Abstract
DNA methylation of different gene components, including different exons and introns, or different lengths of exons and introns is associated with differences in gene expression. To investigate the methylation of porcine gene components associated with the boar taint (BT) trait, this study used reduced representation bisulfite sequencing (RRBS) data from nine porcine testis samples in three BT groups (low, medium and high BT). The results showed that the methylation levels of the first exons and first introns were lower than those of the other exons and introns. The first exons/introns of CpG island regions had even lower levels of methylation. A total of 123 differentially methylated promoters (DMPs), 194 differentially methylated exons (DMEs) and 402 differentially methylated introns (DMIs) were identified, of which 80 DMPs (DMP-CpGis), 112 DMEs (DME-CpGis) and 166 DMIs (DMI-CpGis) were discovered in CpG islands. Importantly, GPX1 contained one each of DMP, DME, DMI, DMP-CpGi, DME-CpGi and DMI-CpGi. Gene-GO term relationships and pathways analysis showed DMP-CpGi-related genes are mainly involved in methylation-related biological functions. In addition, gene–gene interaction networks consisted of nodes that were hypo-methylated GPX1, hypo-methylated APP, hypo-methylated ATOX1, hyper-methylated ADRB2, hyper-methylated RPS6KA1 and hyper-methylated PNMT. They could be used as candidate biomarkers for reducing boar taint in pigs, after further validation in large cohorts.
Highlights
In approximately 80% of non-castrated male pigs, the accumulation of skatole [1] and androstenone [2] in backfat causes offensive boar taint (BT) flavour
Our previous study revealed 32 significant gene differentially methylated cytosines (DMCs) associated with the BT trait [28]; using the same materials used in the first study for this study, we focused on the differentially methylated regions (DMRs) of intragenic regions, especially the promoter, first exon and first intron regions, as a single entity
This study investigated the methylation of porcine gene components in BT trait-related genes and identified the related DMRs of the gene components
Summary
In approximately 80% of non-castrated male pigs, the accumulation of skatole [1] and androstenone [2] in backfat causes offensive boar taint (BT) flavour. DNA methylation is a major epigenetic mechanism that directly causes a chemical modification to DNA [6] conferred by the covalent transfer of a methyl group to the C-5 position of cytosine [7]. DNA methylation in the promoter regions is associated with transcriptional repression at the level of gene regulation [9,10], likely because DNA methylation tends to reinforce chromatin-based silencing [11]. To silence genes at transcription, DNA methylation at high cytosine and guanine dinucleotide (CpG)-density promoters is not necessary [12,13]. Unmethylated CpG islands are found in more than one-half of the gene promoter regions, but they are not associated with the gene transcriptional activity [13]
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