Prenatal and Postnatal Dietary n-3 Fatty Acid Supplementation Alters Buffy Coat DNA Methylation Profile in Pigs

Recent work we have conducted has demonstrated feeding n-3 fatty acids to sows in gestation attenuated the innate immune response of their offspring.  However, the contribution of DNA methylation to differences observed in this phenotypic response is unknown.  The objective of this study was to determine the effect of prenatal and postnatal dietary enrichment of n-3 fatty acids, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), on buffy coat DNA methylation profiles.  Fifteen gilts (n=5 per treatment) were selected from one of three dietary treatments: 1) control diet throughout gestation, lactation, and nursery phase; 2) n-3 fatty acid supplementation in the form of Gromega™, rich in DHA and EPA, fed throughout gestation, lactation and nursery phase; or 3) DHA and EPA supplementation only in the gestation and lactation stage, control diet devoid of DHA and EPA in the nursery.  At 11 weeks of age and after 8 weeks of nursery feeding, buffy coats were collected and DNA isolated.  The DNA was enriched for CpG methylation by an MBD protocol and subjected to next-generation sequencing.  Approximately 77% of total reads were mapped to the pig genome build 10.2, and 623,838 unique methylated regions were identified.  In total, mapped base pairs covered approximately 25% of the genome.  Preliminary analysis revealed distinct chromosome-specific patterns of methylation.  Across the genome, numerous highly methylated regions were detected that were independent of treatment.  Conversely, several treatment-specific methylation patterns were also apparent on specific chromosomes. This work was supported by USDA and Iowa State Experiment Station Animal Health Funds.