Hu Zhenbin, Boschiero Clarissa, Neupane Mahesh, Bhowmik Nayan, Yang Liu, Kilian Levi, DeJarnette James Mel, Sargolzaei Mehdi, Harstine Bo, Li Cong-Jun, Tuo Wenbin, Baldwin Ransom L, Van Tassell Curtis P, Sattler Charles G, Liu George E
Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Select Sires Inc., 11740 U.S. 42 North, Plain City, OH 43064, USA.
Int J Mol Sci. 2025 May 1;26(9):4284. doi: 10.3390/ijms26094284.
DNA methylation is crucial in gene expression regulation and tissue differentiation in livestock. However, genome-wide methylation patterns among tissues remain underexplored in cattle, one of the world's most important farm animals. This study investigates sex- and tissue-specific DNA methylation in cattle using CpG site methylation data generated by an Infinium DNA Methylation array (HorvathMammalMethyl-Chip40) across seven tissues. Our analysis revealed significant tissue-specific methylation differences, with reproductive tissues/cells, such as the sperm, exhibiting distinct profiles compared to somatic tissues like hair and blood. Principal component analysis (PCA) highlighted tissue differentiation as the primary driver of methylation variability. We also identified 222 CpG sites with significant sex-based methylation differences, particularly on the X chromosome, suggesting the potential epigenetic regulation of sex-specific traits. The Gene Ontology (GO) enrichment analysis indicated that these methylation patterns may influence biological processes such as epithelial cell proliferation and blood vessel remodeling. Overall, this study provides important insights into sex- and tissue-specific epigenetic regulation in cattle, with implications for improving livestock breeding strategies through integrating epigenetic data.
DNA甲基化在牲畜的基因表达调控和组织分化中至关重要。然而，作为世界上最重要的农场动物之一，牛组织间的全基因组甲基化模式仍未得到充分研究。本研究利用Infinium DNA甲基化芯片（HorvathMammalMethyl-Chip40）生成的CpG位点甲基化数据，对牛的性别和组织特异性DNA甲基化进行了研究，涉及七个组织。我们的分析揭示了显著的组织特异性甲基化差异，与毛发和血液等体细胞组织相比，生殖组织/细胞（如精子）表现出不同的甲基化模式。主成分分析（PCA）强调组织分化是甲基化变异的主要驱动因素。我们还鉴定出222个具有显著性别甲基化差异的CpG位点，特别是在X染色体上，这表明性别特异性性状可能存在潜在的表观遗传调控。基因本体（GO）富集分析表明，这些甲基化模式可能影响上皮细胞增殖和血管重塑等生物学过程。总体而言，本研究为牛的性别和组织特异性表观遗传调控提供了重要见解，对通过整合表观遗传数据改进牲畜育种策略具有重要意义。
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