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Developmental gene regulatory network architecture across 500 million years of echinoderm evolution
Open accessAbstract
Evolutionary change in morphological features must depend on architectural reorganization of developmental gene regulatory networks (GRNs), just as true conservation of morphological features must imply retention of ancestral developmental GRN features. Key elements of the provisional GRN for embryonic endomesoderm development in the sea urchin are here compared with those operating in embryos of a distantly related echinoderm, a starfish. These animals diverged from their common ancestor 520-480 million years ago. Their endomesodermal fate maps are similar, except that sea urchins generate a skeletogenic cell lineage that produces a prominent skeleton lacking entirely in starfish larvae. A relevant set of regulatory genes was isolated from the starfish Asterina miniata, their expression patterns determined, and effects on the other genes of perturbing the expression of each were demonstrated. A three-gene feedback loop that is a fundamental feature of the sea urchin GRN for endoderm specification is found in almost identical form in the starfish: a detailed element of GRN architecture has been retained since the Cambrian Period in both echinoderm lineages. The significance of this retention is highlighted by the observation of numerous specific differences in the GRN connections as well. A regulatory gene used to drive skeletogenesis in the sea urchin is used entirely differently in the starfish, where it responds to endomesodermal inputs that do not affect it in the sea urchin embryo. Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered.
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In the citing paper
“As in sea urchins, gatae expression is essential for the correct specification of endoderm in A. miniata embryos (6).”
From Evolutionary plasticity of developmental gene regulatory network architecture (2007) · cites this paper as [6]
In the citing paper
“But the foxa gene represses its own transcription in the mesoderm and also represses mesodermal gatae transcription, abolishing expression of both in that territory (6).”
From Evolutionary plasticity of developmental gene regulatory network architecture (2007) · cites this paper as [6]
In the citing paper
“Because bra and foxa are downstream of both gatae and otx 𝛃 1 / 2 (6), the positive input of tbr to these endodermal genes can easily be accounted for as an indirect consequence of Tbr inputs into delta (direct or indirect) plus its direct inputs into otx 𝛃 1 / 2 .”
From Evolutionary plasticity of developmental gene regulatory network architecture (2007) · cites this paper as [6]
In the citing paper
“In the sea star the boundary depends on Foxa repression of gatae in the mesoderm (6), a function that requires a Foxa-responsive gatae cis -regulatory module.”
From Evolutionary plasticity of developmental gene regulatory network architecture (2007) · cites this paper as [6]
In the citing paper
“It is likely a pleisomorphic feature of endoderm specification in echinoderms, like the endomesodermal specification kernel (6) into which it feeds, and unlike the Delta-N function in initial mesoderm specification seen in sea urchins.”
From Evolutionary plasticity of developmental gene regulatory network architecture (2007) · cites this paper as [6]
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Metadata
- Authors
- Hinman, V. F., Nguyen, A. T., Cameron, R. A., & Davidson, E. H.
- Affiliations
- California Institute of Technology (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2003-10-31
- Volume
- 100
- Issue
- 23
- Pages
- 13356-13361
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC263818
- OpenAlex
- W2165937624
- Cited by
- 272
- References
- 31
- Citations by year
- 2026: 7 · 2025: 9 · 2024: 5 · 2023: 6 · 2022: 13 · 2021: 8 · 2020: 5 · 2019: 12 · 2018: 6 · 2017: 13 · 2016: 16 · 2015: 13 · 2014: 16 · 2013: 10 · 2012: 19
- FWCI
- 5.29
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- KiltHub Repository
- Funders
- National Institute on Aging (K07AG021587)
- National Center for Research Resources (P40RR015044, RR15044)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- gene regulatory networks, echinoderm evolution, sea urchins, sea stars, endoderm specification, skeletogenesis, feedback loops, cis-regulatory elements, developmental gene expression, morphological evolution, embryonic development
- MeSH terms
- Animals, Cloning, Molecular, Dose-Response Relationship, Drug, Echinodermata, Biological Evolution, Mesoderm, Phylogeny, RNA, Messenger, Sea Urchins, Starfish, Time Factors, Transcription Factors, Gene Expression Regulation, Developmental, Reverse Transcriptase Polymerase Chain Reaction, Feedback, Physiological
About these checks
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.
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