Additional file 1 of Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

Additional file 1: Figure S1. The Dox inducible ZF-D3A system. Figure S2. ZF-D3A ChIP-seq replicates show equiparable positional enrichments. Figure S3. Nucleosome position dictates mCH deposition on closed and open chromatin. Figure S4. ZF-D3A-wt expression does not lead to a global reduction of transcriptional activity. Figure S5. ZF binding and DMR induction led to diverse transcriptional responses. Figure S6. Characterisation of promoter DMRs. Figure S7. Examples of non-responsive promoter-DMRs. Figure S8. Differential TF-footprinting at promoter-DMRs. Figure S9. Alternative TSS usage upon Dox induction. Figure S10. Differential ATAC-seq peaks. Figure S11. Differential methylation retention at promoters and distal regulatory elements. Figure S12. Prolonged Dox induction does not increase methylation gain. Figure S13. Epigenomic data overview. Table S1. Global WGBS stats for all samples. Table S2. List of promoters with DMRs and transcriptional change. Table S3. Alternative TSS in noDox vs Dox comparison. Table S4. Alternative TSS in noDox-mut vs Dox-mut comparison.