Title: Locus-Specific DNA Methylation Reprogramming during Early Porcine Embryogenesis1 Short title: Diverse DNA Methylation Patterns in Pig Embryos

During early mammalian embryogenesis, there is a wave of DNA demethylation post fertilization and de novo methylation around implantation. The paternal genome undergoes active DNA demethylation whereas the maternal genome is passively demethylated after fertilization in most mammals except sheep and rabbits. However, the emerging genome-wide DNA methylation landscape has revealed a regulatory and locus-specific DNA methylation reprogramming pattern in mammalian preimplantation embryos. Here we optimized a bisulfite sequencing protocol to draw base-resolution DNA methylation profiles of several selected genes in gametes, early embryos and somatic tissue. We observed locus-specific DNA methylation reprogramming in early porcine embryos. First, some pluripotency genes (POU5F1 and NANOG) followed a typical wave of DNA demethylation and remethylation whereas CpG-rich regions of SOX2 and CDX2 loci were hypomethylated throughout development. Second, a differentially methylated region (DMR) of an imprint control region (ICR) in IGF2/H19 locus exhibited differential DNA methylation which was maintained in porcine early embryos. Third, a centromeric repeat element retained a moderate DNA methylation level in gametes, earl