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Cited by 10Developmental Biology and Gene RegulationAdvanced Proteomics Techniques and ApplicationsGenomics and Phylogenetic Studies

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Quantitative proteome dynamics across embryogenesis in a model chordate

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Frese, Alexander N., Mariossi, Andrea, Levine, Michael S., Wühr, Martin·2024·iScience
DOI 10.1016/j.isci.2024.109355PMC PMC10951915

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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.

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Metadata

Authors
Frese, A. N., Mariossi, A., Levine, M. S., & Wühr, M.
Affiliations
Princeton University (US)
Corresponding author
  • Levine, Michael S.
  • Wühr, Martin
ORCID
Venue
iScience
Publisher
Elsevier BV
Published
2024-04
Volume
27
Issue
4
Pages
109355
ISSN
2589-0042 (ISSN-L)
DOI
10.1016/j.isci.2024.109355
PMC
PMC10951915
OpenAlex
W4392302660
Cited by
10
References
11
Citations by year
2026: 6 · 2025: 2 · 2024: 2
FWCI
1.36
Type
journal article
Language
en
Open access
Licence
Locations
  • iScience (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Princeton University (R35GM128813, NS076542)
  • NIH (R35GM128813, NS076542, T32GM007388)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
embryonic development, proteome dynamics, Ciona intestinalis, Xenopus, hourglass model, developmental gene expression, gastrulation, neurulation, vertebrate evolution

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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