The transcriptional activities of developmental genes in time, in space, or in defined cell-types are orchestrated by repertoires of enhancers that communicate in the 3D nuclear space with target promoters. Transcriptional outcomes, necessary to instruct morphogenesis, also involve defined transcriptional durations over which a gene product exerts its function. This aspect implies that genes’ transcriptional activities are initiated in different cells and trans-environment than the one where they are maintained later on or eventually repressed. Despite this intuitive concept, little is known about the cis-regulatory components that enable it. Here, we have established the regulatory trajectory framework to track how regulatory landscapes control gene transcription in vivo over long developmental time periods. Gene regulatory trajectories first involve transcriptional initiation, which corresponds to the onset of gene expression, followed by maintenance over time, and finally decommissioning, leading to gene repression. Using fluorescent sensors and recorders, we can sort cell populations from embryos at different phases of regulatory trajectories to characterize transcription, chromatin states, and genome topologies. Furthermore, we can engineer complex alleles to assess the role of cis-regulatory regions in controlling the phases of a gene’s regulatory trajectory. In summary, our approach aims to characterize the lifespans of developmental gene regulation and their functional dependencies.

Guillaume Andrey is invited by Antoine Zalc.