Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy

Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of the offspring. In previous studies in sheep, we demonstrated that different maternal diets had altered the transcriptome of fetal tissues. However, the mechanisms underlying those transcriptomic changes are poorly understood. DNA methylation is an epigenetic mark regulating transcription and is largely influenced by dietary components of the one-carbon cycle, a generator of the methyl group donor. Therefore, in the present study, we hypothesized that different maternal diets during pregnancy will alter the DNA methylation and gene expression patterns in fetal tissues. Pregnant ewes were randomly divided into two groups each of which received a hay or corn diet from mid-gestation (day 67±5) until necropsy (day 131 ± 1). The diets were formulated to meet the nutritional needs of ewes during pregnancy. On the day of necropsy, longissimus dorsi (LD) muscle tissues were collected from the fetuses and then used for DNA methylation analysis and gene expression profiling. Genomic DNA was extracted from a total of 16 fetal LD samples, eight per dietary treatment, following a salt-chloroform extraction protocol. Methyl-binding domain (MBD) enrichment was performed, subsequently construction of the sequencing library was implemented and libraries were quality checked and quantified. The 16 samples were then used for cluster generation and following sequencing in two lanes of an Illumina Hi-Seq 2000 and 100-base paired-end reads were generated.