Regulation of Transcriptional Bursting by a Naturally Oscillating Signal

Transcription is highly stochastic, occurring in irregular bursts [1–3]. For temporal and spatial precision of gene expression, cells must somehow deal with this noisy behavior. To address how this is achieved, we investigated how transcriptional bursting is entrained by a naturally oscillating signal, by direct measurement of transcription together with signal dynamics in living cells. We identify a Dictyostelium gene showing rapid transcriptional oscillations with the same period as extracellular cAMP signaling waves. Bursting approaches antiphase to cAMP waves, with accelerating transcription cycles during differentiation. Although coupling between signal and transcription oscillations was clear at the population level, single-cell transcriptional bursts retained considerable heterogeneity, indicating that transcription is not governed solely by signaling frequency. Previous studies implied that burst heterogeneity reflects distinct chromatin states [4–6]. Here we show that heterogeneity is determined by multiple intrinsic and extrinsic cues and is maintained by a transcriptional persistence. Unusually for a persistent transcriptional behavior, the lifetime was only 20 min, with rapid randomization of transcriptional state by the response to oscillatory signaling. Linking transcription to rapid signaling oscillations allows reduction of gene expression heterogeneity by temporal averaging, providing a mechanism to generate precision in cell choices during development. •We observe coupled signal and transcriptional oscillations in living cells•Oscillations are collectively robust but heterogeneous at the single-cell level•Response heterogeneity is maintained by a short-term transcriptional persistence•Oscillations can be a mechanism to control gene expression noise in development Corrigan and Chubb, through live imaging of transcriptional bursts, observe coupled oscillations between an extracellular signal and downstream transcription. Oscillations provide a mechanism to reduce transcriptional noise.