Fig. 5
DNA methylation dependent Polycomb targeting is common and reversible. a Left: H3K27me3 ChIPseq heatmap profiles for hiBiv and loBiv in the indicated cell types and associated mutants. Bottom: average profiles of heatmap data. Replicates: E14 serum/2i (n = 1), ES WT/Mbd3−/− (n = 2) and NPC WT/Lsh−/− (n = 1). Right: 5meC liquid chromatography mass spectrometry (LC-MS) comparing wild-type and Lsh−/− NPC (n = 3). b Repeat class DNA methylation (WGBS) boxplots during iPSC reprogramming. Replicates: 2oMEF (n = 8), D8H (n = 11), 2oIPS (n = 8). c H3K27me3 ChIPseq (n = 1) heatmap profiles over hiBiv and loBiv during iPSC reprogramming. Bottom: average profiles of heatmap data. d RNAseq expression barplots for Polycomb components (top) and DNA methylation components (bottom) during iPS cell reprogramming. 2oMEF: secondary reprogrammed MEFs; D8H: OSKM transduced MEFs in high doxycycline after 8 days; 2oiPSC: secondary reprogrammed induced pluripotent stem cells. e Histograms (Satellite, LTR & L1) and boxplots (TSS) of WGBS (n = 1) during DNA methylation manipulation by repression and re-activation of Dnmt1 expression in mESC. f H3K27me3 ChIPseq (n = 1) heatmap profiles over hiBiv and loBiv during DNA methylation manipulation. Bottom: average profiles of heatmap data. See Additional file Table S3 for replicate metrics