San Diego La Jolla CA USA

Department of Orofacial Sciences University of California San Francisco San Francisco CA USA

Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA

Institute for Human Genetics University of California San Francisco San Francisco CA USA

Institute of Molecular Genetics of the ASCR v v i Prague Czech Republic

Institute of Molecular Life Sciences University of Zurich Zurich Switzerland

Max Planck Institute for Molecular Cell Biology and Genetics Dresden Germany

Program in Craniofacial Biology University of California San Francisco San Francisco CA USA

School of Natural Sciences University of California Merced Merced CA USA

Section of Developmental Biology Department of Pediatrics University of Colorado Anschutz Medical Campus Aurora CO USA

Technische Universität Dresden CRTD Center for Regenerative Therapies Dresden Dresden Germany

US Department of Energy Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley CA USA

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Nat Commun. 2023 Oct 18;14(1):6594. doi: 10.1038/s41467-023-42151-3. PubMed

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