NOMe-seq reveals distinct chromatin configurations at CTCF sites and associated with specific histone modifications and promoter types. (A) NOMe-seq demonstrates unmethylated NDRs at CTCF sites in IMR90 and GBM cells, which are marked by a peak in inaccessibility at the CTCF site itself. Well-positioned nucleosomes flank CTCF sites, with DNA methylation peaking in between nucleosomes. 0 indicates the middle of the CTCF binding motif. CTCF binding sites were obtained from GSM935404. (B) NOMe-seq distinguishes the three major promoter states at promoters in IMR90 cells—active H3K4me3-marked promoters are unmethylated and contain a NDR upstream and well-positioned nucleosomes after the TSS. TSSs are indicated on the x-axes as 0. Repressed/poised H3K27me3-marked promoters are unmethylated and nucleosome-occupied. Methylated promoters are nucleosome-occupied. The y-axis indicates M.CviPI inaccessibility (1-CpG; teal) and CpG methylation level. (C) In IMR90 cells, CpG island promoters are characterized by a lack of CpG methylation, an upstream NDR, and well-positioned nucleosomes after the TSS. The majority of CpG island promoters are unmethylated (11,165) and display the same pattern, while methylated CpG island promoters (781) are nucleosome-occupied and inaccessible to M.CviPI. (D) Non-CpG island promoters are generally characterized by CpG methylation and inaccessibility to M.CviPI, indicating nucleosome occupancy. The few unmethylated non-CpG island promoters (1397) are depleted of nucleosomes upstream of the TSS, while the majority of non-CpG island promoters (4668) are nucleosome-occupied and inaccessible to M.CviPI. M.CviPI inaccessibility is plotted (1-GCH) in teal and CpG methylation (CGH) in black.
