3D dynamics of trans enhancer-promoter interactions in living Drosophila embryos reveals spatiotemporal thresholds for transcription activation

While it is well acknowledged that specific enhancer-promoter interactions are essential for transcription, the spatiotemporal thresholds required for transcription initiation remain unclear. Here, we employed the phenomenon of transvection, where an enhancer activates the target gene in trans at the homologous position, to analyze the mechanism of long-range enhancer-promoter interactions. We combined the MS2- and PP7-based RNA labeling with the ParB/ parS DNA labeling to simultaneously visualize active transcription and a target DNA locus in living Drosophila embryos. By quantifying the 3D enhancer-promoter distances in nuclei that exhibited active or inactive transcription, we found that sustained proximity between the enhancer and promoter is necessary and sufficient to initiate transcription. The enhancer-promoter proximity was established before transcription initiation and remained stable after the termination, suggesting the localization of an enhancer and the target promoters in a “transcription hub.” When transvection occurred, the cis -linked reporter gene showed a delayed activation and reduced mRNA production, suggesting homologous promoter competition in the hub. Our DNA-labeled co-transvection assay sheds insights into the activation criteria for the long-range enhancer-promoter interactions and provides a stepping stone for future endeavors to understand the complex gene regulation in 3D space.