Design of genetic networks with specified functions by evolution <i>in silico</i>

TLDR

Genetic regulatory networks are modular, and quantitative functional descriptions are increasingly sought. The study introduces an in silico evolutionary procedure to generate small gene networks that perform basic tasks. The algorithm evolves networks that function as bistable switches or oscillators. The resulting circuits display diverse designs, highlight the critical role of post‑transcriptional interactions, and reveal design principles common to natural networks, providing a useful framework for understanding and building functional modules.

Abstract

Recent studies have provided insights into the modular structure of genetic regulatory networks and emphasized the interest of quantitative functional descriptions. Here, to provide a priori knowledge of the structure of functional modules, we describe an evolutionary procedure in silico that creates small gene networks performing basic tasks. We used it to create networks functioning as bistable switches or oscillators. The obtained circuits provide a variety of functional designs, demonstrate the crucial role of posttranscriptional interactions, and highlight design principles also found in known biological networks. The procedure should prove helpful as a way to understand and create small functional modules with diverse functions as well as to analyze large networks.