Reduced Representation Bisulfite Sequencing (RRBS) and RNA-Seq Reveal Effects of Methyl-Donor Rich Maternal Diet on Hepatic Transcriptome and DNA Methylome Landscapes of the Fetuses and Adult Pig Offspring

Epigenetic mechanisms regulate gene transcriptions in spatio-temporal manner by introducing chemical modifications to DNA/nucleosomes such as DNA methylation and histone acetylation without changing the underlying DNA sequence. Besides critical roles in embryonic development and genomic stability, evidence suggests that epigenetics enable plasticity of the genome function in response to environmental factors and shape the phenotypic outcomes. Maternal diet represents an in-utero environmental factor for the fetuses and may have a life-long impact on the offspring phenotype. Therefore, we investigated the effects of maternal diets supplemented with substrates and co-factors of the one-carbon cycle on hepatic DNA methylation and gene expression of 32 offspring at 91d post-conception and 150d post-natal in German Landrace and Pietrain pigs using Reduced Representation Bisulfite Sequencing (RRBS) and RNA-Seq. The RNA-Seq results showed that nucleic acid metabolism pathways of the fetuses were influenced by methyl-donor-rich maternal diet compared to control, while lipid metabolism pathways of the adult offspring were affected. The RRBS preferentially targeted CpG islands and CpG-rich promoters and moderately CDS, intron, 5´- and 3´-UTR. Mean percentage of global methylated cytosine was 43.73 ± 2.4, 0.35 ± 0.06 and 0.41 ± 0.09 in the CpG, CHG and CHH context, respectively. Dynamic pattern of the DNA methylomes revealed differentially methylated regions (DMRs) associated with maternal diet, developmental stage, and breed. Adipogenesis was among top canonical pathways whose gene members were linked to maternal-diet associated DMRs. Our results provide evidence reinforcing the epigenetic influence of maternal diet on phenotypic outcomes of the offspring and suggest its implication in livestock.