Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle.
Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle.
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日本黑牛（和牛）和中国红草原牛背最长肌的全基因组甲基化比较分析
DOI：
10.1371/journal.pone.0182492
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Yu X
中科院分区：
文献类型：
--
作者：
Fang X;Zhao Z;Yu H;Li G;Jiang P;Yang Y;Yang R;Yu X
DNA甲基化是一种重要的表观遗传学机制，参与了包括肌肉生长和发育在内的许多生物学过程中的基因表达。它对重要经济性状的影响表现在日本黑牛（Wagyu）和中国草原红牛（Red Steppes）肉质性状的显著差异上，从而为分析DNA甲基化对这些性状的影响提供了一个独特的模型。在本研究中，我们进行了全基因组DNA甲基化分析在两个品种的全基因组亚硫酸氢盐测序（WGBS）。总体上，鉴定了23150个差异甲基化区域（DMR），其位于9922个GO术语中富集的8596个基因中，其中1046个GO术语显著富集（p<0.05），包括脂质易位（GO：0034204）和脂质转运（GO：0015914）。KEGG分析表明DMR相关基因分布在276条通路中。相关性分析发现，331个DMR与差异表达基因（DEG）的表达水平呈负相关，其中21个DMR位于启动子区。这些结果为今后肌肉发育的基因组学和表观基因组学研究以及肉质性状的标记辅助选择奠定了基础。
DNA methylation is an important epigenetic mechanism involved in expression of genes in many biological processes including muscle growth and development. Its effects on economically important traits are evinced from reported significant differences in meat quality traits between Japanese black (Wagyu) and Chinese Red Steppes cattle, thus presenting a unique model for analyzing the effects of DNA methylation on these traits. In the present study, we performed whole genome DNA methylation analysis in the two breeds by whole genome bisulfite sequencing (WGBS). Overall, 23150 differentially methylated regions (DMRs) were identified which were located in 8596 genes enriched in 9922 GO terms, of which 1046 GO terms were significantly enriched (p<0.05) including lipid translocation (GO: 0034204) and lipid transport (GO: 0015914). KEGG analysis showed that the DMR related genes were distributed among 276 pathways. Correlation analysis found that 331 DMRs were negatively correlated with the expression levels of differentially expressed genes (DEGs) with 21 DMRs located in promoter regions. Our results identified novel candidate DMRs and DEGs correlated with meat quality traits, which will be valuable for future genomic and epigenomic studies of muscle development and for marker assisted selection of meat quality traits.
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