Clock-driven waves of Tbx6 expression prefigure somite boundaries
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ABSTRACT:
PROVIDER: PRJNA1024523 | ENA |
REPOSITORIES: ENA
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Project description:One of the major events of vertebrate embryonic development is the segmentation of the body axis into transient blocks of tissue, called somites, that ultimately give rise to vertebrae, ribs, and skeletal muscles of the adult body. Somites bud off from the presomitic mesoderm (PSM) by the sequential and rhythmic formation of new boundaries. The periodicity of the process is controlled by the segmentation clock, which manifests as spatiotemporal waves of Hes/Her gene expression travelling anteriorly in the PSM and reiterating during the formation of each somite. In zebrafish, the genes her1 and her7 form a the core of this genetic oscillator. We discovered that the protein expression of the gene Tbx6 oscillates, driven by the Her1;Her7 loop. Although Her binding to gene regulatory sequences has been tested in vitro, the binding of Her1 or Her7 to regulatory regions in the embryo remains unknown. To assess whether Her1 and Her7 directly bind to tbx6, we performed CUT&Tag using anti-GFP antibodies to address the genomic binding landscape of the fusion proteins Her1-YFP and Her7-YFP from their respective transgenic lines, as no antibodies against Her1 and Her7 currently exist.
2023-11-09 | GSE244768 | GEO
Project description:Axial development of mammals is a dynamic process involving several coordinated morphogenetic events, including axial elongation, somitogenesis, and neural tube formation. To gain insight into the signals control the dynamics of human axial morphogenesis, we generated hundreds of axially elongating organoids by inducing anteroposterior symmetry breaking of spatially coupled epithelial cysts derived from human pluripotent stem cells. Each organoid was composed of a neural tube flanked by presomitic mesoderm sequentially segmented into somites. Periodic activation of the somite differentiation gene MESP2 coincided in space and time with anteriorly traveling segmentation clock waves in the presomitic mesoderm of the organoids, recapitulating critical aspects of somitogenesis. Through timed perturbations of organoids, we demonstrated that FGF and WNT signaling play distinct roles in axial elongation and somitogenesis and that FGF signaling gradients drive the segmentation clock waves. By generating and perturbing organoids that robustly recapitulate the architecture and dynamics of multiple axial tissues in human embryos, this work offers a means to dissect complex mechanisms underlying human embryogenesis.
2022-12-12 | GSE220563 | GEO
Project description:All vertebrates share a segmented body axis. Segments form from the rostral end of the presomitic mesoderm (PSM) with a periodicity that is regulated by the segmentation clock. The segmentation clock is a molecular oscillator that exhibits dynamic clock gene expression across the PSM with a periodicity that matches somite formation. Notch signalling is crucial to this process. Altering Notch intracellular domain (NICD) stability affects both the clock period and somite size. However, the mechanism by which NICD stability is regulated in this context is unclear. We identified a highly conserved site crucial for NICD recognition by the SCF E3 ligase, which targets NICD for degradation. We demonstrate both CDK1 and CDK2 can phosphorylate NICD in the domain where this crucial residue lies and that NICD levels vary in a cell cycle-dependent manner. Inhibiting CDK1 or CDK2 activity increases NICD levels both in vitro and in vivo, leading to a delay of clock gene oscillations and an increase in somite size.
2020-03-24 | PXD013038 | Pride
Project description:The number of vertebrae is strictly defined for any given species1, and depends on the number of somites, which are periodically formed as perfectly matched cell masses during mid-embryogenesis, where the somite segmentation clock prescribes the timing2. The tempo of the clock is affected by surrounding condition, despite which the same number of somites is formed3, suggesting that the clock may be tunable to adapt to the environmental condition. Here, we demonstrate a tunability of the segmentation clock in the period depending on the level of Notch signaling that senses the surrounding information to adjust the number of somites and vertebrae precisely, in which we propose a mechanism of the clock with a feedback loop of Notch signaling by Notch-regulated ankyrin repeat protein (Nrarp). Disruption of Nrarp in mouse resulted in the loss of two vertebrae, due to 4-min extension of the period of the clock elicited by the up-regulation of Notch activity, whereas pharmacological diminishment of Notch activity shortens it by a few min. The Notch inhibitor rescues the phenotype of Nrarp knockout mice in the period. These results are comprehended by mathematical analyses, in which the period of the clock is fine-tuned by Notch activity that Nrarp adjusts. Overall, our results are the first to provide molecular evidence of fine-tuning of the segmentation clock that preserves the number of somites and vertebrae.
2010-10-01 | GSE18419 | GEO
Project description:The number of vertebrae is strictly defined for any given species1, and depends on the number of somites, which are periodically formed as perfectly matched cell masses during mid-embryogenesis, where the somite segmentation clock prescribes the timing2. The tempo of the clock is affected by surrounding condition, despite which the same number of somites is formed3, suggesting that the clock may be tunable to adapt to the environmental condition. Here, we demonstrate a tunability of the segmentation clock in the period depending on the level of Notch signaling that senses the surrounding information to adjust the number of somites and vertebrae precisely, in which we propose a mechanism of the clock with a feedback loop of Notch signaling by Notch-regulated ankyrin repeat protein (Nrarp). Disruption of Nrarp in mouse resulted in the loss of two vertebrae, due to 4-min extension of the period of the clock elicited by the up-regulation of Notch activity, whereas pharmacological diminishment of Notch activity shortens it by a few min. The Notch inhibitor rescues the phenotype of Nrarp knockout mice in the period. These results are comprehended by mathematical analyses, in which the period of the clock is fine-tuned by Notch activity that Nrarp adjusts. Overall, our results are the first to provide molecular evidence of fine-tuning of the segmentation clock that preserves the number of somites and vertebrae. Nrarp mutant mouse which have LacZ gene instead of Nrarp coding region was generated by homologous recombinant. Fragnant female heterozygous mutant mice, mated with heterozygous mutant male, were dissected at embryonic day 10.5 (E10.5). 12 PSMs were collected in each genotype to extract total RNA.
2010-10-01 | E-GEOD-18419 | biostudies-arrayexpress
Project description:Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves
| PRJNA910218 | ENA
Project description:Mammalian circadian clocks precisely control the rhythms of behavior and physiology, and can be reset by various environmental signals. While the light-dark (LD) cycle resets the master clock, timed food intake is a potent synchronizer of peripheral clocks. As the largest metabolic organ, the liver sensitively responds to the food signals and secrets hepatokines, leading to the robust regulation of metabolic and clock processes. However, it remains unknown which hepatokine mediates the food-driven resetting of the liver clock independent of the master clock. In our current study, we clustered high-throughput RNA sequencing results to screen out candidate genes that mediate the food-driven resetting of the liver clock
2019-06-27 | GSE133342 | GEO
Project description:A Clock-Driven Neural Network Critical for Arousal
| PRJNA609641 | ENA
Project description:Somite segmentation depends on a gene expression oscillator or clock in the posterior presomitic mesoderm (PSM) and on read-out machinery in the anterior PSM to convert the pattern of clock phases into a somite pattern. Notch pathway mutations disrupt somitogenesis, and previous studies have suggested that Notch signalling is required both for the oscillations and for the read-out mechanism. By blocking or overactivating the Notch pathway abruptly at different times, we show that Notch signalling has no essential function in the anterior PSM and is required only in the posterior PSM, where it keeps the oscillations of neighbouring cells synchronized. Using a GFP reporter for the oscillator gene her1, we measure the influence of Notch signalling on her1 expression and show by mathematical modelling that this is sufficient for synchronization. Our model, in which intracellular oscillations are generated by delayed autoinhibition of her1 and her7 and synchronized by Notch signalling, explains the observations fully, showing that there are no grounds to invoke any additional role for the Notch pathway in the patterning of somite boundaries in zebrafish.
| S-EPMC2222926 | biostudies-literature
Project description:RNAseq from somite-matched frontonasal prominence (FNP) from E10.5 embryos at the 29-somite developmental stage
2021-05-08 | GSE174090 | GEO