Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
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DOI：
10.1111/1365-2656.13645
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发表时间：
2021-12-21
影响因子：
4.8
通讯作者：
Kelly, Morgan W.
中科院分区：
文献类型：
--
作者：
Johnson, Kevin M.;Sirovy, Kyle A.;Kelly, Morgan W.
据推测，环境引起的基因体甲基化变化可以促进对不断变化的环境的适应性跨代反应。我们比较了来自 6 个全同胞科的 80 只东部牡蛎 Crassostrea virginica 的全局基因表达 (Tag-seq) 和基因体甲基化（简化代表性亚硫酸氢盐测序）模式，这些牡蛎在墨西哥湾北部平均盐度不同的两个地点共同养殖 14 个月。采样时，两个地点的牡蛎质量相差 60%，寄生虫含量相差近两个数量级。他们还差异表达了 35% 的测量转录本。然而，在来自这些不同环境的个体之间进行比较时，我们观察到仅 1.4% 的潜在甲基化位点存在差异甲基化，并且差异甲基化与差异基因表达之间几乎没有对应关系。相反，甲基化模式很大程度上是由家族之间的遗传差异驱动的，PERMANOVA 分析表明，家族之间差异甲基化的基因数量比环境之间的差异甲基化基因数量多出近两个数量级。对 C. virginica 基因组的 CpG 观察值/预期值 (CpG O/E) 的分析显示出明显的双峰分布，来自第一个簇的基因显示出较低的 CpG O/E 值、更大的甲基化以及更高且更稳定的基因表达，而来自第二簇的基因则显示出更低的甲基化、更低且更可变的基因表达。总而言之，差异甲基化结果表明，只有一小部分维吉尼亚基因组受到环境诱导的甲基化变化的影响。目前，几乎没有证据表明环境诱导的甲基化状态在调节基因表达对新环境的反应中起主导作用。
It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments. We compared patterns of global gene expression (Tag-seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters Crassostrea virginica from six full-sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments. An analysis of CpG observed/expected values (CpG O/E) across the C. virginica genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation and higher and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression. Taken together, the differential methylation results suggest that only a small portion of the C. virginica genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.