Edge usage, motifs and regulatory logic for cell cycling genetic networks

TL;DR

This study investigates the structural features and motifs of genetic regulatory networks involved in cell cycling across different species, revealing common motifs and a regulatory logic based on feed-forward cascades.

Contribution

It introduces an in silico ensemble approach to identify shared network motifs and regulatory principles underlying cell cycle control across species.

Findings

Networks reuse a few key interactions as building blocks.

Enrichment of similar network motifs in yeast systems.

Regulatory logic involves feed-forward cascades.

Abstract

The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression patterns? We tackle this question in silico by examining the ensemble of all regulatory networks which satisfy the constraint of producing a given sequence of gene expressions. We focus on three cell cycle profiles coming from baker's yeast, fission yeast and mammals. First, we show that the networks in each of the ensembles use just a few interactions that are repeatedly reused as building blocks. Second, we find an enrichment in network motifs that is similar in the two yeast cell cycle systems investigated. These motifs do not have autonomous functions, but nevertheless they reveal a regulatory logic for cell cycling based on a feed-forward cascade of activating interactions.