The regulation of cellular protein levels is a complex process involving many regulatory mechanisms. These regulatory mechanisms introduce a cascade of stochastic events leading to variability of protein levels between cells. Previous studies have shown that perturbing genes involved in transcription regulation alters variability of protein levels, but to date, there has been no systematic characterization of these effects. Here we utilize single-cell expression levels of two fluorescent reporters under a wide range of genetic perturbations in Saccharomyces cerevisiae to identify proteins that affect expression variability.

We introduce computational methodology to determine the variability introduced by each perturbation, and distinguish between global variability, affecting both reporters in a coordinated manner, and local variability, affecting individual reporters independently. Classifying genes by their variability phenotype identifies functionally coherent groups, which broadly correlate with the different stages of transcriptional regulation. Specifically, we find that perturbation of processes related to DNA maintenance, chromatin regulation and RNA synthesis affect local variability, while processes related to protein synthesis and transport, cell morphology and cell size affect global variability. In addition, we find that perturbations of many processes related to chromatin regulation affect both global and local variability. Finally, we demonstrate that the variability phenotypes of different protein complexes provide insights into their cellular functions. Our methodology provides tools for examining arising data on variability, and establishes the utility of this phenotype as a tool in dissecting the regulatory mechanisms involved in gene expression.