Nuclear microenvironments modulate transcription from low-affinity enhancers

Transcription factors regulate gene expression by binding to DNA for short durations and by often binding to low-affinity DNA sequences. It is not clear how such temporally brief, low-affinity interactions can drive efficient transcription. Here we report that the transcription factor Ultrabithorax (Ubx) functionally utilizes low-affinity binding sites in the Drosophila melanogaster shavenbaby ( svb ) locus in nuclear microenvironments of relatively high Ubx concentration. By manipulating the affinity of svb enhancers, we revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. A Ubx cofactor, Homothorax (Hth), was enriched together with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. These results suggest that low affinity sites overcome their kinetic inefficiency by utilizing microenvironments with high concentrations of transcription factors and cofactors. Mechanisms that generate these microenvironments are likely to be a general feature of eukaryotic transcriptional regulation.