Mitotic reactivation and transcriptional bursting govern transcriptional noise in the early Drosophila embryo

Isogenic cells often exhibit variability in gene expression. Because of its stochastic nature, transcription is thought to lie at the heart of gene expression variability. While beneficial in some contexts, this transcriptional noise must be dampened to ensure the deployment of accurate gene expression programs. Here, we have investigated how the cis-regulatory code affects inter-nuclear variability in transcription, quantified at the level of individual RNA Polymerase II initiation events. Combining quantitative imaging in Drosophila embryos with mathematical modeling, we discovered that transcriptional noise is time dependent with two major components: mitotic exit and transcriptional bursting. Transcriptional noise peaks after mitosis due to the stochastic timing of postmitotic reactivation and the temporal heterogeneity of transcriptional bursting. When a steady-state regime is reached, transcriptional noise is then primarily driven by the kinetics of bursting. We demonstrate that the TATA box is necessary and sufficient to generate transcriptional noise, and assess the contribution of shadow enhancers to noise. Our work reveals the major contribution of the first polymerase passage after mitotic exit to transcriptional noise.