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Review
. 2009 Dec;19(6):535-40.
doi: 10.1016/j.gde.2009.10.007. Epub 2009 Nov 11.

Network design principles from the sea urchin embryo

Eric H Davidson  1
Affiliations
Review

Network design principles from the sea urchin embryo

Eric H Davidson. Curr Opin Genet Dev. 2009 Dec.

Abstract

As gene regulatory network models encompass more and more of the specification processes underlying sea urchin embryonic development, topological themes emerge that imply the existence of structural network 'building blocks'. These are subcircuits which perform given logic operations in the spatial control of gene expression. The various parts of the sea urchin gene regulatory networks offer instances of the same subcircuit topologies accomplishing the same developmental logic functions but using different genes. These subcircuits are dedicated to specific developmental functions, unlike simpler 'motifs', and may indicate a repertoire of specific devices of which developmental gene regulatory networks are composed.

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Figures

Fig. 1
Fig. 1. Putative “building block” subcircuits of the sea urchin GRNs
(A, B) Double negative gate subcircuits. The first gene of the double negative gate is shown in red and the second in brown; target gene outputs are in green. In this and the following panels, thick lined linkages are backed by both trans-perturbation analysis and by direct published or unpublished cis-regulatory analysis, and thin lines are linkages deduced from trans-perturbation analysis. (A) Subcircuit from the skeletogenic mesoderm lineage (1); (B) Subcircuit from the oral ectoderm GRN (3). (C, D) Dynamic feedback lockdown subcircuits. The genes participating in the triple feedback subcircuit are colored in blue, yellow, and purple, and in each case an upstream gene receiving an additional feedback input from the triple loop is in red. (C) Subcircuit from the skeletogenic mesoderm lineage (1); (D) Subcircuit from the aboral ectoderm GRN (3). (E, F) Community effect subcircuits. The ligand genes are in blue, the signal transduction system is black, and downstream genes are in orange and red .(E) Subcircuit from the oral ectoderm GRN (22); (F) Subcircuit from the endomesoderm GRN (25).
See this image and copyright information in PMC

References

    1. Oliveri P, Tu Q, Davidson EH. Global regulatory logic for specification of embryonic cell lineage. Proc Natl Acad Sci USA. 2008;105:5955–5962. This paper for the first time provides direct evidence that the regulatory linkages of a near complete GRN suffice to explain why each of the developmental processes that can be observed biologically occurs as it does. It shows that the topology of the GRN explains the initial specification of the skeletogenic lineage, its emission of inductive signals, its stabilization of regulatory state, its activation of skeletogenic gene batteries and other functions.

    1. Kim HD, Shay T, O’Shea EK, Regev A. Transcriptional regulatory circuits: predicting numbers from alphabets. Science. 2009;326:429–432. This review considers the variety of ways transcriptional regulatory circuits can be solved and computationally dealt with, focusing on the problems of scale from small circuits to genome scale networks. It covers both prokaryote and animal gene networks and cis- and trans-oriented models.

    1. Su Y-H, Li E, Geiss GK, Krämer WJR, Davidson EH. A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev Biol. 2009;329:410–421. This paper provides the first sea urchin embryo ectoderm GRN, based on a system wide analysis of thousands of perturbation results.

    1. Wei Z, Yaguchi J, Yaguchi S, Angerer RC, Angerer LM. The sea urchin animal pole domain is a Six3-dependent neurogenic patterning center. Development. 2009;136:1179–1189. This paper focuses on the role of six3, a key early expressed upstream component of the apical domain GRN, which eventually causes activation of neurogenic genes. This is the first published work on the apical neurogenic GRN.

    1. Yaguchi S, Yaguchi J, Burke RD. Sp-Smad2/3 mediates patterning of neurogenic ectoderm by nodal in the sea urchin embryo. Dev Biol. 2007;302:494–503. - PubMed

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