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Fig. 6 | Genome Biology

Fig. 6

From: Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

Fig. 6

Active chromatin is compatible with DNA methylation. A Number of differentially called ATAC-seq peaks (DEseq2 FDR < 0.05) classified as gain or loss with respect to the noDox sample, DoxWD corresponds to 7-day withdrawal. B Average methylation and ATAC signal and C TF binding motifs at differential ATAC-seq peaks in noDox versus Dox conditions. D TFAP2C (MCF-7 ENCODE) and ZF-D3A-wt ChIP-seq signal on differential ATAC-seq peaks, color coded as in B. E Genome browser snapshot showing the TFAP2C locus, where DoxWD corresponds to 7-day withdrawal. Average methylation levels on F H3K4me3 and G RNA polymerase II phosphorylated serine 5 peaks called from bisulfite-ChIP-seq data. On the left hand side are the methylation values obtained as per WGBS and on the right hand side as per BS-ChIP-seq. One asterisk indicates a p-value < 0.01 in a one-sided Wilcoxon rank-sum test. Boxplot center lines are medians, box limits are quartiles 1 (Q1) and 3 (Q3), whiskers are 1.5 × interquartile range (IQR), and points are outliers

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