Exploiting fluctuations in gene expression to detect causal interactions between genes

Abstract

Characterizing and manipulating cellular behaviour requires a mechanistic understanding of the causal interactions between cellular components. We present an approach that can detect causal interactions between genes without the need to perturb the physiological state of cells. This approach exploits naturally occurring cell-to-cell variability which is experimentally accessible from static population snapshots of genetically identical cells without the need to follow cells over time. Our main contribution is a simple mathematical relation that constrains the propagation of gene expression noise through biochemical reaction networks. This relation allows us to rigorously interpret fluctuation data even when only a small part of a complex gene regulatory process can be observed. This relation can be exploited to detect causal interactions by synthetically engineering a passive reporter of gene expression, akin to the established “dual reporter assay”. While the focus of our contribution is theoretical, we also present an experimental proof-of-principle to illustrate the approach. Our data from synthetic gene regulatory networks in E. coli are not unequivocal but suggest that the method could prove useful in practice to identify causal interactions between genes from non-genetic cell-to-cell variability.