title: Exploring the behavior of small eukaryotic gene networks.
abstract: Analysis of the genome organization of higher eukaryotes indicates that it contains many clusters of functionally related genes. In these clusters, the activity of a single gene is regulated hierarchically at a local gene-level and a global cluster-level. Whether a single gene can be activated by a dedicated transcription factor depends on the epigenetic status of the cluster, i.e. whether it is epigenetically permissive or silenced. The consequence of gene clusters for the functioning of gene networks is largely unexplored. The accumulating biological knowledge about mechanisms for epigenetic regulation, signal transduction, and gene clusters makes such explorations a timely challenge. We explore the steady-state behavior of two gene clusters that mutually inhibit each other. This gives rise to multiple steady states in this simple system of interacting clusters. We illustrate that a gene cluster encoding a module composed of a signal transduction network and a transcription factor can generate versatile temporal dynamics that resembles cellular differentiation. The gene cluster can be epigenetically silenced and activated by a dedicated transcription factor. This module displays transient signal sensitivity, and irreversible decisions (commitment; hysteresis) depending on the identity and temporal sequence of external signals.
authors.affiliation: Molecular Cell Physiology, Vrije Universiteit, De Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands. Frank.Bruggeman@falw.vu.nl
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Bruggeman
authors.forename: Ionela
authors.initials: I
authors.lastname: Oancea
authors.forename: Roel
authors.initials: R
authors.lastname: van Driel
mesh_terms: D000818:Animals; D044127:Epigenesis, Genetic; D005057:Eukaryotic Cells / Q000166:cytology*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D005810:Multigene Family; D015398:Signal Transduction / Q000235:genetics; D014157:Transcription Factors / Q000502:physiology
chemical_list: D014157:Transcription Factors