Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals (original) (raw)
Figure 8
Poly(dA:dT) elements have a reduced affinity for nucleosome formation in vitro.
(A–C) Experimental maps of nucleosome occupancy at three genomic loci for which we measured the relative nucleosome affinity of Poly(dA:dT)-containing sequences (blue triangles). Every cyan oval represents the genomic location of one nucleosome that we sequenced in its entirety. Also shown is the average nucleosome occupancy per basepair predicted by the sequence-based nucleosome model that we developed here (red), the raw hybridization signals of two microarray-based nucleosome maps [5],[10] (green and purple traces), and the locations of nucleosomes that were computationally inferred from these hybridization signals [5],[10] (green and purple ovals). Annotated genes [63], transcription factor binding sites [47], and TATA sequences [53] in the region are indicated. (D) Poly(dA:dT)-containing sequences have low nucleosome affinities. Shown are measurements of relative affinity for nucleosome formation of seven Poly(dA:dT)-containing sequences (blue bar; shown are mean and standard deviation for seven measured sequences: three boundary regions from yeast that each contain multiple Poly(dA:dT) elements, and four sequence variants that disrupt one of the Poly(dA:dT) elements in each sequence). For comparison, also shown are the relative affinities of sequences selected for their relative resistance to nucleosome formation [45] (yellow bars), and of sequences selected for their high nucleosome affinity from the mouse genome [18] (green bars) and from chemically synthesized random sequences [7],[19] (red bars). All results are presented relative to the 5S reference sequence, defined as 0. (E) The sequences of the Poly(dA:dT)-containing elements of (a–c) that we measured, along with their chromosomal locations.