Figure 8

Proposed model of interaction between two HOT regions and resulting signals from high-throughput sequencing experiments. An enhancer is looped over and connected by a complex of many TFs, which recruit the preinitiation complex and ultimately RNA polymerase II to the TSS. Proteins A are directly bound to DNA, while protein B is recruited to the site through only protein-protein interactions. These mechanisms are indistinguishable from the ChIP-seq signal, but presence of a known sequence motif suggests which protein binds directly.