DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1) showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns.These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a good predictor of whether the foetus would develop to term or not.Somatic cell nuclear transfer (SCNT) has been used to successfully produce cloned animals from several mammalian species since a sheep was cloned using a differentiated somatic donor cell [1]. However, to date widespread application of SCNT in agricultural breeding programs has not yet been captured because the technology remains inefficient despite more than 10 years of research. Irrespective of the species being cloned, there is still a high rate of pregnancy failure throughout gestation [2-6]. The most common SCNT foetal phenotypes across species are foetal overgrowth and loss of allometric growth regulation (collectively known as "large offspring syndrome"), musculoskeletal defects, and acute, excessive accumulation of allantoic fluid (hydrallantois or hydrops) accompanied by perturbations in the co