Abstract
BackgroundDNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation.ResultsA total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver.ConclusionsIn this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.
Highlights
DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli
The overall methylation composition was inclined towards liver (Fig. 2A) and methylation in the CpG context was higher in backfat than in the liver, with 77 % of total methylation vs. 71 %, respectively (Fig. 2B & Additional file: File S1)
CpG methylation help in stabilizing chromatin structure as well as it controls the regulation of related gene expression and these effects could overall responsible for stabilization of genome (Fig. 2C)
Summary
DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. In the course of the intensive breeding program and continued close monitoring using modern biological methods, a pig breed referred to as ‘Nanchukmacdon’ was developed It has increased fat deposition, a better metabolism rate and maintained superior characteristics features in subsequent generations. The enhanced characteristics displayed by the mixed breed involve the expression of genes and different biological pathways in different tissues that play important roles in maintaining the harmony of the cells and the development of tissue from single cells [7, 8]
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