Wang Xiao, Kadarmideen Haja N
Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
Vet Sci. 2020 Jun 13;7(2):77. doi: 10.3390/vetsci7020077.
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, 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 , hypo-methylated , hypo-methylated , hyper-methylated , hyper-methylated and hyper-methylated . They could be used as candidate biomarkers for reducing boar taint in pigs, after further validation in large cohorts.
不同基因成分（包括不同外显子和内含子，或不同长度的外显子和内含子）的DNA甲基化与基因表达差异相关。为了研究与公猪膻味（BT）性状相关的猪基因成分的甲基化情况，本研究使用了来自三个BT组（低、中、高BT）的九个猪睾丸样本的简化代表性亚硫酸氢盐测序（RRBS）数据。结果表明，第一个外显子和第一个内含子的甲基化水平低于其他外显子和内含子。CpG岛区域的第一个外显子/内含子的甲基化水平甚至更低。共鉴定出123个差异甲基化启动子（DMP）、194个差异甲基化外显子（DME）和402个差异甲基化内含子（DMI），其中在CpG岛中发现了80个DMP（DMP-CpGis）、112个DME（DME-CpGis）和166个DMI（DMI-CpGis）。重要的是， 分别包含一个DMP、DME、DMI、DMP-CpGi、DME-CpGi和DMI-CpGi。基因-基因本体术语关系和通路分析表明，与DMP-CpGi相关的基因主要参与甲基化相关的生物学功能。此外，基因-基因相互作用网络由低甲基化的 、低甲基化的 、低甲基化的 、高甲基化的 、高甲基化的 和高甲基化的 节点组成。在大型队列中进一步验证后，它们可作为减少猪公猪膻味的候选生物标志物。
