Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes that Govern Cardiomyocyte Maturation [RNA-seq]

To test the hypothesis that the disruption caused by TCDD in cardiomyocytes results from changes in DNA methylation and gene expression patterns, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under the control of the cardiomyocyte-specific Nkx2.5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 122 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue towards the elucidation of the complex interactions between genetic and epigenetic mechanisms, and environmental factors that may contribute to CHD incidence. Overall design: To analyze gene expression and DNA methylation changes across time, we compared Nkx2-5- positive cells treated with vehicle (control) with a) untreated ES cells, and b) Nkx2-5- positive cells treated with 5 nM TCDD for 24, 72, and 96 hours.