A genetic regulatory network for Xenopus mesendoderm formation

Dev Biol. 2004 Jul 15;271(2):467-78. doi: 10.1016/j.ydbio.2004.04.014.


We have constructed a genetic regulatory network (GRN) summarising the functional relationships between the transcription factors (TFs) and embryonic signals involved in Xenopus mesendoderm formation. It is supported by a relational database containing the experimental evidence and both are available in interactive form via the World Wide Web. This network highlights areas for further study and provides a framework for systematic interrogation of new data. Comparison with the equivalent network for the sea urchin identifies conserved features of the deuterostome ancestral pathway, including positive feedback loops, GATA factors, SoxB, Brachyury and a previously underemphasised role for beta-catenin. In contrast, some features central to one species have not yet been found in the other, for example, Krox and Otx in sea urchin, and Mix and Nodal in Xenopus. Such differences may represent evolved features or may eventually be resolved. For example, in Xenopus, Nodal-related genes are positively regulated by beta-catenin and at least one of them is repressed by Sox3, as is the uncharacterised early signal (ES) inducing endomesoderm in the sea urchin, suggesting that ES may be a Nodal-like TGF-beta. Wider comparisons of such networks will inform our understanding of developmental evolution.

Publication types

  • Comparative Study

MeSH terms

  • Animals
  • Databases, Genetic*
  • Endoderm / metabolism*
  • Gene Expression Regulation, Developmental*
  • Mesoderm / metabolism*
  • Phylogeny
  • Sea Urchins / genetics
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Xenopus / embryology*


  • Transcription Factors