Figure 2. The Nucleosome-Free Region on the GRP78 Core Promoter Is Minimally 350 bp Long.

(A) The diagram on top, drawn to scale, represents the region analyzed and indicates the distribution density of the 73 CpG sites (tick marks) included in this region. The position of the ERSEs (E1–E3), TATA box (T), and transcription initiation site (bent arrow) are indicated. Nuclei were extracted from actively growing LD419 cells, followed by 15 min M.SssI treatment, bisulfite conversion of extracted DNA, PCR amplification of three regions of the promoter covering 1100 bp, and cloning and sequencing of individual clones. Each horizontal line with a string of circles represents the methylation profile for one DNA molecule. White circles indicate unmethylated, and black circles, methylated CpG sites.

(B) Summed protection levels at individual CpG sites. The striped bar represents the inferred nucleosome-free region. Note that the relatively high protection levels at CpGs 40 to 50 are contributed by distinct footprints which are too small to reflect nucleosomes. The ovals represent the predicted nucleosome positions (solid line, well positioned nucleosome; dotted line, less well positioned nucleosomes or no nucleosome boundary).