title: Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function.
abstract: Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure.
authors.affiliation: GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France. Electronic address: olivier.martin@moulon.inra.fr.
authors.forename: O C
authors.initials: OC
authors.lastname: Martin
authors.affiliation: Laboratoire de Physique Théorique, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Orsay, 91405, France.
authors.forename: A
authors.initials: A
authors.lastname: Krzywicki
authors.affiliation: Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria; Institute of Physics, Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland. Electronic address: marcin.zagorski@ist.ac.at.
authors.forename: M
authors.initials: M
authors.lastname: Zagorski
mesh_terms: D000818:Animals; D001703:Biophysics; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D010641:Phenotype; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors
keywords: Genetic regulation; Graph motif; Network function; Network structure