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

M. Zagorski 1, A. Krzywicki 2, O. C. Martin 34

Physical Review E 87 (2013) 012727

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.

  • 1 : Marian Smoluchowski Institute of Physics and Mark Kac Complex Systems Research Center
    Jagellonian University
  • 2 : Laboratoire de Physique Théorique d'Orsay (LPT)
    CNRS : UMR8627 – Université Paris XI - Paris Sud
  • 3 : Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS)
    CNRS : UMR8626 – Université Paris XI - Paris Sud
  • 4 : Génétique Végétale (GV)
    CNRS : UMR8120 – Institut national de la recherche agronomique (INRA) : UMR0320 – Université Paris XI - Paris Sud – AgroParisTech