## 4 Discussion  
Cloning has become a powerful tool for analysing gene functions, genomic imprinting, genomic re-programming, development, neurodegenerative diseases, gene therapy, and more [34; 35; 36]. Somatic cell nuclear transfer is an essential cloning tool for biomedical and epigenetic research [37]. This method enables significant development in biomedicine and disease modeling, where genome-edited mammals can be bred and used for disease research, transplantation, or to protect endangered species [5; 38; 39; 40; 41]. Due to its similarity to humans, somatic cell nuclear transfer (SCNT) and precise genome editing to generate transgenic pigs carrying the required disease phenotype may be applied to swine [6; 7]. Here, we showed that according to methylation patterns, there is a clear definition of groups with low and high cloning efficiency [42; 43; 44]. Figure 4: Hierarchical cluster analysis according to methylation patterns across analysed samples. Blue colour—low cloning efficiency cells; red colour—high cloning efficiency cells. Dendrograms were produced using correlation distance and ward clustering methods. Numbers represent the individual sample ID. DNA methylation in a promoter usually correlates with the repression [45]. Methylated genes are known to be linked with genomic region-specific DNA methylation patterns [46; 47]. We investigated promoter, exon, and intron regions along the porcine genome and localised CpG islands to these genic features. Most differentially methylated sites were intergenic (Figure 2), and 37% were located in previously described CpG islands. We showed that methylation levels of CpG islands were lower than CpG island shores in the promoter, exon, and intron regions. These results demonstrated that CpG islands located in different genic features displayed effects on the methylation patterns of the associated genes. A strong relation between methylations in CpG island shores located within 2 kb of an annotated transcription start site (TSS) and the expression of related genes was reported by [PERSON] and others [48]. CpG islands in exon regions showed different methylation levels than those in intron regions, suggesting that exons may affect the methylation patterns of CpG islands [49; 50]. Completing the swine reference genome sequence [41; 42] provides a great ability to perform porcine studies for human diseases and disorders and opens the door for targeted approaches to produce models for diseases [51; 52; 53]. Our results provide novel information for future studies of porcine epigenomics. The results based on RRBS are a powerful technology for epigenetic profiling of cell populations relevant to developmental biology and genetic engineering for porcine disease models. Further studies are necessary to investigate the similarities in methylation levels between humans and pigs for specific genomic regions. This knowledge will give us a chance to analyse disease progression, the differences observed in intron and exon methylation patterns between pig tissues and human cell lines, and the proposed adaptive evolutionary role of CpG methylation. Recent advances in single-cell multi-omics data have shed light on the complexity of epigenetic regulation and the potential for using this information to understand the mechanisms underlying the epigenetic reprogramming process [54]. As a result, this information may be used to design more effective and efficient strategies for reprogramming the donor nucleus in SCNT. The study by [PERSON] et al. (2018) highlights the importance of single-cell multi-omics data in exploring the molecular mechanisms underlying epigenetic reprogramming and suggests that this information could be valuable in the development of new techniques for SCNT in the future [55]. In conclusion, new perspectives in SCNT and the use of single-cell multi-omics data as a tool for understanding the mechanisms of epigenetic regulation offer novel possibilities for the future of epigenetic research.