Eric H. Davidson,^1* Jonathan P. Rast,¹ Paola Oliveri,¹ Andrew Ransick,¹ Cristina Calestani,¹ Chiou-Hwa Yuh,¹ Takuya Minokawa,¹ Gabriele Amore,¹ Veronica Hinman,¹ César Arenas-Mena,¹ Ochan Otim,¹ C. Titus Brown,¹ Carolina B. Livi,¹ Pei Yun Lee,¹ Roger Revilla,¹ Alistair G. Rust,² Zheng jun Pan,² Maria J. Schilstra,² Peter J. C. Clarke,² Maria I. Arnone,³ Lee Rowen,⁴ R. Andrew Cameron,¹ David R. McClay,⁵ Leroy Hood,⁴ Hamid Bolouri²

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

¹ Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
² Science and Technology Research Centre, University of Hertfordshire, AL10 9AB, UK.
³ Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.
⁴ Institute for Systems Biology, Seattle, WA 98105, USA.
⁵ Department of Zoology, Duke University, Durham, NC 27708-0325, USA.
^*   To whom correspondence should be addressed. E-mail: davidson{at}caltech.edu

   Present address: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB101 1SD, UK.

   Present address: Altera European Technology Centre, Holmers Farm Way, High Wycombe, Buckinghamshire HP12 4XF, UK.