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Fig. 1 | Genome Biology

Fig. 1

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

Fig. 1

A synthetic zinc finger fused to D3A binds to thousands of loci leading to widespread 5mC gain. A Schematic representation of the ZF-D3A doxycycline inducible system. The ZF-D3A-mut has 4 amino-acid changes in the DNMT3A catalytic domain compared to the wild type (ZF-D3A-wt) that abrogate the DNA methyltransferase catalytic activity. The constructs only include the DNMT3A catalytic domain, not the full-length human gene. B Diagram of the experimental approach used in this study, highlighting stage names and sample harvesting points. After 3 days of Dox induction, only GFP expressing cells were collected for both Dox and Dox withdrawal (DoxWD) timepoints. For DoxWD-3d, no RNA-seq data was generated. C Genome browser representation of the SOX2 locus. D Genomic distribution of identified ZF-D3A-wt binding sites, differentially methylated regions (DMRs) between ZF-D3A-wt noDox and Dox, and unmethylated regions (UMRs) in the ZF-D3A-wt control. Distal ATAC are ATAC-seq peaks > 2kb away from a TSS. E Overlaps between ZF-D3A-wt peaks and DMRs, and UMRs versus DMRs. Intersection values are shown for the top category (peaks and DMRs respectively). F Heatmap of the all DMRs and associated features, showing the binding signal of ZF-D3A constructs, mCG by WGBS, ATAC-seq and H3K4me3 ChIP-seq signal, and CpG density (p-value < 0.01, mCG gain >20%). Genome-wide consistency across epigenomic samples depicted in this figure is shown in Additional file 1: Fig. S13

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