Transcription Factor

Transcription Factor

Transcription Factor

Target Gene

Target Gene

Figure 3.3

Genetic regulatory logic

A model hierarchy, pathway, circuit, battery, and network are depicted. The signaling pathways contain several obligately linked components, but their deployment is controlled by potentially diverse regulators. The target genes they control in regulatory circuits are also diverse and context-specific. Tiers of regulators and targets constitute a hierarchy. Connections between independent regulatory circuits constitute a network.

depend on one another to conduct the signal to the cell nucleus, the nature of the pathway output is usually context-dependent. When gene regulation is the output, the target genes of a given individual pathway usually differ between developmental stages and spatial locations in the developing embryo. We use the term "circuit" to describe a regulatory pathway that includes particular target genes. Thus two circuits that employ the same pathway are different if they regulate different target genes.

A group of connected circuits constitutes a regulatory network. These circuits may be connected in series or they may consist of parallel circuits that are connected by one or more links (Fig. 3.3). Some genes in the network may act earlier than others, or control the activity of many genes, organizing the network into a hierarchy. Hierarchies may be vertically organized, comprising many tiers of genes that control lower tiers of genes (Fig. 3.3). Alternatively, they may be organized more horizontally, with single genes directly controlling the expression of a large group or battery of target genes (Fig. 3.3).

Model regulatory hierarchies and the key genetic switches that operate them

The regulatory mechanisms that underlie a large number of developmental processes in the several model species belonging to a few different phyla have been analyzed in recent years. In this book, we concentrate primarily on insect and vertebrate examples because they illustrate general mechanisms of the control of toolkit gene expression and function during development. Importantly, knowledge derived from these model systems forms the foundation of the comparative approaches to the evolution of morphology described in subsequent chapters.

Our discussion focuses on the regulatory hierarchies that control the sequential generation of spatial coordinate systems that unfolds during embryogenesis—from the generation of the major body axes, to the formation of primary and secondary fields, to the patterning of individual fields. We examine at the molecular level how organizers function within embryos and fields, how gradients of morphogens are interpreted within fields, how selector genes regulate the formation and identity of individual fields, and how cz's-regulatory elements integrate combinations of regulatory inputs to control complex spatial patterns of toolkit gene expression.

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