Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

While gene expression noise has been shown to drive dramatic phenotypic variations, the molecular basis for this variability in mammalian systems is not well understood. Gene expression has been shown to be regulated by promoter architecture and the associated chromatin environment. However, the exact contribution of these two factors in regulating expression noise has not been explored. Using a dual‐reporter lentiviral model system, we deconvolved the influence of the promoter sequence to systematically study the contribution of the chromatin environment at different genomic locations in regulating expression noise. By integrating a large‐scale analysis to quantify mRNA levels by smFISH and protein levels by flow cytometry in single cells, we found that mean expression and noise are uncorrelated across genomic locations. Furthermore, we showed that this independence could be explained by the orthogonal control of mean expression by the transcript burst size and noise by the burst frequency. Finally, we showed that genomic locations displaying higher expression noise are associated with more repressed chromatin, thereby indicating the contribution of the chromatin environment in regulating expression noise. Synopsis Analyses of the molecular basis of gene expression noise by smFISH and flow cytometry show that in mammalian cells, mean expression and noise are uncorrelated across genomic locations and are affected by the local chromatin environment. Using a dual‐reporter lentiviral system, the influence of the promoter sequence is deconvolved to systematically study how the chromatin environment regulates gene expression noise. Analysis of 418 single‐integration clones reveals that the mean expression is uncorrelated with the coefficient of variation (CV). Single‐molecule mRNA FISH distributions are fit to a two‐state model of gene expression to show orthogonal control of mean expression by burst size and gene expression noise (CV) by burst frequency. DNase I sensitivity assays reveal that promoters within more repressed chromatin are associated with reduced burst frequency and increased gene expression noise. Graphical Abstract Analyses of the molecular basis of gene expression noise by smFISH and flow cytometry show that in mammalian cells, mean expression and noise are uncorrelated across genomic locations and are affected by the local chromatin environment.