Flexible and robust patterning by centralized gene networks

TL;DR

This paper explores how centralized gene networks with a bow-tie architecture can generate diverse dynamic patterns and exhibit robust control, with implications for understanding cellular processes.

Contribution

It introduces a theoretical framework for centralized gene networks, demonstrating their ability to produce complex dynamics and switch attractors efficiently.

Findings

Centralized networks can generate any prescribed patterning dynamics.

Activation or silencing of a node can sharply switch network attractors.

Centralized networks are more robust to perturbations in the PC regime.

Abstract

We consider networks with two types of nodes. The v-nodes, called centers, are hyperconnected and interact one to another via many u-nodes, called satellites. This centralized architecture, widespread in gene networks, realize a bow-tie scheme and possesses interesting properties. Namely, this organization creates feedback loops that are capable to generate any prescribed patterning dynamics, chaotic or periodic, and create a number of equilibrium states. We show that activation or silencing of a node can sharply switch the network attractor, even if the activated or silenced node is weakly connected. We distinguish between two dynamically different situations, "power of center" (PC) when satellite response is fast and "satellite power" (SP) when center response is fast. Using a simple network example we show that a centralized network is more robust with respect to time dependent perturbations, in the PC relative to the SP case. In theoretical molecular biology, this class of models can be used to reveal a non-trivial relation between the architecture of protein-DNA and protein-protein interaction networks and controllability of space-time dynamics of cellular processes.