Benchmarking DNA methylation assays in a reef-building coral
Benchmarking DNA methylation assays in a reef-building coral
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DOI：
10.1111/1755-0998.13282
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发表时间：
2020-11-14
影响因子：
7.7
通讯作者：
Matz, Mikhail
中科院分区：
文献类型：
--
作者：
Dixon, Groves;Matz, Mikhail
对染色质修饰（例如DNA甲基化）的研究有可能改善海洋生态系统的预测和保护。然而，检测DNA甲基化的标准方法（全基因组亚硫酸氢盐测序）目前成本太高，无法应用于生态研究所需的规模。在这里，我们评估不同的方法来测量生态表观遗传学的DNA甲基化。我们比较了全基因组亚硫酸氢盐测序（WGBS）与甲基化CpG结合结构域测序（MBD-seq），以及甲基化RAD的修改版本，我们称之为甲基化依赖性限制性位点相关DNA测序（mdRAD）。我们评估这三种测定方法在测量甲基化的变化在整个基因组，基因型之间，和珊瑚礁建筑珊瑚鹿角珊瑚的息肉类型之间。我们发现，所有三种检测方法测量的绝对甲基化水平类似的基因体（gbM），以及外显子和1 Kb的窗口与最小皮尔逊相关0.66。gbM差异估计值的相关性较低，但在各检测试剂盒之间仍然一致。我们得出结论，MBD-seq和mdRAD是WGBS的可靠且具有成本效益的替代品。mdRAD产生可比较的甲基化估计所需的相当低的测序工作使其对生态表观遗传学特别有用。
Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is currently too costly to apply at the scales required for ecological research. Here, we evaluate different methods for measuring DNA methylation for ecological epigenetics. We compare whole genome bisulphite sequencing (WGBS) with methylated CpG binding domain sequencing (MBD-seq), and a modified version of MethylRAD we term methylation-dependent restriction site-associated DNA sequencing (mdRAD). We evaluate these three assays in measuring variation in methylation across the genome, between genotypes, and between polyp types in the reef-building coral Acropora millepora. We find that all three assays measure absolute methylation levels similarly for gene bodies (gbM), as well as exons and 1 Kb windows with a minimum Pearson correlation 0.66. Differential gbM estimates were less correlated, but still concurrent across assays. We conclude that MBD-seq and mdRAD are reliable and cost-effective alternatives to WGBS. The considerably lower sequencing effort required for mdRAD to produce comparable methylation estimates makes it particularly useful for ecological epigenetics.