Alterations in gene expression and DNA methylation in the bovine blastocyst in response to choline supplementation...

Exposure of the preimplantation bovine embryo to choline programs development to alter postnatal phenotype. To understand potential mechanisms, actions of choline on gene expression and DNA methylation of the bovine blastocyst were characterized. Embryos produced in vitro were cultured for 7 days with either 1.8 mM choline chloride or vehicle and RNA was extracted to assess gene expression. Using an adjusted p value of 0.05, the total number of differentially expressed genes (DEG) was 263 with 208 downregulated by choline. Analysis of gene ontologies of DEG indicated choline causes reduced protein synthesis. DNA methylation was determined using whole genome enzymatic methyl sequencing. A total of 7983 differentially methylated regions (DMR) were identified, with 6174 hypermethylated (choline>vehicle) and 1809 hypomethylated. Thus, as expected given its role as a methyl donor, the major action of choline was to promote methylation. The correlation coefficient between DNA methylation percent in promoters and gene expression was -0.18 for both vehicle and choline groups. Comparison of a DNA methylation data set of blood cells from heifers derived from choline- or vehicle-treated embryos identified 26 overlapping DMR for the blastocyst and blood datasets. Twelve of these DMR exhibited a consistent trend of hypermethylation in both heifer blood cells and blastocysts, whereas two DMR consistently showed a trend toward hypomethylation. It was concluded that choline alters blastocyst gene expression in a manner consistent with reduced protein synthesis and causes small changes in DNA methylation. Moreover, a small number of DMR are retained into the postnatal period.