Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States.
Department of Animal Science, Cornell University, Ithaca, NY, United States.
Genome Biol. 2024 Jul 15;25(1):185. doi: 10.1186/s13059-024-03307-6.
We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle.
Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction.
Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.
我们最近在人类基因组中鉴定出了约 10000 个系统性个体间的表观遗传变异相关区域（CoRSIVs）。这些甲基化变体适用于人群研究，因为血液中的 DNA 甲基化测量提供了关于整个身体的表观遗传调控的信息。此外，人类 CoRSIVs 的 DNA 甲基化建立是易受围孕期影响的，如营养。在这里，我们分析了两个荷斯坦奶牛的多种组织的公开全基因组亚硫酸氢盐测序数据，以确定 CoRSIVs 是否存在于牛中。
我们专注于具有至少 5 个 CpG 和至少 20 的系统性个体间变异指数的基因组块，我们的方法鉴定了 217 个牛 CoRSIVs，其中一部分我们通过亚硫酸氢盐焦磷酸测序独立验证。与人类 CoRSIVs 相似，牛中的 CoRSIVs 与遗传变异强烈相关。同样在人类中，我们表明，在辅助生殖过程中胚胎培养的背景下，牛 CoRSIVs 的 DNA 甲基化建立特别容易受到早期胚胎环境的影响。
我们的数据表明，CoRSIVs 存在于牛中，与人类相似，这表明这些系统性的表观遗传变体可能在哺乳动物中普遍存在。在牛 CoRSIVs 的个体表观遗传变异影响表型结果的程度上，出生时 CoRSIV 甲基化的评估可能成为优化农业重要性状的重要工具。此外，通过工程 CoRSIV 甲基化谱，调整辅助生殖过程中的胚胎培养条件，可能为定制农业结果提供机会。
