Fig. 1

Genome-wide DNA methylation dynamics during cellular senescence. a HMECs progressively cease proliferation with serial passage. Early proliferating (EP) and deeply senescent (DS) cells as used throughout are indicated. Error bars = SD of three independent experiments. b DS cells display increased p16 expression (green, top row) and SA-β-gal staining (blue, bottom row). c A scatter plot of the average beta value differences between triplicate samples of DS and EP cultures for those sites found significantly differentially methylated (F-test; genome wide corrected P value <0.01 and a minimum beta value difference of 0.3 between EP and DS cells) in either experiment 1 or experiment 2 (grey points). Those sites which are senDMPs in experiment 1 which show a beta value difference <0.1 in experiment 2 (926 probes, ‘experiment 1’) are highlighted in blue; those senDMPs in experiment 2 which show a beta value difference <0.1 in experiment 1 (1,807 probes, ‘experiment 2 only’:) are highlighted in red and those common senDMPs between experiment 1 and 2 which change in the same direction (725 probes, ‘agree’) are highlighted in green. Those senDMPs in common between experiments 1 and 2 which show opposite directions are highlighted in red. The number of sites for each quadrant are shown in the four corners with the appropriate colour. d DS–EP beta value differences of neighbouring Illumina 450K probes within 500 bp of ‘index’ senDMP. The hypermethylated index senDMPs (left) and hypomethylated index senDMPs (right) are shown for both experiment 1 and experiment 2. Each panel row represents the three different sites (experiment 1 only (blue), experiment 2 only (green) and agree (purple)). e Comparison of DNA methylation profiles between unsorted EP cells versus each of the three different EP sub-fractionated populations (left, middle and right panels). The beta values for all 401,915 CpGs are plotted on each axis (black points). senDMPs, as defined in the text, are illustrated in blue (experiment 1 only), green (experiment 2 only) and purple (agree). No genome-wide statistical significant differences were found between EP and any of the sub-fractionated populations, or indeed between any of the FACs sorted populations (Additional file 5: Table S8)