Regulatory genome information processing during early development in the sea urchin

Smadar Ben-Tabou De-Leon and Eric Davidson (California Institute of Technology)

Abstract

The regulatory genome functions through development as an immense information processor. The basic information processing units are individual cis-regulatory modules that receive multiple inputs in form of the transcription factors that bind to them. The cid-regulatory modules action on these inputs can be described in terms of OR, AND, and NOT logical functions, the combination of which is the resulting expression output. The regulatory genes that play a part in development are functionally interconnected through their cis-regulatory modules to form structures with increasing complexity, such as network motifs, network subcircuits, and, eventually, gene regulatory networks. Gene regulatory networks are essentially the genomic program of development. The sea urchin gene regulatory network provides a clear view of the information processing that is done by the different organization levels of the regulatory apparatus. It enables a thorough analysis of both the subcircuits' topology and of the individual cis-regulatory modules that comprise the subcircuits. Here we demonstrate how high fidelity developmental output is achieved at the various levels of the regulatory apparatus. First we analyze the subcircuit that is responsible for processing the asymmetric distributions of cellular components in the egg and transforms them into the onset of spatially localized specification state. Then we show how the network regulates the timely differential activation of signaling molecules, transcription factors and differentiation genes.

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