Modulation of the promoter activation rate dictates the transcriptional response to graded BMP signaling levels in theDrosophilaembryo

SUMMARY Morphogen gradients specify cell fates during development, with a classic example being the BMP gradient’s conserved role in embryonic dorsal-ventral axis patterning. Here we elucidate how the BMP gradient is interpreted in the Drosophila embryo, by combining live imaging with computational modelling to infer transcriptional burst parameters at single cell resolution. By comparing burst kinetics in cells receiving different levels of BMP signaling, we show that BMP signaling controls burst frequency by regulating the promoter activation rate. We provide evidence that the promoter activation rate is influenced by both enhancer and promoter sequences, whereas Pol II loading rate is primarily modulated by the enhancer. Consistent with BMP-dependent regulation of burst frequency, the numbers of BMP target gene transcripts per cell are graded across their expression domains. We suggest that graded mRNA output is a general feature of morphogen gradient interpretation and discuss how this can impact on cell fate decisions.