Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Figure 10
Boundaries enhance the accessibility of transcription factors to their cognate binding sites.
(A) Nucleosome depletion over factor sites increases with their proximity to, and with the strength of, boundaries. Shown is the combined nucleosome fold depletion over factor sites (y-axis) that are within a certain range of distances from boundaries that themselves have a particular nucleosome fold depletion (boundary strength; x-axis). Plots are shown for four different ranges of factor-boundary distances and for the four boundary strength groups of nucleosome fold depletions that we defined based on sequence rules (see Methods). (B) Factor binding sites near boundaries are depleted of nucleosomes. For each factor, shown is the combined nucleosome fold depletion over its annotated sites [47],[67] that are within 30 bp from a boundary whose fold depletion is at least 5 (blue bars), and over the rest of its sites (green bars). The combined fold depletion of a set of genomic elements is the ratio between their expected and observed nucleosome coverage (see Methods).