CHAPTER 9: Using Single-cell RNA Measurements to Decipher the Stochastic Kinetics of Transcription

This chapter describes how single-cell microscopy studies in Escherichia coli are used to obtain information on the stochastic kinetics of mRNA production from a gene of interest. By measuring the distribution of mRNA copy number across many individual cells, under a range of experimental conditions, and directly comparing the experimental data with predictions by mathematical models for the underlying stochastic process, it is possible to test mechanistic hypotheses and estimate physiological parameters of mRNA life history. After surveying the key elements of this approach, we provide examples of how single-cell RNA measurements aid understanding of the integration of regulatory processes that drive transcription in the cell. The results of these experiments reveal the strong correlation between the transcriptional states of two sister copies within the same cell, and a tight coupling between transcription from a repressed promoter and the cell-cycle event of gene replication.