Cooperative reliable response from sloppy gene-expression dynamics

TL;DR

This paper explores how complex gene networks achieve reliable responses despite individual gene expression being unreliable, revealing three network types and highlighting the role of cooperation in cellular responses.

Contribution

It introduces a classification of gene expression networks based on their response dynamics and explains the emergence of complex networks in cells for reliable functioning.

Findings

Three types of gene networks identified: direct, amplified, and cooperative responses.

Cooperative networks involve many genes responding collectively with specific structures.

Sloppy gene responses favor the evolution of complex, cooperative networks in cells.

Abstract

Gene expression dynamics satisfying given input-output relationships were investigated by evolving the networks for an optimal response. We found three types of networks and corresponding dynamics, depending on the sensitivity of gene expression dynamics: direct response with straight paths, amplified response by a feed-forward network, and cooperative response with a complex network. When the sensitivity of each gene's response is low and expression dynamics is sloppy, the last type is selected, in which many genes respond collectively to inputs, with local-excitation and global-inhibition structures. The result provides an insight into how a reliable response is achieved with unreliable units, and on why complex networks with many genes are adopted in cells.