A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

Eric H. Davidson, Jonathan P. Rast, Paola Oliveri, Andrew Ransick, Cristina Calestani, Chiou Hwa Yuh, Takuya Minokawa, Gabriele Amore, Veronica Hinman, César Arenas-Mena, Ochan Otim, Charles Brown, Carolina B. Livi, Pei Yun Lee, Roger Revilla, Maria J. Schilstra, Peter J.C. Clarke, Alistair G. Rust, Zhengjun Pan, Maria I. ArnoneLee Rowen, R. Andrew Cameron, David R. McClay, Leroy Hood, Hamid Bolouri

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Abstract

We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/∼mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the β-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg2 endomesodermal domain; the blastula-stage separation of the central veg2 mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg2 endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages.

Original languageEnglish (US)
Pages (from-to)162-190
Number of pages29
JournalDevelopmental Biology
Volume246
Issue number1
DOIs
StatePublished - Jun 1 2002
Externally publishedYes

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Keywords

  • Gene network
  • Gene regulation
  • Sea urchin embryo

ASJC Scopus subject areas

  • Molecular Biology
  • Developmental Biology
  • Cell Biology

Cite this

Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C. H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C., Livi, C. B., Lee, P. Y., Revilla, R., Schilstra, M. J., Clarke, P. J. C., Rust, A. G., Pan, Z., ... Bolouri, H. (2002). A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Developmental Biology, 246(1), 162-190. https://doi.org/10.1006/dbio.2002.0635