Properties of developmental gene regulatory networks

Abstract

The modular components, or subcircuits, of developmental gene regulatory networks (GRNs) execute specific developmental functions, such as the specification of cell identity. We survey examples of such subcircuits and relate their structures to corresponding developmental functions. These relations transcend organisms and genes, as illustrated by the similar structures of the subcircuits controlling the specification of the mesectoderm in the Drosophila embryo and the endomesoderm in the sea urchin, even though the respective subcircuits are composed of nonorthologous regulatory genes.

Fig. 1.

GRN subcircuits used in both Drosophila and sea urchin development. Horizontal lines indicate the relevant cis-regulatory modules of the indicated genes, and the bent arrows attached represent the transcription unit; incident vertical arrows indicate positive transcription factor inputs into these cis-regulatory systems, and barred stems indicate negative inputs; double sideways “v” indicates the Notch receptor for the Delta ligand; “Regulatory State” represents the sum of expressed transcription factors at the given time and place. (A) The double negative gate. (B) Notch signaling circuitry. In Drosophila, the delta ligand is expressed in mesoderm (Meso), and Notch signaling occurs in adjacent neurogenic ectoderm causing expression of the midline gene sim; in the sea urchin, the Delta ligand is expressed in the skeletogenic mesoderm (SM), and Notch signaling occurs in adjacent nonskeletogenic mesoderm, causing expression of the pigment cell regulator gcm.