Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity

• DOI: 10.1093/bioinformatics/btn229
• Publication Date: 2008-05-09T00:34:00Z
• Authors: Junil Kim; Tae-Geon Kim; Sung Hoon Jung; Jeong-Rae Kim; Taesung Park; Pat Heslop-Harrison; Kwang-Hyun Cho
• Keywords: 0303 health sciences; Models, Genetic; Proteome; Evolution; Molecular; Gene Expression Regulation, Developmental; Cell Differentiation; 612; Feedback; Evolution, Molecular; 03 medical and health sciences; Gene Expression Regulation; Genetic; Models; Developmental; Computer Simulation; Signal Transduction

Abstract Motivation: Gene regulatory networks (GRNs) govern cellular differentiation processes and enable construction of multicellular organisms from single cells. Although such networks are complex, there must be evolutionary design principles that shape the network to its present form, gaining complexity from simple modules. Results: To isolate particular design principles, we have computationally evolved random regulatory networks with a preference to result either in hysteresis (switching threshold depending on current state), or in multistationarity (having multiple steady states), two commonly observed dynamical features of GRNs related to differentiation processes. We have analyzed the resulting evolved networks and compared their structures and characteristics with real GRNs reported from experiments. Conclusion: We found that the artificially evolved networks have particular topologies and it was notable that these topologies share important features and similarities with the real GRNs, particularly in contrasting properties of positive and negative feedback loops. We conclude that the structures of real GRNs are consistent with selection to favor one or other of the dynamical features of multistationarity or hysteresis. Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.