Transcription factor hubs exhibit gene-specific properties that tune expression

The spatial and temporal control of gene expression relies on transcription factors binding to and occupying their target sites. Transcription factor hubs—localized, high-concentration microenvironments—promote transcription by facilitating binding and recruitment of transcriptional machinery and co-factors. Hubs are often thought to have emergent nucleus-wide properties depending on transcription factor nuclear concentrations and intrinsic, protein sequence-dependent properties. This global model does not account for gene-specific hub regulation. Using high-resolution lattice light-sheet microscopy in Drosophila embryos, we examined hubs formed by the morphogen transcription factor, Dorsal, at reporter genes with distinct enhancer compositions. We found that snail recruits long-lived, high-intensity hubs; sog exhibits shorter-lived, lower-intensity hubs; and hunchback , lacking Dorsal binding sites, shows only transient hub interactions. Hub intensity and interaction duration correlate with burst amplitude, RNAPII loading rate, and transcriptional output. These findings challenge the global view of hub formation and support a model where hub properties are locally tuned in a gene-specific manner to regulate transcriptional kinetics.