Degrees of nucleosome depletion around 6-mer motif sites and the relationships between occupancy and DNase I hypersensitivity (DHS) in A. thaliana. (A) Volcano plot showing the relationships between normalized NOC scores (x-axis) and the statistical significance (−log10 [P-value], y-axis) testing whether the distribution of normalized NOCs of 200-bp regions around sites of each 6-mer differs from the normalized NOC distribution of randomly chosen sites with the same relative positions (Mann-Whitney U test). The NOC score here is determined according to the nucleosome gDNA data. (Red) 6-mers that have significant nucleosome depletion (P < 1 × 10−10), have normalized NOC scores <−0.5, and are enriched among the top 10% highly expressed genes (Type I, n = 59); (blue) 6-mers with significant nucleosome depletion but not enriched among highly expressed genes (Type II, n = 213); (orange) 6-mers enriched among the highly expressed genes but with no significant nucleosome depletion (Type III, n = 66). (B) Volcano plot as in A but determined using naked gDNA data. (C) Relationships between normalized NOC and DHS scores for regions surrounding 6-mer motifs based on nucleosome gDNA data. (D) Same as in C except naked gDNA data were used. (E) The normalized NOC and DHS (per base) profiles in regions surrounding genomic sites of the G-box (CACGTG) and a shuffled G-box sequence (CTGCAG) located in proximal (500 bp upstream of TSS) and distal (1 kb to 500 bp upstream of TSS) promoters. The x-axis represents the distance to motif sites.
