Methylation Genome-Wide Profiling in Lowly and Highly Efficient Somatic Cell Nuclear Transfer in Pigs

Swine is a common model organism for biomedical research. Epigenetic reprogramming in somatic cell nuclear transfer (SCNT) embryos does not fully recapitulate the natural DNA demethylation events at fertilisation. This study aimed to conduct genome-wide methylation profiling detect differentially methylated regions (DMRs) responsible epigenetic differences stem cells that displayed high and low efficiency of SCNT elucidate cloning rate pigs. Adipose tissue mesenchymal (AMSC)s lines were isolated from adipose adult male pigs (n = 20; high-efficiency 10; low-efficiency 10). Reduced representation bisulfite sequencing (RRBS) was performed on an Illumina HiSeq1500. Paired-end reads filtered remove adapter contamination, low-quality using TrimGalore! Filtered mapped reference genome Bismark. MethylKit used identify (bases tiles), showing statistically significant differential between AMSCs. Hierarchical cluster analysis according patterns clearly defined groups with efficiency. We report 3704 bases 10062 tiles methylation. Most sites are intergenic 62%, 31% intronic, 4% exons, promoters. Moreover, 37% located known CpG islands (CGIs), island shores (CGSs).