Cell subpopulation imbalance induced by TGFβ correlates with a methylome reconfiguration. a. Huh7 and HepG2 cells were treated with TGF-β for 4 days, or 4 + 4 days post-release, as described above. Biological triplicates were used to assess DNA methylation changes with HM450 arrays. b. heatmap represents probes differentially methylated (FDR < 0.05) with a delta-beta of at least 20% (n = 41) between control and TGF-β treated cells, in both cell lines, and both time points. For a full list of DMPs (FDR < 0.05 and delta-beta of at least 10%) see Table S3. Blue indicates lower methylation, and red indicates higher methylation. The unsupervised clustering distinguishes TGF-β from control conditions regardless of cell line or time of exposure. c. 555 DMPs (FDR < 0.05, delta > 10%) were mapped to known enhancer regions in the human hg19 genome assembly. Enrichment is observed in DMPs, relative to a random selection of the same number of probes and the total of HM450 probes mapping to an enhancer (hg19). d. in similar way, GC content was compared between DMPs, random probes, and all HM450 probes (HM450). (*) indicates a significantly lower GC content in DMPs relative to any of the other probe lists. e. DMPs were distributed according to their relationship to CpG islands (CGI: islands, SHO: shores, SHE: shelves, or NC: non-CpG islands) or genes (DP: distal promoter, DS: distal sequence, GB: gene body, IG: intergenic, and PP: proximal promoter), as described in Materials and Methods. f. A selection of significant loci were validated by pyrosequencing (as described in Materials and Methods), in both cell lines. (*) indicates P value < 0.05 relative to non-treated cells at the corresponding time point and cell line. IL-6 was included for comparison.