Dissecting the dynamics of coordinated active transcriptional repression in a multicellular organism

The ability to refine transcriptional levels via active repression in an euchromatic context represents a critical regulatory process during development. While the molecular players of active repression are well described, their dynamics remain largely obscure. By monitoring expression dynamics of the pro-EMT developmental gene snail in Drosophila embryos, we uncovered and quantified the timescale of kinetic bottlenecks tuning transcription during repression. Repression is associated with the transition of the promoter from two states to a three-state regime, comprising two temporally distinct inactive periods. Surprisingly, repression occurs without abrupt changes in Pol II initiation rates. By monitoring nuclear Sna protein levels, we show that Sna-mediated repression operates with high cooperativity, a feature dictating the degree of cell-cell coordination in the imposition of repression. Our approach offers quantitative insights into the dynamics of repression mediated by short-range repressors and how their cooperativity may coordinate cell fate decisions within a tissue.