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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.

 Authorship: Fernandez-Lopez R., Del Campo I., Ruiz R., Lanza V., Vielva L., De La Cruz F.,

 Fuente: BioEssays, 2010, 32(4), 346-355

 Publisher: Wiley

 Year of publication: 2010

 No. of pages: 10

 Publication type: Article

 DOI: 10.1002/bies.200900164

 ISSN: 0265-9247,1521-1878

 Spanish project: BFU2008-00995

 Publication Url: https://doi.org/10.1002/bies.200900164

Authorship

RAUL FERNANDEZ LOPEZ

RAUL RUIZ GONZALEZ

VAL FERNANDEZ LANZA

LUIS ANTONIO VIELVA MARTINEZ