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Related Experiment Video

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Quantitative Analysis of Protein Expression to Study Lineage Specification in Mouse Preimplantation Embryos
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Quantitative proteome dynamics across embryogenesis in a model chordate.

Alexander N Frese1,2, Andrea Mariossi1,2, Michael S Levine1,2

  • 1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

Iscience
|March 21, 2024
PubMed
Summary

This study presents a proteome atlas of the chordate Ciona, challenging the hourglass model of vertebrate evolution. Gene expression shows maximal divergence during key developmental stages, not peak conservation.

Keywords:
AnimalsEmbryologyEvolutionary developmental biologyProteomicsTranscriptomics

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Area of Science:

  • Developmental Biology
  • Evolutionary Biology
  • Proteomics

Background:

  • The evolution of gene expression in vertebrate development is not well understood.
  • Existing models, like the hourglass model, are primarily based on transcriptomic data.

Purpose of the Study:

  • To create a comprehensive proteome atlas for the model chordate Ciona across eight developmental stages.
  • To analyze the co-evolution of proteomic and transcriptomic profiles with the vertebrate Xenopus.
  • To re-evaluate the hourglass model of vertebrate development using proteomic data.

Main Methods:

  • Generated a proteome atlas of Ciona, covering approximately 7,000 translated genes.
  • Performed multi-omics analysis comparing Ciona and Xenopus developmental stages.
  • Conducted quantitative proteome comparisons to assess evolutionary conservation and divergence.

Main Results:

  • Quantitative proteome data contradicts the hourglass model, which predicts peak conservation in mid-development.
  • Maximal evolutionary divergence was observed during gastrulation and neurulation stages.
  • Significant differences were found between proteomic and transcriptomic profiles regarding evolutionary conservation.

Conclusions:

  • The hourglass model, based on transcriptomics, may not accurately reflect proteome evolution in vertebrates.
  • Proteome divergence, particularly during gastrulation and neurulation, plays a crucial role in vertebrate diversification.
  • This study provides a valuable multi-omics resource for understanding vertebrate evolutionary diversification.