Abstract

The methylation status of pivotal genes involved in fat deposition in chickens has been extensively studied. However, the whole-genome DNA methylation profiles of broiler abdominal adipose tissue remain poorly understood. Using whole-genome bisulfite sequencing, we generated DNA methylation profiles of chicken abdominal adipose tissue from Northeast Agricultural University broiler lines divergently selected for abdominal fat content. We aimed to explore whether DNA methylation was associated with abdominal fat deposition in broilers. The whole-genome DNA methylation profiles of fat- and lean-line broilers abdominal adipose tissue were constructed. The DNA methylation levels of functional genomic regions in the fat broiler were higher than those in the lean broiler, especially in the 3′ untranslated regions (UTRs) and exons in the non-CG contexts. Additionally, we identified 29,631 differentially methylated regions and, subsequently, annotated 6,484 and 2,016 differentially methylated genes (DMGs) in the gene body and promoter regions between the two lines, respectively. Functional annotation showed that the DMGs in promoter regions were significantly enriched mainly in the triglyceride catabolic process, lipid metabolism-related pathways, and extracellular matrix signal pathways. When the DMG in promoter regions and differentially expressed genes were integrated, we identified 30 genes with DNA methylation levels that negatively correlated with their messenger RNA (mRNA) expression, of which CMSS1 reached significant levels (false discovery rate < 0.05). These 30 genes were mainly involved in fatty acid metabolism, peroxisome-proliferator-activated receptor signaling, Wnt signaling pathways, transmembrane transport, RNA degradation, and glycosaminoglycan degradation. Comparing the DNA methylation profiles between fat- and lean-line broilers demonstrated that DNA methylation is involved in regulating broiler abdominal fat deposition. Our study offers a basis for further exploring the underlying mechanisms of abdominal adipose deposition in broilers.

中文翻译：

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腹部脂肪的全基因组亚硫酸氢盐测序揭示了根据脂肪不同选择的肉鸡品系的 DNA 甲基化模式变化

摘要

参与鸡脂肪沉积的关键基因的甲基化状态已得到广泛研究。然而，肉鸡腹部脂肪组织的全基因组 DNA 甲基化谱仍然知之甚少。使用全基因组亚硫酸氢盐测序，我们生成了来自东北农业大学肉鸡品系的鸡腹部脂肪组织的 DNA 甲基化图谱，这些组织根据腹部脂肪含量进行了不同的选择。我们旨在探讨 DNA 甲基化是否与肉鸡腹部脂肪沉积有关。构建了肥肉和瘦肉肉鸡腹部脂肪组织的全基因组 DNA 甲基化图谱。肥肉鸡功能基因组区域的 DNA 甲基化水平高于瘦肉鸡，尤其是在非 CG 环境中的 3' 非翻译区 (UTR) 和外显子。DMG s) 分别位于基因体和两条线之间的启动子区域。功能注释表明启动子区域的DMGs显着富集，主要在甘油三酯分解代谢过程、脂质代谢相关通路和细胞外基质信号通路中。当启动子区域的 DMG 和差异表达的基因被整合时，我们确定了 30 个 DNA 甲基化水平与其信使 RNA (mRNA) 表达负相关的基因，其中CMSS1达到显着水平（错误发现率 < 0.05）。这30个基因主要参与脂肪酸代谢、过氧化物酶体-增殖物激活受体信号、Wnt信号通路、跨膜转运、RNA降解和糖胺聚糖降解。比较肥肉和瘦肉肉鸡之间的 DNA 甲基化图谱表明 DNA 甲基化参与调节肉鸡腹部脂肪沉积。我们的研究为进一步探索肉鸡腹部脂肪沉积的潜在机制提供了基础。