Approaches to Whole-Genome Methylome Analysis in Plants.
Approaches to Whole-Genome Methylome Analysis in Plants.
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DOI：
10.1007/978-1-0716-0179-2_2
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发表时间：
2020
影响因子：
--
通讯作者：
Xiaodong Yang;S. Mackenzie
中科院分区：
文献类型：
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作者：
Xiaodong Yang;S. Mackenzie
胞嘧啶甲基化作为一种可逆的染色质标记，由于其对基因沉默的影响以及对其在真核基因组中特定位置的动态结合-解离的调节而被广泛研究。随着全基因组DNA序列分析的成本和时间的显著降低，再加上亚硫酸氢盐处理的DNA测序的高保真，即使是非常大的基因组中胞嘧啶甲基化重塑的单核苷酸解析也越来越有可能实现。仍然是一个挑战，是对全基因组甲基组数据集的分析，从而清楚地了解甲基化重塑对基因表达的总体影响，反之亦然。报告的数据有时会受到严格的数据过滤方法的影响，这可能会扭曲下游的生物解释。这些并发症源于甲基组分析程序，这些程序在方法和参数设置上有很大的差异。DNA甲基化作为一种影响DNA稳定性的染色质特征，可以对环境变化做出动态和快速的反应。因此，在某些类型的实验中，从响应特定扰动的生物信号中区分系统的背景噪声的方法是必不可少的。我们描述了必须考虑的全基因组亚硫酸盐序列数据的许多方面，以及影响最终输出的生物学解释的甲基组数据分析的各个步骤。
Cytosine methylation as a reversible chromatin mark has been investigated extensively for its influence on gene silencing and the regulation of its dynamic association–disassociation at specific sites within a eukaryotic genome. With the remarkable reductions in cost and time associated with whole-genome DNA sequence analysis, coupled with the high fidelity of bisulfite-treated DNA sequencing, single nucleotide resolution of cytosine methylation repatterning within even very large genomes is increasingly achievable. What remains a challenge is the analysis of genome-wide methylome datasets and, consequently, a clear understanding of the overall influence of methylation repatterning on gene expression or vice versa. Reported data have sometimes been subject to stringent data filtering methods that can serve to skew downstream biological interpretation. These complications derive from methylome analysis procedures that vary widely in method and parameter setting. DNA methylation as a chromatin feature that influences DNA stability can be dynamic and rapidly responsive to environmental change. Consequently, methods to discriminate background “noise” of the system from biological signal in response to specific perturbation is essential in some types of experiments. We describe numerous aspects of whole-genome bisulfite sequence data that must be contemplated as well as the various steps of methylome data analysis which impact the biological interpretation of the final output.