用DNA甲基化分析来区分牛基因组时代的参考,品种和父系原生效应
Callum MacPhillamy1, Tong Chen1, Stefan Hiendleder1,2
1The Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy SA 5371, Australia.
GigaScience
|October 22, 2024
概括
选择正确的参考基因组对于准确的DNA甲基化分析至关重要. 错误的基因组选择可以引入偏见并掩盖特定品种的表观遗传差异,影响基因调节研究.
科学领域:
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 基因组学就是基因组学.
- 比较生物学的比较生物学
背景情况:
- 大多数DNA甲基化研究依赖于单个参考基因组,可能引入因SNP和SVs等遗传变异而导致的偏差.
- 这些变异可能导致同一物种的个体之间甲基化位点 (CpG) 的差异.
- 参考基因组选择对甲基组分析的影响在很大程度上被忽视了.
研究的目的:
- 在甲基组分析中,研究参考基因组选择对品种和原始基因的影响.
- 分析来自Angus和Brahman牛及其交叉的全基因组二硫酸盐测序数据.
- 通过使用不正确的参考基因组来量化引入的偏差.
主要方法:
- 来自Angus和Brahman牛的胎儿肝脏DNA的全基因组双硫酸盐测序.
- 使用了来自Bovine Pangenome Consortium的特定品种参考基因组.
- 分析了CPG站点重叠,量化偏差以及SNP和SV对CPG的影响.
主要成果:
- 大约75%的CpG地点是Angus和Brahman共享的,其中5%是品种特定的.
- 使用不正确的参考基因组在全球甲基化中引入了高达2%的量化偏差.
- SNPs和SVs对CpG产生了显著影响,SNP对它们的影响是其他自体位的13倍.
结论:
- 对遗传和表观遗传差异的准确探索需要仔细考虑参考基因组效应.
- 识别差异甲基化区域 (DMR) 需要考虑参考基因组选择.
- DMRs可能会影响控制差异表达基因 (DEGs) 的增强剂,DGAT1被确定为相关的印记基因.
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