Fig. 3: Histone mark-specific 5mC and 5hmC signatures define different mESC enhancer states.
From: Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features
a Genome browser views of representative active, primed and poised enhancer loci. Tracks show histone mark levels and percentages of 5mC and 5hmC obtained with 6B-C&T for enhancer-associated histone marks, in addition to an IgG control. The genomic location of each annotated enhancer is indicated with a horizontal bar and shaded area coloured according to enhancer type (active—blue, primed—green and poised—red). Tracks within each group (CUT&Tag fragment enrichments, %5mC and %5hmC) have the same y-axis scale. b Stacked bar plots showing average (mean) relative percentages of CpG methylation states for each enhancer type at different associated histone marks (data from biologically independent replicates: H3K27me3, N = 2; H3K27ac, N = 3; H3K4me1, N = 3). Error bars show standard deviation. The top bar graph shows the total distribution of detected unmodified C, 5mC, and 5hmC, while the bottom graph shows the relative abundances of 5mC and 5hmC. c Normalised 6B-C&T read coverages in primed enhancer regions for H3K27ac, H3K4me1 and H3K27me3. Data from one representative experiment plotted relative to the centre of each enhancer region. Replicate information as in (b). d Stacked bar plots of mean CpG methylation percentages for each histone modification at primed enhancers. Top: all 6-base-seq CpG states (C, 5mC, and 5hmC). Bottom: quantification of the relative abundances of 5mC and 5hmC at each histone mark across biologically independent replicates (H3K27me3, N = 2; H3K4me1, N = 3; H3K27ac, N = 3). Error bars represent standard deviation. Source data are provided as a Source Data file.
