Characterization of physical interactions between the Drosophila insulator binding protein BEAF and...

Originally identified as a chromatin domain insulator binding protein, Drosophila melanogaster BEAF (Boundary Element-Associated Factor of 32 kDa) is predominantly associated with transcription start sites (TSSs) of housekeeping genes. It was previously shown that BEAF directly interacts with the transcription factor Serendipity-δ (Sry-δ). TSS-proximal BEAF can interact with distantly bound Sry-δ to activate a reporter gene. However, it is unknown if the ability of BEAF to communicate with transcription-associated factors from a distance is a common property. Here, we use yeast 2-hybrid assays to show that BEAF directly interacts with a variety of transcription-associated factors: both FACT subunits (Dre4 and SSRP), DREF, Rib, ROW, Map60, Apt, Wds, Cdk1, GFZF, and weakly with Adf1 and Kdm5. We further explored the interaction of BEAF with the histone chaperone FACT and transcription factors DREF, Rib, and ROW, including interrogating communication from a distance with a reporter gene assay and by analysis of S2 cell high-throughput chromosome conformation capture (Hi-C) data. When tagged with a VP16 activation domain, all five proteins activated RpS12 and yellow promoters cooperatively with adjacent, promoter-proximal BEAF. Only ROW and the FACT subunit SSRP communicated with BEAF from a distance, and only ROW exhibited long-range interaction with BEAF in Hi-C data. Our results provide evidence for three mechanisms by which promoter-proximal BEAF might facilitate gene activation. First, it might affect promoter chromatin accessibility by recruiting chromatin proteins like FACT. Second, consistent with the model of housekeeping gene regulation by promoter-proximal elements, BEAF might cooperate with adjacent interacting transcription factors for promoter activation. Third, a subset of interacting transcription factors, including ROW and Sry-δ, might interact with BEAF from a distance, modifying the traditional paradigm of local regulation of housekeeping genes.