Input-response function for spatiotemporally modulated input transcription factor and target gene outputs

During embryonic development, cell specification is tightly regulated in space and time by specific DNA-binding proteins called transcription factors (TFs). However, the input-response functions between transcription factors and the gene outputs that will eventually give rise to distinct cell fates are largely unknown. To address this issue, we engineered embryos with no natural input sources and with a fast optogenetically tunable single-input system. Our custom-built light delivery platform allows acute temporal and spatial light patterns to instruct light-sensitive TF concentrations in living fly embryos. These tools enable us to induce and control input TF concentration on a minute-time scale and record output gene transcription in real-time. We found the target genes showing differential transcriptional activity in response to acute TF concentration perturbations in time and space. Our synthetic approach to modulate TF concentration while concurrently recording transcriptional gene output in real-time presents a powerful approach to study transcriptional dynamics in vivo.