A Genome‐Wide Analysis of Placental Epigenetic Markers in Response to Maternal Choline Supplementation

Abstract

Choline is an essential micronutrient that provides methyl groups for cellular DNA methylation, an epigenetic modification with downstream effects on gene expression. Maternal choline supplementation (MCS) during pregnancy has many beneficial effects on placental and fetal development, which may be mediated in part by an altered placental methylation profile. In addition to DNA methylation, other epigenetic mechanisms such as genomic imprinting and microRNA (miRNA) regulation are also important to normal placental and fetal development, but whether these markers are modulated by choline remains largely unknown. We sought to investigate the impact of MCS on these epigenetic markers using a subset of placental samples collected at gestational day 15.5 from dams consuming 1× or 4× the recommended choline level. Placental mRNA and miRNA were extracted and sequenced, and the RNAs with differential expression were determined using the edgeR package developed in R. In response to MCS, three imprinted genes (Dcn, Qpct and Tnfrsf23) were downregulated in the male placentas (Padj≤0.01) whereas four imprinted genes (Ampd3, Tfpi2, Gatm, and Aqp1) were upregulated in the female placentas (Padj≤0.05). Furthermore, five miRNAs (miR‐712‐5p, miR‐3470a, miR‐6538, miR‐6240 and miR‐5126) were significantly downregulated in the female placentas from the 4× choline group (Padj≤0.033). Consistent with the downregulation of these miRNAs, some of their predicted mRNA targets showed a higher expression (P<0.05). These target genes are involved in processes such as cell signaling, immune response and macronutrient transport, all of which are crucial to placental development and fetal health. In contrast, none of the miRNAs in the male placentas remained significant after correction for false discovery rate (Padj>0.05). Overall, these data indicate that the placental imprintome and miRNA profile are responsive to MCS, but the effects may differ between the male and the female placentas.Support or Funding InformationUSDA, NIH, Graduate Women in Science, Egg Nutrition Center