Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes

Gene regulatory networks contain several substructures called network motifs, which frequently exist throughout the networks. One of such motifs found in Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster is the feed-forward loop, in which an effector regulates its target by a direct regulatory interaction and an indirect interaction mediated by another gene product. Here, we theoretically analyze the behavior of networks that contain feed-forward loops cross talking to each other. In response to levels of the effecter, such networks can generate multiple rise-and-fall temporal expression profiles and spatial stripes, which are typically observed in developmental processes. The mechanism to generate these responses reveals the way of inferring the regulatory pathways from experimental results. Our database study of gene regulatory networks indicates that most feed-forward loops actually cross talk. We discuss how the feed-forward loops and their cross talks can play important roles in morphogenesis.