Distributions of nucleosomes around transcription start sites (TSSs) with and without CpG islands. Distributions of nucleosomes containing H3K4me3 (A, B) and H3 (C, D) around broad and peak promoters are shown. The analyses were conducted separately for TSSs that were associated with CpG islands (A, C) and those that were not (B, D). Broad promoters had aligned patterns of nucleosomes containing H3 and H3K4me3, regardless of the existence of CpG islands, and were enriched in H3K4me3. In contrast, peak promoters had little alignment of the H3 pattern, regardless of the presence of CpG islands. The proportion of nucleosomes containing H3K4me3 associated with peak promoters was lower than that associated with broad promoters, particularly in the absence of CpG islands.