Long-lived epigenetic states convert all-or-none single-cell responses to graded population responses in mammalian expression systems

However, even minimal synthetic systems often exhibit unexplained behaviors. In a widely used inducible mammalian expression system, we show that transcriptional responses appear graded and sigmoidal at the population level but are largely all-or-none at the single-cell level.

By combining single-cell sorting and single-molecule footprinting with mathematical modeling of transcriptional regulation, we found that this behavior is not caused by bursty transcription or bistability, but by long-lived, chromatin-encoded variability in TF occupancy and activation strength. This variability produced a range of activation thresholds in switchlike single-cell responses that were stable over time, resulting in bimodal gene expression across the population.