Distribution of essential interactions in model gene regulatory networks under mutation-selection balance.
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these degree distributions? Starting with an accepted framework of the binding of transcription factors to DNA, we consider a simple model of gene regulatory dynamics. There, we show that selection for a target expression pattern leads to the emergence of minimum connectivities compatible with the selective constraint. As a consequence, these gene networks have low in-degree and "functionality" is parsimonious, i.e., is concentrated on a sparse number of interactions as measured for instance by their essentiality. Furthermore, we find that mutations of the transcription factors drive the networks to have broad out-degrees. Finally, these classes of models are evolvable, i.e., significantly different genotypes can emerge gradually under mutation-selection balance.
Burda
Z
Z
Marian Smoluchowski Institute of Physics and Mark Kac Complex Systems Research Centre, Jagellonian University, Reymonta 4, 30-059 Krakow, Poland.
Krzywicki
A
A
Martin
O C
OC
Zagorski
M
M
D000818:Animals; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D012641:Selection, Genetic / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*
D020543:Proteome