Comparative Methylation and RNA-Seq Expression Analysis in CpG Context to Identify Genes Involved in Backfat vs Liver Diversification in Nanchukmacdon Pig

Abstract Background: DNA methylation and demethylation at CpG island is one of the main regulatory mechanisms at the transcriptional level that give cells the possibility to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergone selection. Liver and Backfat play important role in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue stores plethora of information and their understanding are required to enhance tissue characteristics in the future generation. Results: In this study, to understand the differentiation mechanism we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis and identified 16 CpG islands were involved in differentially methylation regions (DMRs) as well differentially expressed genes (DEGs) between liver and backfat. Among the identified differentially-methylated genes (C7orf50, ACTB, MLC1) in backfat and (TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A, HOXA5) in the liver were identified. Motif analysis for DMRs was also performed to understand the major role of methylated motif for tissue-specific differentiation. Gene ontology studies revealed the association with collagen fibril organization, BMP signaling pathway in backfat and Cholesterol biosynthesis, bile acid and bile salt transport, immunity-related pathways in methylated genes expressed in the liver. Conclusion: Our finding could help in understanding how methylation on certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.