Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF

Housekeeping and regulated genes have distinct core promoter motif usage and architecture. The Boundary Element-Associated Factor of 32 kDa, BEAF, was identified as a chromatin domain insulator protein that affects chromatin structure and plays a role in insulator function. Genome-wide mapping found that it usually binds near transcription start sites of housekeeping genes found at topologically associating domain (TAD) boundaries, suggesting roles in both insulator function and gene activation. This was substantiated when it was found to activate the RpS12 and aurA promoters, and that BEAF-dependent promoter activation could be separated from BEAF-dependent insulator activity. Here, we use luciferase assays after transient transfection of Drosophila S2 cells to show that adding an upstream BEAF binding site leads to activation of housekeeping promoters without showing a preference for particular housekeeping core promoter motifs, and also activates core promoters lacking motifs or with only an Inr. Regulated core promoters with a TATA box or with an Inr plus MTE or DPE or both are not activated. Activation by BEAF has a weak negative correlation with promoter basal activity. We additionally show that BEAF activates promoters synergistically with DRE or Motif 1 housekeeping promoter motifs. This establishes BEAF as an activator for a large set of promoters.