Fig. 2: Epigenetic characteristics of MeCP2 binding or non-binding mononucleosomes.

a Examples of MeCP2 ChIP-seq and MNase-seq tracks for MeCP2-absent mononucleosome occupied loci (left), MeCP2-enriched mononucleosome occupied loci (center), and MeCP2 binding in unstable nucleosome loci (right). b Venn diagram showing the number of peaks in MeCP2-absent mononucleosome loci (group1), MeCP2-enriched mononucleosome loci (group2) and nucleosome-free MeCP2-binding loci (group3). c Comparison of methylation levels of CpG, CAG, and CAH in each of 10,000 loci randomly selected from the three groups defined in b. N = 2 (WT) from biologically independent mice. For CpG, p = 1.11 × 10⁻¹¹⁵ (group1 vs group2); p = 2.4 × 10⁻⁸⁵ (group1 vs group3); p = 1.16 × 10⁻⁴ (group2 vs group3). For CAG, p = 1.06 × 10⁻⁷⁵ (group1 vs group2); p = 1.55 × 10⁻⁶³ (group1 vs group3); p = 0.17 (group2 vs group3). For CAH, p = 1.69 × 10⁻²² (group1 vs group2); p = 9.85 × 10⁻²⁷ (group1 vs group3); p = 1.08 (group2 vs group3). d Heatmap of Input, MeCP2, H3K27me3, H3K9ac ChIP-seq peaks and MNase-seq with flanking regions, of Chr19 by the types of regions defined in b. Aggregate plot of average Input, MeCP2, H3K27me3, H3K9ac and MNase-seq reads below. e, f Comparison of H3K27me3 (e) or H3K9ac (f) levels among the three groups of loci at chr19 (group1, n = 101,549; group2, n = 67,051; group3, n = 33,644). N = 2 (WT) from biologically independent mice. For H3K27me3, p < 0.0001 (group1 vs group2); p < 0.0001 (group1 vs group3); p = 0.02 (group2 vs group3). For H3K9ac, p < 0.0001 (group1 vs group2); p < 0.0001 (group1 vs group3); p = 2.34 ×10⁻³³ (group2 vs group3). p = 0.00 were reported as p < 0.0001. g Scatter plots showing inter-correlation between H3K27me3 and H3K9ac ChIP-seq and MeCP2 enrichment (binning size = 1000 bp). Two-tailed Mann–Whitney testing with Bonferroni corrections, ***p < 0.0001 (c, e, and f). Box-and-whisker plots show median, 10 to 90 percentile, and min and max values (c, e, and f). Mean is marked by “+.” .