DNA Methylation Affects Phenotypic Variation in Cattle Possessing Extreme Phenotypes for Residual Feed Intake

DNA methylation is an environmentally influenced epigenetic modification that regulates gene transcription and has the potential to influence variation in economically important phenotypes in agricultural species.  We have integrated RNA-Seq and methyl binding domain sequencing (MBD-Seq) data in order to determine the extent to which DNA methylation affects phenotypic variation of residual feed intake in Angus steers. MBD-Seq is a technique that involves the sample enrichment of methylated genomic regions followed by their next-generation sequencing.  This study utilized Illumina next generation sequencing technology to perform both RNA-Seq and MBD-Seq.  Subsequently, differential methylation and differential gene expression were characterized in the livers, small intestines and longissimus dorsci muscles of 8 animals that are phenotypically extreme for residual feed intake (4 high and 4 low RFI).  Finally, Partial Correlation with Information Theory (PCIT) was performed to determine if methylation events regulate transcriptional networks.  Here we provide evidence that RFI QTL and GWAS regions overlay genomic regions where methylation may regulate transcription.