Function does not follow form in gene regulatory circuits.
Gene regulatory circuits are to the cell what arithmetic logic units are to the chip: fundamental components of information processing that map an input onto an output. Gene regulatory circuits come in many different forms, distinct structural configurations that determine who regulates whom. Studies that have focused on the gene expression patterns (functions) of circuits with a given structure (form) have examined just a few structures or gene expression patterns. Here, we use a computational model to exhaustively characterize the gene expression patterns of nearly 17 million three-gene circuits in order to systematically explore the relationship between circuit form and function. Three main conclusions emerge. First, function does not follow form. A circuit of any one structure can have between twelve and nearly thirty thousand distinct gene expression patterns. Second, and conversely, form does not follow function. Most gene expression patterns can be realized by more than one circuit structure. And third, multifunctionality severely constrains circuit form. The number of circuit structures able to drive multiple gene expression patterns decreases rapidly with the number of these patterns. These results indicate that it is generally not possible to infer circuit function from circuit form, or vice versa.
University of Zurich, Institute of Evolutionary Biology and Environmental Studies, Zurich, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Joshua L
JL
Payne
University of Zurich, Institute of Evolutionary Biology and Environmental Studies, Zurich, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.|The Santa Fe Institute, Santa Fe, New Mexico, United States of America.
Andreas
A
Wagner
D053263:Gene Regulatory Networks; D005838:Genotype; D008957:Models, Genetic; D059372:Nucleotide Motifs / Q000235:genetics