The cell type-specific expression of key transcription factors is central to development and disease. 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 conserved Brachyury-controlling notochord enhancers, T3, C, and I, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, in cis deletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The three Brachyury-driving notochord enhancers are conserved beyond mammals in the brachyury/tbxtb loci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers for Brachyury/T/TBXTB notochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development.

• MeSH
• Notochord * metabolism   MeSH
• Zebrafish * genetics   metabolism   MeSH
• Fetal Proteins genetics   metabolism   MeSH
• Humans MeSH
• Mice MeSH
• Brachyury Protein MeSH
• T-Box Domain Proteins genetics   metabolism   MeSH
• Mammals genetics   MeSH
• Gene Expression Regulation, Developmental MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Names of Substances
• Fetal Proteins MeSH
• Brachyury Protein MeSH
• T-Box Domain Proteins MeSH
• TBX1 protein, human MeSH Browser
• Tbx1 protein, mouse MeSH Browser

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.

• Publication type
• Journal Article MeSH
• Preprint MeSH

The σI sigma factor from Bacillus subtilis is a σ factor associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide a comprehensive characterization of this transcriptional regulator. By transcriptome sequencing (RNA-seq) of wild-type (wt) and σI-null strains at 37°C and 52°C, we identified ∼130 genes affected by the absence of σI Further analysis revealed that the majority of these genes were affected indirectly by σI The σI regulon, i.e., the genes directly regulated by σI, consists of 16 genes, of which eight (the dhb and yku operons) are involved in iron metabolism. The involvement of σI in iron metabolism was confirmed phenotypically. Next, we set up an in vitro transcription system and defined and experimentally validated the promoter sequence logo that, in addition to -35 and -10 regions, also contains extended -35 and -10 motifs. Thus, σI-dependent promoters are relatively information rich in comparison with most other promoters. In summary, this study supplies information about the least-explored σ factor from the industrially important model organism B. subtilisIMPORTANCE In bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ factors) is the key for understanding how bacteria cope with the changing environment and could be instrumental for biotechnologically motivated rewiring of gene expression. Here, we characterize the σI regulon from the industrially important model Gram-positive bacterium Bacillus subtilis We reveal that σI affects expression of ∼130 genes, of which 16 are directly regulated by σI, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for σI-dependent transcription. This study thus provides a comprehensive view on this underexplored component of the B. subtilis transcription machinery.

• Keywords
• RNA-seq, RNAP, iron metabolism, promoter, sigma factor,
• MeSH
• Bacillus subtilis genetics   MeSH
• Bacterial Proteins genetics   metabolism   MeSH
• DNA-Directed RNA Polymerases genetics   MeSH
• Transcription, Genetic * MeSH
• Operon MeSH
• Promoter Regions, Genetic * MeSH
• Gene Expression Regulation, Bacterial * MeSH
• Regulon MeSH
• Sigma Factor genetics   MeSH
• Transcriptome MeSH
• Iron metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Bacterial Proteins MeSH
• DNA-Directed RNA Polymerases MeSH
• Sigma Factor MeSH
• Iron MeSH

Generation of neurons in the embryonic neocortex is a balanced process of proliferation and differentiation of neuronal progenitor cells. Canonical Wnt signalling is crucial for expansion of radial glial cells in the ventricular zone and for differentiation of intermediate progenitors in the subventricular zone. We detected abundant expression of two transcrtiption factors mediating canonical Wnt signalling, Tcf7L1 and Tcf7L2, in the ventricular zone of the embryonic neocortex. Conditional knock-out analysis showed that Tcf7L2, but not Tcf7L1, is the principal Wnt mediator important for maintenance of progenitor cell identity in the ventricular zone. In the absence of Tcf7L2, the Wnt activity is reduced, ventricular zone markers Pax6 and Sox2 are downregulated and the neuroepithelial structure is severed due to the loss of apical adherens junctions. This results in decreased proliferation of radial glial cells, the reduced number of intermediate progenitors in the subventricular zone and hypoplastic forebrain. Our data show that canonical Wnt signalling, which is essential for determining the neuroepithelial character of the neocortical ventricular zone, is mediated by Tcf7L2.

• Keywords
• Neocortex, Neurogenenesis, Tcf7L1, Tcf7L2, Wnt signalling,
• MeSH
• Cell Differentiation genetics   MeSH
• Chloride-Bicarbonate Antiporters MeSH
• Down-Regulation genetics   MeSH
• Embryo, Mammalian MeSH
• Hippocampus cytology   embryology   MeSH
• Mutation genetics   MeSH
• Mice, Transgenic MeSH
• Mice MeSH
• Neocortex cytology   embryology   MeSH
• Neural Stem Cells physiology   MeSH
• Neurogenesis physiology   MeSH
• Neuroglia MeSH
• Neurons physiology   MeSH
• Cell Count MeSH
• Cell Proliferation genetics   MeSH
• Transcription Factor 7-Like 2 Protein genetics   metabolism   MeSH
• T-Box Domain Proteins metabolism   MeSH
• Wnt Proteins metabolism   MeSH
• Retinal Ganglion Cells physiology   MeSH
• Signal Transduction genetics   MeSH
• SOXB1 Transcription Factors metabolism   MeSH
• Animals MeSH
• Check Tag
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Chloride-Bicarbonate Antiporters MeSH
• Eomes protein, mouse MeSH Browser
• Transcription Factor 7-Like 2 Protein MeSH
• T-Box Domain Proteins MeSH
• Wnt Proteins MeSH
• Sox2 protein, mouse MeSH Browser
• Tcf7l2 protein, mouse MeSH Browser
• SOXB1 Transcription Factors MeSH