Fig. 3

ZF binding and widespread methylation gain are not limited to transcriptional repression. A Heatmaps representing the mCG % in noDox versus Dox DMRs indicating the level of methylation gain in ZF-D3A-wt Dox, major loss of methylation on Dox withdrawal (DoxWD), and absence of methylation in ZF-D3A-mut expression (Dox-mut). B Overlap of differentially expressed (DE) genes (DEseq2 fdr < 0.05) between ZF-D3A-wt noDox vs Dox and ZF-D3A-mut noDox vs Dox. C Transcriptional change of differentially expressed genes classified as having a ZF-D3A-mut peak on the promoter (−2000, +500 bp). D Scatter plot of the DMR methylation gain (as defined by dmrseq statistic), versus the fold change in mRNA abundance of promoter-DMR associated genes, between noDox and Dox. Point color indicates the gene differential expression significance: red indicates FDR <0.05, black indicates FDR >0.05 (DEseq2). Trend line (blue) was fitted using a local polynomial regression. Depicted genes are not differentially expressed in the ZF-D3A-mut. E Proportion of genes with a promoter-DMR classified by transcriptional change. On the left, genes not differentially expressed in the ZF-D3A-mut and on the right all genes