Effect of epigenotoxic chemicals on transcriptomic profiles of human induced pluripotent stem cells [RNA-seq]

We studied the effects of chemical exposure on global DNA methylation by using mCherry-methyl-CpG-binding domain (MBD)-nls human induced pluripotent stem cells (iPSCs). According to the fluorescent MBD parameters, we divided the effects of 135 chemical on global DNA methylation into 3 categories; reduction (hypomethylation), increase (hypermethylation) and little/no effect. We performed RNA-seq analysis to examine the effects of chemicals on the expression of 100 stemness-related genes. In this series of experiment, we selected 5 compounds for genome-wide analyses. Etoposide, propyl gallate, and biotin were selected as representative chemicals of hypermethylation agents. Theophylline and bisphenol A were selected as representative chemicals of hypomethylation agents and undefined-epigenetic agents, respectively. Our results indicated that hypermethylation agents increased DNA methylation and downregulated the expression of genes involved in cell cycle or development. Human iPSCs cells were exposured to DMSO, biotin, etoposide, propyl gallate, theophylline, or bisphenol A for 48 hrs and then total RNA was isolated for RNA-seq analysis.