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

Abstract

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.

Design and implementation of three incoherent feed-forward motif based biological concentration sensors

“…Theoretical protein expression profiles of coherent (type 1) and incoherent (type 3, 4) FFL were computationally investigated by Ishihara et al (2005). They show that the levels of Z monotonically change in a coherent FFL, and that monotonic and bell-shaped curves, convex or concave, can be produced depending on which type of incoherent FFL is used.…”

“…Such biphasic responses have also been discussed in other systems (Wolf and Arkin 2003;Mayya and Loew 2005). Recently Ishihara et al (2005), discussed the band properties of such networks and used this to explain pulsed behavior and patterning in Drosophila developmental processes.…”

“…This has been suggested to be a mechanism for speeding response times in transcriptional networks (Mangan and Alon 2003). Ishihara et al (2005) showed in silico that the concentration sensitive bell shaped pattern described by Basu et al (2005) could be produced by the FFL architecture, using three genes instead of five. We have built three networks that satisfy the three gene feed-forward topology capable of validating modeling predictions.…”

Design of artificial genetic regulatory networks with multiple delayed adaptive responses*

“…, N out . Therefore, equation (12) indicates that the first output node (node-12 in Fig. 5) shows an up-regulation with τ d = 0, the second one (node-13 in Fig.…”

“…We even study adaptive responses with time delays; the output nodes show no response at all for a period of time after stimulus to input receptors, but then they suddenly start to show adaptive responses. Such responses with time-delay are observed ubiquitously [4,12], however, adaptive responses with time delays have been rarely studied.…”