Large distances separate coregulated genes in living Drosophila embryos

Significance The prevailing model of gene activation is the looping of a distal enhancer to its target promoter, although it remains uncertain whether enhancers must come into direct contact. Recent studies suggest that clusters of RNA polymerase II are recruited to active genes, raising the possibility that enhancers cannot get too close to their target promoters due to molecular crowding. Here, we use live imaging methods to visualize genes that are simultaneously regulated by a single enhancer both in cis and in trans. We present evidence that these coregulated genes are separated by a substantial distance—at least 100–200 nm—during transcription. These observations challenge the textbook view of enhancer function and raise the possibility of an action-at-a-distance model for gene expression.