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Fig. 2 | Genome Biology

Fig. 2

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

Fig. 2

EpiMethylTag is a reproducible method for testing whether DNAme can coexist with TF binding (CTCF) or chromatin accessibility genome-wide. a Pearson correlation of read counts comparing M-ATAC with unconverted samples (NC) and regular ATAC-seq (top), and CTCF M-ChIP with unconverted samples, a sample from the Schubeler lab generated using ChIP-BisSeq [1] (GSE39739) and regular CTCF ChIP-seq (bottom). b Representative IGV screenshots of EpiMethylTag, at the Klf4 locus (left panel), the Pisd-ps1 locus (middle panel), and the Slc5a8 locus (right panel). ATAC and M-ATAC in green, CTCF in purple and DNA methylation from merged M-ATAC, merged CTCF M-ChIP and WGBS (methylation from 0% in blue to 100% in red). A zoom-in of methylation at the highlighted region is shown at the bottom of each example. The Klf4 locus illustrates a region that has low methylation as detected by M-ATAC, CTCF M-ChIP, and WGBS. The Pisd-ps1 locus illustrates a region that has high methylation as detected by M-ATAC, CTCF M-ChIP, and WGBS. The Slc5a8 locus illustrates a region that has low methylation as detected by M-ATAC and high methylation as detected by WGBS. c Density plots of methylation from EpiMethyltag compared with WGBS. Only CpGs inside peaks and with at least five reads were considered. Top: average methylation of CpGs per M-ATAC peak in M-ATAC versus WGBS (Pearson correlation = 0.69, p value < 2.2e−16; bottom left corner: 27977 peaks, top left corner: 8408 peaks, top right corner: 1019 peaks, bottom right corner: 113 peaks). Bottom: average methylation per CTCF M-ChIP peak of CpGs in CTCF M-ChIP versus WGBS (Pearson correlation = 0.74, p value < 2.2e−16; bottom left corner: 6549 peaks, top left corner: 198 peaks, top right corner: 304 peaks, bottom right corner: 310 peaks)

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