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Cited by 156Developmental Biology and Gene RegulationEchinoderm biology and ecologyMarine Invertebrate Physiology and Ecology

Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution

Open access
Gao, Feng, Davidson, Eric H.·2008·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0801201105PMC PMC2329712
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Abstract

Of the five echinoderm classes, only the modern sea urchins (euechinoids) generate a precociously specified embryonic micromere lineage that ingresses before gastrulation and then secretes the biomineral embryonic skeleton. The gene regulatory network (GRN) underlying the specification and differentiation of this lineage is now known. Many of the same differentiation genes as are used in the biomineralization of the embryo skeleton are also used to make the similar biomineral of the spines and test plates of the adult body. Here, we determine the components of the regulatory state upstream of these differentiation genes that are shared between embryonic and adult skeletogenesis. An abrupt “break point” in the micromere GRN is thus revealed, on one side of which most of the regulatory genes are used in both, and on the other side of which the regulatory apparatus is entirely micromere-specific. This reveals the specific linkages of the micromere GRN forged in the evolutionary process by which the skeletogenic gene batteries were caused to be activated in the embryonic micromere lineage. We also show, by comparison with adult skeletogenesis in the sea star, a distant echinoderm outgroup, that the regulatory apparatus responsible for driving the skeletogenic differentiation gene batteries is an ancient pleisiomorphic aspect of the echinoderm-specific regulatory heritage.

Verified 2026-10-06 · 2 references not checked yet

AI snapshot

Written from the paper’s full text.

TL;DR

This study maps which components of the sea urchin micromere gene regulatory network are shared with juvenile adult skeletogenic centers, revealing an abrupt break point just downstream of the pmar1-hesC double-negative gate. It argues that a large, ancient skeletogenic regulatory apparatus was transferred into the embryonic micromere lineage, with additional cooptions, and that this apparatus is shared with sea stars.

Key findings

  • The micromere GRN contains 31 genes, of which 23 are regulatory/signaling genes (one unidentified) and the remainder are differentiation genes. In juvenile skeletogenic centers, the initial micromere specification and signaling portions are not used, but most regulatory genes upstream of the differentiation batteries and downstream of initial specification are shared; the junction is just downstream of the pmar1-hesC linkage.
  • At least four genes are used in micromeres but not in juvenile centers: foxB, foxO, tel, and tbrain (tbr). tbr provides an explicit case of cooption, because it is expressed in endomesoderm in other echinoderms, including sea stars, but in echinoids is expressed only in the skeletogenic micromere lineage.
  • In the sea star Asterina miniata, eight key skeletogenic regulatory genes and one downstream gene were tested in juvenile skeletogenesis centers, and results were identical to those in sea urchin larvae, suggesting the skeletogenic regulatory apparatus may be an ancient pleisiomorphic GRN unit.
  • In sea urchins, the larval cells producing adult skeletal structures are not descendants of the skeletogenic micromere lineage but an independently arising postembryonic mesodermal cell population.

Methods

  • Sea urchin (Strongylocentrotus purpuratus) and sea star (A. miniata) larvae were cultured and fed Rhodomonas lens and/or R. salina; adult skeleton was first visible at 2 and 4 weeks after fertilization, respectively, and larvae required 6 and 9 weeks after fertilization to reach metamorphosis competence.
  • Fixation and RNA extraction were done weekly from embryo through late larval stages. Twenty-four sea urchin skeletogenic micromere genes from the GRN and nine sea star orthologs were studied by whole-mount in situ hybridization (WMISH) using digoxigenin-labeled riboprobes of ≈1 kb, with 1-week hybridization; unclear patterns were examined in 8-μm cryosections or 4-μm Durcupan sections.
  • The authors first used QPCR measurements of staged larval RNA and then WMISH to determine whether genes functionally linked in the micromere GRN are expressed in juvenile skeletogenic centers, superimposing these data on the micromere GRN map.

Limitations

  • The paper states that it cannot be certain the genes in the shared region of the map are linked similarly in the two developmental contexts, though it can be fairly certain of the micromere-specific parts. It also notes there could be additional genes used in juvenile centers but not in micromeres, and that little comparative evidence exists on the underlying vegetal specification GRN.
  • The paper states that the proposed evolutionary pathway is a plausible reconstruction rather than a proven one, and that the pleisiomorphic nature of the skeletogenic regulatory apparatus could only be substantiated by determining whether the actual cis-regulatory linkages are as conserved as the gene expression complex.
  • Evident from the text: functional linkages in larval skeletogenesis were not established, expression presence/absence does not demonstrate causality, and the analysis sampled a limited set of genes, including one unidentified regulatory gene and only eight regulatory genes plus one downstream gene in the sea star comparison.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1073/pnas.0801201105

Cites

27 of 29 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 22 cited sources checked · 0 supported · 0 flagged

  • Findingown data
    § Discussion

    The skeletogenic regulatory apparatus of micromeres differs from that of juvenile skeletogenesis centers by at least four genes used in micromeres but not juvenile centers: foxB, foxO, tel, and tbrain.

    “The skeletogenic regulatory apparatus of the micromeres differs from that of the juvenile skeletogenesis centers by at least four genes that are used in the micromeres but not in the juvenile centers (of course, there could be others used in the juvenile and not in the micromeres). These are foxB, foxO, tel, and tbrain (tbr) (blue regions in Fig. 3).”
    Quote in the paperSubstantial claim
  • Findingown data
    § Results

    The part of the micromere GRN that presents inductive signals to adjacent cells is not used in juvenile skeletogenic centers.

    “nor is the part of the GRN the function of which is presentation of inductive signals to the adjacent cells (green in Fig. 3).”
    Quote in the paperSubstantial claim
  • Findingown data
    § Results

    In sea star larvae, the juvenile skeletogenesis centers express eight key skeletogenic regulatory genes and one downstream gene, with results identical to those seen in sea urchin larvae.

    “We tested the juvenile skeletogenesis centers of advanced sea star larvae for expression of eight key skeletogenic regulatory genes and one downstream gene (Table S1) and found results identical to those seen in sea urchin larvae.”
    Quote in the paperSubstantial claim
  • Findingown data
    § Results

    The exact point at which the micromere-specific regulatory apparatus and the definitive skeletogenic regulatory systems are joined, or were joined in evolution, is just downstream of the pmar1-hesC linkage in the GRN.

    “The exact point at which the micromere-specific regulatory apparatus and the definitive skeletogenic regulatory systems are joined, or were joined in evolution, is just downstream of the pmar1-hesC linkage in the GRN (Fig. 3).”
    Quote in the paperSubstantial claim
  • Findingown data
    § Results

    The expressed differentiation genes tested, and with few exceptions the complete repertoire of expressed regulatory genes upstream of these gene batteries and downstream of the initial specification system, are shared with juvenile skeletogenic centers.

    “But the expressed differentiation genes tested, and, with few exceptions, the complete repertoire of expressed regulatory genes upstream of these gene batteries and downstream of the initial specification system is shared with the juvenile skeletogenic centers (red in Fig. 3).”
    Quote in the paperSubstantial claim
  • May combine two claims. 5
  • Classified as probably not a substantial claim. 4

  • May combine two claims.

    Findingown data
    § Results

    The part of the micromere GRN that installs the initial state of micromere specification is particular to micromeres and is not used in juvenile skeletogenic centers.

    “The part of the GRN the function of which is to install the initial state of micromere specification is particular to the micromeres and is not used in the juvenile skeletogenic centers (violet region in Fig. 3)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data
    § Abstract

    The micromere GRN has an abrupt break point: on one side most regulatory genes are used in both embryonic and adult skeletogenesis, and on the other side the regulatory apparatus is entirely micromere-specific.

    “An abrupt “break point” in the micromere GRN is thus revealed, on one side of which most of the regulatory genes are used in both, and on the other side of which the regulatory apparatus is entirely micromere-specific.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given
    § Discussion

    The subnetwork was inserted into an also-pleisiomorphic regulatory apparatus operating to define the vegetal endomesoderm of the egg.

    “Of course, the subnetwork was inserted not into a vacuum but rather into an also-pleisiomorphic regulatory apparatus operating to define the vegetal endomesoderm of the egg.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based). May combine two claims.

    Interpretationnone given
    § Discussion

    Cooption of additional regulatory genes, erection of stabilizing intergenic circuitry, and formulation of biomineralization gene batteries by linking them into modified mesodermal regulatory circuitry must have taken place in the remote preskeletogenic stem group echinoderm lineage.

    “Cooption of some additional regulatory genes, erection of stabilizing intergenic circuitry, and formulation of biomineralization gene batteries by linking them into the modified mesodermal regulatory circuitry must have taken place in the remote preskeletogenic stem group echinoderm lineage.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Many genes of the pleisiomorphic skeletogenic regulatory apparatus are also expressed in nonskeletogenic mesoderm.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation
    § Discussion

    The near universal eumetazoan nuclearization of β-catenin in embryonic cells at the vegetal poles of eggs in deuterostomes, lophotrochozoans, and cnidarians suggests the underlying vegetal specification GRN could be phylogenetically widespread.

    “But this could be a phylogenetically widespread system judging from clues such as the near universal eumetazoan nuclearization of β-catenin in embryonic cells at the vegetal poles of eggs in deuterostomes, lophotrochozoans, and cnidarians (22–25).”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [22] Logan CY, Miller JR, Ferkowicz MJ, McClay DR. Nuclear beta-catenin is required to specify vegetal cell fates in the sea urchin embryo. Development. 1999;126:345–357. doi: 10.1242/dev.126.2.345. [DOI] [PubMed] [Google Scholar]

      Not checked in the free run.

    • cites [23] Imai K, Takada N, Satoh N, Satou Y. β-catenin mediates the specification of endoderm cells in ascidian embryos. Development. 2000;127:3009–3020. doi: 10.1242/dev.127.14.3009. [DOI] [PubMed] [Google Scholar]

      Not checked in the free run.

    • cites [24] Schneider SQ, Bowerman B. Beta-catenin asymmetries after all animal/vegetal-oriented cell divisions in Platynereis dumerilii embryos mediate binary cell-fate specification. Dev Cell. 2007;13:73–86. doi: 10.1016/j.devcel.2007.05.002. [DOI] [PubMed] [Google Scholar]

      Not checked in the free run.

    • cites [25] Wikramanayake AH, et al. An ancient role for nuclear beta-catenin in the evolution of axial polarity and germ layer segregation. Nature. 2003;426:446–450. doi: 10.1038/nature02113. [DOI] [PubMed] [Google Scholar]

      Not checked in the free run.

  • May combine two claims.

    Premisecitation
    § Discussion

    tbr provides an explicit case of cooption because it is expressed in endomesoderm in other echinoderms including sea stars, where it is obligatory for endomesoderm specification, whereas in echinoids it is expressed only in the skeletogenic micromere lineage.

    “tbr provides an explicit case of cooption, because this gene is expressed in endomesoderm in other echinoderms, including sea stars (20, 21), where it is obligatory for endomesoderm specification (21); in echinoids, tbr is expressed only in the skeletogenic micromere lineage.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [20] Maruyama YK. A sea cucumber homolog of the mouse T-Brain-1 is expressed in the invaginated cells of the early gastrula in Holothuria leucospilota. Zool Sci. 2000;17:383–389. doi: 10.2108/jsz.17.383. [DOI] [PubMed] [Google Scholar]

      Not checked in the free run.

    • cites [21] Hinman VF, Nguyen AT, Davidson EH. Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci USA. 2007;104:19404–19409. doi: 10.1073/pnas.0709994104. [DOI] [PMC free article] [PubMed] [Google Scholar] source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data
    § Results

    The skeletogenic regulatory apparatus may have existed as a modular GRN unit since early in echinoderm history, and it was this same unit that was placed into the embryological control system defining the micromere lineage regulatory state.

    “The skeletogenic regulatory apparatus may thus have existed as a modular GRN unit since early in echinoderm history, and it was this same unit that was placed into the embryological control system defining the micromere lineage regulatory state.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).

    Interpretationnone given
    § Discussion

    A similar sequence of events engaging other kinds of mesodermal structural genes, superimposed on a broadly distributed mesodermal regulatory state, must underlie the evolutionary diversification of mesoderm in Bilateria.

    “A similar sequence of events engaging other kinds of mesodermal structural genes, superimposed on a broadly distributed mesodermal regulatory state, must underlie the evolutionary diversification of mesoderm in Bilateria.”
    Quote in the paperNot a substantial claim
8 of 8

  • The paper relies on this without support.

    Expression of a gene in juvenile skeletogenic centers is sufficient to indicate its use in adult skeletogenesis.

    “Although it is not easy to establish functional linkages in larval skeletogenesis, we could determine first by QPCR measurements of staged larval RNA, and then by whole-mount in situ hybridization (WMISH), whether or not the genes that are known to be functionally linked in the micromere GRN are expressed in the specific juvenile skeletogenic centers of the larva.”

  • The paper relies on this without support.

    Genes in the shared region of the GRN map are linked similarly in the two developmental contexts.

    “Although we cannot be certain that the genes in the shared region of the map are indeed linked similarly in the two developmental contexts, we can be fairly certain of the parts that are micromere-specific.”

  • The paper relies on this without support.

    The sea star genes studied are orthologs of the sea urchin skeletogenic regulatory genes.

    “Twenty-four skeletogenic micromere genes from the sea urchin GRN and nine sea star orthologs isolated by library screening and degenerate PCR were studied by WMISH.”

  • The paper relies on this without support.

    Many genes of the pleisiomorphic skeletogenic regulatory apparatus are also expressed in nonskeletogenic mesoderm.

    “Although it lies beyond the scope of this article, an essential point is that many of the genes of this GRN circuitry are also expressed in nonskeletogenic mesoderm.”
4 of 4

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In sea urchins, a Class-specific evolutionary modification caused the acquisition of an embryonic skeleton not present in other echinoderms.

    “One example of a subcircuit-level co-option event has been discovered in sea urchins, in which a Class-specific evolutionary modification has caused the acquisition of an embryonic skeleton not present in other echinoderms.”

    From Evolution of Gene Regulatory Networks Controlling Body Plan Development (2011) · cites this paper as Gao and Davidson, 2008

    The Discussion (Heterochrony; page unavailable) describes an evolutionary transfer of a skeletogenic gene-regulatory subnetwork to an embryonic developmental address in sea urchins. But the paper’s introductory passage says that ophiouroid embryos also have skeletons, built differently. The modification is therefore supported; the claim that an embryonic skeleton is absent from all other echinoderms is not. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Regulatory genes exclusive to the embryonic GRN determine the embryonic location in which the skeletogenic GRN is activated.

    “Regulatory genes exclusive to the embryonic GRN are those determining the embryonic location in which the skeletogenic GRN is activated.”

    From Evolution of Gene Regulatory Networks Controlling Body Plan Development (2011) · cites this paper as Gao and Davidson, 2008

    The Results and Discussion identify a micromere-specific specification system that establishes the embryonic regulatory state into which the shared skeletogenic apparatus is linked. But the Discussion also identifies genes used in embryonic micromeres and not juvenile skeletogenic centers—including foxB, foxO, tel, and tbr—as parts of the skeletogenic apparatus or possible cell-biology controls. Thus, the paper does not support saying that all regulatory genes exclusive to the embryonic GRN determine its location of activation. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • A comparison of regulatory gene expression in embryonic and adult skeletogenic precursor cells revealed a large overlap at least at the nodes of these GRNs, which very likely extends also to the linkages between them.

    “A comparison of regulatory gene expression in embryonic and adult skeletogenic precursor cells revealed a large overlap at least at the nodes of these GRNs which very likely extends also to the linkages between them (Gao and Davidson, 2008; Oliveri et al., 2008).”

    From Evolution of Gene Regulatory Networks Controlling Body Plan Development (2011) · cites this paper as Gao and Davidson, 2008

    The Results report that, with few exceptions, embryonic micromeres and juvenile skeletogenic centers express the same regulatory genes in the skeletogenic portion of the network. The Discussion proposes transfer of a GRN subnetwork but explicitly says it cannot be certain that the shared genes are linked similarly in the two contexts. The claimed overlap in nodes is supported; the assertion that it very likely extends to linkages is stronger than the comparison establishes. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • The entire skeletogenic network was highjacked from the portion of the genomic regulatory system that controls adult skeletogenesis.

    “we discovered that the entire skeletogenic network was highjacked from the portion of the genomic regulatory system that controls adult skeletogenesis (spines and body wall plates; Gao and Davidson 2008).”

    From An integrated view of precambrian eumetazoan evolution (2009) · cites this paper as Gao and Davidson 2008

  • Given regulatory states can be redeployed during evolution for use in developmental contexts other than immediate cell-type specification, and this redeployment probably is a major mechanism of evolutionary change in body plan.

    “Given regulatory states can be redeployed during evolution for use in developmental contexts other than immediate cell-type speci fi cation, this redeployment probably is a major mechanism of evolutionary change in body plan (22).”

    From Transphyletic conservation of developmental regulatory state in animal evolution (2011) · cites this paper as [22]

Cites

Flagged first, then by citations

1 of the 30 references couldn’t be matched to a known paper.

Research works printed but not linked: 3

  1. DH Tennent, The early influence of the spermatozoan upon the characters of echinoid larvae. Carnegie Inst Wash Publ 182, 129–138 (1914).
  2. LH Hyman The Invertebrates: Echinodermata (McGraw–Hill, New York), pp. 1–763 (1955).
  3. P Leahy Methods in Cell Biology, ed TE Schroeder (Academic, Orlando, FL), pp. 1–13 (1986).

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Related

Authors
Gao, F., & Davidson, E. H.
Affiliations
California Institute of Technology (US)
ORCID
Gao, Feng
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2008-04-22
Volume
105
Issue
16
Pages
6091-6096
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0801201105
PMC
PMC2329712
OpenAlex
W2031766495
Semantic Scholar
0f29504aa73db836d267b6e949a45534261170a5
Cited by
155
References
30
Citations by year
2026: 2 · 2025: 5 · 2024: 8 · 2023: 8 · 2022: 11 · 2021: 9 · 2020: 6 · 2019: 11 · 2018: 5 · 2017: 7 · 2016: 15 · 2015: 11 · 2014: 10 · 2013: 5 · 2012: 9
FWCI
4.52
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • CaltechAUTHORS (California Institute of Technology) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Echinoderm biology and ecology
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
Keywords
echinoid evolution, gene regulatory networks, biomineralization, skeletogenesis, sea urchins, sea stars, regulatory evolution, echinoderm phylogeny
MeSH terms
Animals, Biological Evolution, Gene Expression Regulation, Larva, Skeleton, Strongylocentrotus purpuratus, Asterina, Gene Regulatory Networks

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