Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans.

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences
Wen-Jou Chang, Maria S Baker, Eleonora Laritsky, Chathura J Gunasekara, Uditha Maduranga, Justine C Galliou, Joseph W McFadden, Jessica R Waltemyer, Bruce Berggren-Thomas, Brianna N Tate, Hanxue Zhang, Benjamin D Rosen, Curtis P Van Tassell, George E Liu, Cristian Coarfa, Yi Athena Ren, Robert A Waterland
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Abstract

Background: 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.

Results: 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.

Conclusions: 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.

牛的系统性个体间 DNA 甲基化变异与人类具有相同的主要特征。
背景:我们最近在人类基因组中发现了约 10,000 个系统性个体间表观遗传变异相关区域(CoRSIVs)。这些甲基化变异可用于群体研究,因为血液中的 DNA 甲基化测量可提供全身表观遗传调控的信息。此外,人类 CoRSIVs 上 DNA 甲基化的建立不易受到围孕期影响(如营养)的影响。在这里,我们分析了公开的全基因组亚硫酸氢盐测序数据,分别对两头荷斯坦奶牛的多个组织进行了分析,以确定牛体内是否存在CoRSIVs:我们的方法以 CpGs ≥ 5 个且系统个体间变异指数至少为 20 的基因组区块为重点,识别出 217 个牛 CoRSIVs,我们通过亚硫酸氢盐热测序独立验证了其中的一部分。与人类的 CoRSIV 相似,牛的 CoRSIV 也与遗传变异密切相关。与人类一样,我们的研究表明,在辅助生殖过程中胚胎培养的背景下,牛CoRSIVs上DNA甲基化的建立对早期胚胎环境特别敏感:我们的数据表明,与人类一样,牛体内也存在 CoRSIVs,这表明这些系统性表观遗传变异可能是哺乳动物的共性。由于牛 CoRSIV 的个体表观遗传变异会影响表型结果,因此评估牛出生时的 CoRSIV 甲基化情况可能会成为优化重要农业性状的重要工具。此外,在辅助生殖过程中调整胚胎培养条件可能会提供机会,通过设计 CoRSIV 甲基化图谱来定制农业结果。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
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