Binary transcriptional control of pattern formation in development

During development, stochastic promoter switching between active and inactive states results in transcriptional bursts. We tested whether burst kinetics are sufficient to quantitatively recapitulate the formation of patterns of accumulated mRNA in Drosophila embryos by dissecting the transcriptional dynamics of even-skipped stripe 2. Using a novel memory-adjusted hidden Markov model, single-cell live imaging and theoretical modeling, we show that the regulation of bursting in space and time alone is insufficient to predict stripe formation. In addition to bursting, we discovered that the duration of the window of time over which genes transcribe is regulated, and that this binary (on/off) control of where and when gene expression occurs, not transcriptional bursting, is the main regulatory strategy governing stripe formation. Thus, a quantitative description of the regulation of both bursting and the transcriptional time window are necessary to capture the full complement of molecular rules governing the transcriptional control of pattern formation.