Fig. 7

Methylation loss is concentrated at regions normally repressed by polycomb. a Distribution of probes showing significant loss per chromatin state—numbers of probes are shown at left, chromatin states below: tcn, transcription; heterochrom/Lo, heterochromatin or low signal; repetitive, repeat DNA. b Region around the LEP gene: tracks as before, with the addition of data from cells treated with siRNA for 72 h (top). A track showing ChromHMM chromatin states from NHLF foetal lung fibroblasts is shown at bottom: grey, polycomb-repressed; green, transcriptionally active (full colour key at top right). c DNMT1 mRNA levels by qPCR following treatment with siRNA (+) for 72 h compared with scrambled control (Scr). ACTB is shown as a control; ladder as above. d Median β values for all regions (WT) compared to medians for polycomb-repressed regions (Polycomb), or all other regions (Other) in the cell lines indicated at top; remeth, remethylated. e Numbers of probes showing loss and gain in methylation in hTERT cells following treatment with siRNA for 72 h compared with the shRNA lines (averaged); #, number. f mRNA levels for the indicated genes in shRNA lines treated with the EzH2 inhibitor DZNeP; UNT, untreated; bars represent SEM, experiment carried out in duplicate. g Median β values for all variable exons at the PCDHG locus (left) and for fat/body mass genes (FBM, right): compare d16 shRNA lines with cells treated with siRNA. h DNMT1 mRNA levels in WT cells exposed to siRNA for 48 h, then allowed to recover in normal medium; comparisons were made to a scrambled siRNA negative control (Scr). i Methylation levels by pyroassay at the loci indicated during the transient KD and recovery shown in (h); timepoints are in days. All loci showed significant loss of methylation: LEP and SNRPN showed no significant gain versus lowest methylation level, while PCDHGA2 showed no significant gain between d22 and d36