| The vertebrate body plan is characterized by a segmented organization which is visible at the level of the vertebral column, its associated muscles and the peripheral nervous system. This basic organization is first established during embryogenesis through the periodic formation of embryonic segments called somites. This process is associated with a molecular oscillator---the segmentation clock---which drives the expression of cyclic genes in the tissue precursor of the somites, the presomitic mesoderm (PSM). Thus far, a handful of cyclic genes has been identified using a candidate gene approach, with the majority of them belonging to the Notch pathway. The work presented here utilizes the power of microarray genomic tools to search for new cyclic genes, allowing the first quantitative and systematic analyses of the segmentation clock systems in mouse and chick.;We first generated a time series microarray dataset of mouse PSMs during one clock oscillation cycle. Due to the limiting amount of starting material, our protocol included two rounds of amplification controlled for reproducibility and quality. We performed a mathematical (Lomb-Scargle) analysis to identify periodic expression profiles. By hierarchically clustering expression profiles, we identified a first cluster containing cyclic genes related to Notch and FGF signaling. A second cluster contained almost exclusively genes related to Wnt signaling, cycling in antiphase with the genes from the first cluster. Candidate genes were validated by in situ hybridization on mouse embryos. Consistently, mouse mutants for some newly identified cyclic genes exhibit segmentation defects. A second time series was generated using whole mouse expression arrays. Approximately a hundred of candidates, commonly found by the two time series, as well as additional candidates were identified, enlarging the Wnt and Notch-FGF clusters. Finally, analysis of a time series microarray dataset generated in chick, identified FGF genes cycling in phase with Notch genes, and Wnt genes cycling in antiphase.;In conclusion, this work uncovers a complex oscillating network of common signaling pathways (organized in negative feedback loops) underlying the segmentation clock. However, cross-species comparison reveals little conservation of the cyclic genes, suggesting that the clock regulates different components of these pathways in mouse and chick. |
