Measuring Transcription at a Single Gene Copy Reveals Hidden Drivers of Bacterial Individuality

Single-cell measurements of mRNA copy-number inform our understanding of stochastic gene expression [1-3], but these measurements coarse-grain over the individual copies of the gene, where transcription and its regulation stochastically take plasce [4, 5]. Here we combine single-molecule quantification of mRNA and gene loci to measure the transcriptional activity of an endogenous gene in individual Escherichia coli bacteria. Interpreted using a theoretical model for mRNA dynamics, the single-cell data allows us to obtain the probabilistic rates of promoter switching, transcription initiation and elongation, mRNA release and degradation. Unexpectedly, we find that gene activity can be strongly coupled to the transcriptional state of another copy of the same gene present in the cell, and to the event of gene replication during the bacterial cell cycle. These gene-copy and cell-cycle correlations demonstrate the limits of mapping whole-cell mRNA numbers to the underlying stochastic gene activity, and instead highlight the contribution of previously hidden variables to the observed population heterogeneity.