Although the average level of DNA methylation per chromosome was increased after EtOH treatment, it does not mean that all the genes in the chromosome are affected the same way. To examine the effect of EtOH on the DNA methylation change in undifferentiated hESCs at the gene level, we calculated the changes in % of genes that are hyper- or hypomethylated upon EtOH treatment, after normalization against untreated cells. Using this type of analysis we observed that EtOH treatment induced overall increases in both hyper- and hypomethylation of the promoter regions in each and all chromosomes (Fig. S2). Interestingly, the % of genes hyper or hypomethylated by EtOH at the promoter regions was relatively similar, whereas a much higher % of genes were hypomethylated at CGIs compared to the % of hypermethylated genes (Fig. S2). Although this first appears counterintuitive to the observed global increases in methylation at promoter regions and CGIs (Figs. 2 & 3), these data demonstrate that while a greater number of genes were hypomethylated, the increases in methylation of a smaller number of genes on individual
