Figure 6

A model to account for zinger motif enrichment across ChIP-seq datasets. A TF loading station model is presented that is compatible with the observed enrichment of zinger motifs across diverse TF ChIP-seq data and cell lines. The dark blue oval represents the ChIPped TF, the magenta oval represents the zingers, the remaining coloured ovals represent TFs or other proteins or complexes that engage with the DNA, and the red loop represents cohesin and polycomb group proteins. The grey strands are chromatin. (A) Overview of a loading station. Multiple proteins may interact within a local region, from which TFs may disperse to search for other regulatory regions. Zingers and structural components such as cohesin and polycomb group proteins are key features. Panels B, C, and D present specific scenarios under which DNA loading station segments might be recovered in a ChIP-seq experiment. (B) Direct binding. The ChIPped TF directly binds to a TFBS, while a zinger motif is present in trans (upper) or in cis (lower). (C) Indirect binding. The ChIPped TF is present due to an indirect interaction, involving a mediating protein. The zinger motif is again present in trans (upper) or in cis (lower). (D) Non-specific events. Numerous proteins are present at the loading station, providing an abundance of epitopes, thus increasing the probability of being recovered in a ChIP-seq experiment.