Figure 2.

TF‐DNA recognition involves multiple levels of interactions. Top: The first level of recognition involve chromatin accessibility, where nucleosome‐depleted regions (i.e. open chromatin) are associated with TF binding while closed chromatin is often thought as inaccessible to most TFs. Middle: The unique features of the environment in which the motif is embedded can further direct the TF to its cognate binding site. Bottom: Specific TF interactions with the DNA occur through the interplay of base and shape readout at the core motif and its proximal flanks.