Skip to main content
Fig. 3 | Genome Biology

Fig. 3

From: EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation

Fig. 3

M-ATAC reveals a complex interplay between accessible chromatin and DNA methylation. a CpGs in M-ATAC peaks from merged replicates were divided into four groups according to methylation and coverage status: 1. Low Methylation (< 20%) + High coverage (> 50 reads) (22,932 CpGs). 2. Low Methylation + Low coverage (5 to 50 reads) (1,348,931 CpGs). 3. Intermediate methylation (20–80) + Low coverage (5 to 50 reads) (39,321 CpGs). 4. High methylation (> 80%) + Low coverage (5 to 50 reads) (1652 CpGs). *** P < 1e−300 between groups #1 + 2 and group #3, ***P = 3.25e−109 between groups #3 and 4 (Wilcoxon text). b Genomic annotations for M-ATAC peaks corresponding to the 4 groups from Fig. 3a as well as the full list of M-ATAC peaks. Promoter: TSS − 3 kb and + 3 kb; intragenic: introns, exons, 5′UTR, 3′UTR and TTS, intergenic: distal from promoter > 1 kb and non-coding RNAs. c Expression level of genes associated with the four groups of methylated CpGs from in Fig. 3a, for the CpGs at promoters. ***P = 4.2e−33 between groups #1 and 2, ***P = 2.8e−75 between groups #2 and 3, *P = 0.034 between groups #3 and 4 (Wilcoxon test). d Average profile of M-ATAC, H3K4me1, H3K4me3, and H3K27ac signal associated with the four groups of methylated CpGs from Fig. 3a at promoters versus non-promoters. Of note, the small number of promoters in group 4 gives an unsmooth pattern for marks such as H3K4me1 and H3K27ac

Back to article page