title: Numbers on the edges: a simplified and scalable method for quantifying the gene regulation function.
abstract: The gene regulation function (GRF) provides an operational description of a promoter behavior as a function of the concentration of one of its transcriptional regulators. Behind this apparently trivial definition lies a central concept in biological control: the GRF provides the input/output relationship of each edge in a transcriptional network, independently from the molecular interactions involved. Here we discuss how existing methods allow direct measurement of the GRF, and how several trade-offs between scalability and accuracy have hindered its application to relatively large networks. We discuss the theoretical and technical requirements for obtaining the GRF. Based on these requirements, we introduce a simplified and easily scalable method that is able to capture the significant parameters of the GRF. The GRF is able to predict the behavior of a simple genetic circuit, illustrating how addressing the quantitative nature of gene regulation substantially increases our comprehension on the mechanisms of gene control.
authors.affiliation: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-IDICAN, Cardenal Herrera Oria s/n, 39011 Santander, Spain.
authors.forename: Raul
authors.initials: R
authors.lastname: Fernandez-Lopez
authors.forename: Irene
authors.initials: I
authors.lastname: Del Campo
authors.forename: Raúl
authors.initials: R
authors.lastname: Ruiz
authors.forename: Val
authors.initials: V
authors.lastname: Lanza
authors.forename: Luis
authors.initials: L
authors.lastname: Vielva
authors.forename: Fernando
authors.initials: F
authors.lastname: de la Cruz
mesh_terms: D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks