Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Figure 7
Nucleosome depleted regions are created in the vicinity of Poly(dA:dT) boundaries.
(A) A boundary constraint creates, on average, a larger nucleosome-depleted region that extends far into regions flanking the boundary. Shown is a simple example focusing only on the immediate neighborhood of the boundary. All (five) possible nucleosome configurations are illustrated, in which a nucleosome (cyan ovals) can be placed within five basepairs of the boundary (blue triangle). The number and set of nucleosome configurations occupying each of the five basepairs immediately adjacent to the boundary are shown in the graph and table, respectively. If all configurations are equally likely, then basepairs closer to the boundary will exhibit lower nucleosome occupancy. (B) Boundaries exhibit strong and long-range nucleosome depletion regardless of whether they are near transcription factor binding sites or whether they are in promoters or non-promoter intergenic regions. Shown is the average number of nucleosome reads in our data at locations k (for k = 1,2,…,150) basepairs away from boundaries (strength >5) that are: more than 30 bp from any factor site (green); within 30 bp of a factor site bound by its cognate factor [47] (purple); in intergenic regions that are not promoters (orange). The strength of a boundary is defined by properties of the DNA sequence of the boundary, based on the length and perfection of the Poly(dA:dT) components of the boundary (see Methods). Plots are symmetric by construction. (C) Boundaries enhance the accessibility of transcription factors to cognate sites. Shown is the average number of nucleosome reads in our data at locations k (for k = 1,2,…,150) basepairs away from annotated factor binding sites bound by their cognate factor [47] that are: more than 30 bp from any boundary (boundary strength >5) (blue); within 30 bp of any boundary (strength >5) (red). Plots are symmetric by construction.