Mariossi, A. | bioRxiv Science

bioRxiv2023

Quantitative proteome dynamics across embryogenesis in a model chordate

The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and [~]7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.

developmental biology↗

bioRxiv2022

Cereblon controls the timing of muscle differentiation in Ciona embryos

Thalidomide has a dark history as a teratogen, but in recent years it has been shown to function as a chemotherapeutic agent. Thalidomide binds cereblon, a component of E3 ubiquitin ligase complex and modifies its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ the simple proto-vertebrate model, Ciona intestinalis, to address this question. We observed a "hotspot" of Crbn expression in the developing tail muscles and identify its enhancer containing both Myod activator sites and a Snail repressive element. Overexpression of Crbn in tail muscles decreases expression of contractility genes. We suggest that this reduction is due to premature degradation of Tbx6. Drug inhibition studies using lenalidomide, a derivative of thalidomide, lead to a striking increase of Crbn expression. This autofeedback regulation could be induced by neomorphic degradation of Snail, contributing to the efficacy of lenalidomide in treating metastatic melanoma. In summary, our analysis of Crbn suggests that its normal function in Ciona is to time expression of contractility genes during muscle differentiation thereby ensuring coordination of tail morphogenesis and hatching of swimming tadpoles.

developmental biology↗