216 CATALYZING INQUIRY
FIGURE 6.1 The endomesoderm specification network in the sea urchin species Strongylocentrotus purpuratus.
The period of activity represented spans embryonic growth from single cell to gastrulation (approximately 600
cells). The different background colors denote different cell types, as indicated on the cartoon of an early blastula-
stage embryo on the top right. The short, thick horizontal lines represent regulatory DNA of a particular gene in
the network, to which transcription factors bind to activate or repress transcription. The bent arrow emanating
from each regulatory domain represents the basal transcription apparatus of the gene, and the line(s) emerging
from it represent the interactions of the product of the gene with other proteins (via the white and black interaction
boxes) or cis-regulatory DNA.
The architecture of the network is based on perturbation and expression data, on data from cis-regulatory
analyses for several genes, and on other experiments discussed in the references below. For quantitative results of
perturbation experiments and temporal details and the latest view of the network, see http://sugp.caltech.edu/
endomes/.
The repression cascade motif referred to in the text is indicated by the thick black (upstream gene) and gray
(downstream genes) arrows. This work is described in the following:
- E.H. Davidson, J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.H. Yuh, T. Minokawa, et al., “A Genomic
Regulatory Network for Development,” Science 295(5560):1669-1678, 2002. - H. Bolouri and E.H. Davidson, “Modeling DNA Sequence-based cis-Regulatory Gene Networks,” Develop-
mental Biology 246(1):2-13, 2002. - C.T. Brown, A.G. Rust, P.J.C. Clarke, Z. Pan, M.J. Schilstra, T. De Buysscher, G. Griffin, et al., “New Compu-
tational Approaches for Analysis of cis-Regulatory Networks,” Developmental Biology 246(1):86-102, 2002. - A. Ransick, J.P. Rast, T. Minokawa, C. Calestani, and E.H. Davidson, “New Early Zygotic Regulators of
Endomesoderm Specification in Sea Urchin Embryos Discovered by Differential Array Hybridization,” Develop-
mental Biology 246(1):132-147, 2002. - C.H. Yuh, C.T. Brown, C.B. Livi, L. Rowen, P.J.C. Clarke, and E.H. Davidson, “Patchy Interspecific Sequence
Similarities Efficiently Identify Positive cis-Regulatory Elements in the Sea Urchin,” Developmental Biology
246(1):148-161, 2002.