Quantitative proteome dynamics across embryogenesis in a model chordate

Alexander N Frese; Andrea Mariossi; Michael S Levine; Martin Wühr

doi:10.1016/j.isci.2024.109355

Quantitative proteome dynamics across embryogenesis in a model chordate

iScience. 2024 Feb 29;27(4):109355. doi: 10.1016/j.isci.2024.109355. eCollection 2024 Apr 19.

Authors

Alexander N Frese^{1

2}, Andrea Mariossi^{1

2}, Michael S Levine^{1

2}, Martin Wühr^{1

2}

Affiliations

¹ Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
² Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Abstract

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.

Keywords: Animals; Embryology; Evolutionary developmental biology; Proteomics; Transcriptomics.

Grants and funding

R35 GM128813/GM/NIGMS NIH HHS/United States