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. Overall design: 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.