Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases
Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases
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无脊椎动物甲基化组提供了对环境耐受机制的深入了解并揭示了方法学偏差
DOI：
10.1111/1755-0998.13542
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发表时间：
2021
影响因子：
7.7
通讯作者：
Puritz, Jonathan B.
中科院分区：
文献类型：
--
作者：
Trigg, Shelly A.;Venkataraman, Yaamini R.;Gavery, Mackenzie R.;Roberts, Steven B.;Bhattacharya, Debashish;Downey‐Wall, Alan;Eirin‐Lopez, Jose M.;Johnson, Kevin M.;Lotterhos, Katie E.;Puritz, Jonathan B.
DNA甲基化在海洋无脊椎动物快速应对不断变化的环境因素和人为影响的能力中的作用越来越受到关注。然而，非模式生物的全基因组DNA甲基化研究目前受到方法学偏差的有限理解的阻碍。在这里，我们比较了三种以单碱基对分辨率定量DNA甲基化的方法-全基因组亚硫酸氢盐测序（WGBS），减少代表性亚硫酸氢盐测序（RRBS）和甲基CpG结合结构域亚硫酸氢盐测序（MBDBS）-使用来自两种造礁珊瑚物种的多个个体，具有对比的环境敏感性。所有的方法都显示出Montipora capitata的甲基化程度（11.4%）明显高于更敏感的Pocillopora acuta（2.9%）。两个物种中的大多数CpG甲基化发生在基因体和侧翼区域。在这两个物种中，MBDBS在我们的测序深度下具有检测编码区中CpG的最大能力，但MBDBS可能受到样本内甲基化异质性的影响。RRBS产生特定基因座的稳健信息，尽管没有任何特定基因组特征的富集并且基因组覆盖率显著降低。当测序深度有限时，相对基因组大小强烈影响每种方法检测到的CpG的数量和位置，从而阐明跨物种比较中的细微差别。由于全基因组甲基化差异得到亚硫酸氢盐测序方法数据的支持，可能有助于关键海洋无脊椎动物分类群的环境敏感性表型，这些数据为研究DNA甲基化在环境耐受性中的功能作用提供了基因组资源。
There is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome‐wide DNA methylation studies in nonmodel organisms are currently hampered by a limited understanding of methodological biases. Here, we compare three methods for quantifying DNA methylation at single base‐pair resolution—whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and methyl‐CpG binding domain bisulfite sequencing (MBDBS)—using multiple individuals from two reef‐building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation inMontipora capitata(11.4%) than the more sensitivePocillopora acuta(2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, but MBDBS may be influenced by intrasample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross‐species comparisons. As genome‐wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
7.7
作者：
Dixon, Groves;Matz, Mikhail
通讯作者：
Matz, Mikhail
影响因子：
5.3
作者：
Tweedie, S;Charlton, J;Bird, A
通讯作者：
Bird, A
DOI：
10.1073/pnas.1813749115
发表时间：
2018-12-26
影响因子：
11.1
作者：
Dixon, Groves;Liao, Yi;Matz, Mikhail V.
通讯作者：
Matz, Mikhail V.
影响因子：
4.5
作者：
L. Rodrigues;A. Grottoli
通讯作者：
L. Rodrigues;A. Grottoli