Ulahannan Netha, Greally John M
Department of Genetics, Albert Einstein College of Medicine, Center for Epigenomics and Division of Computational Genetics, 1301 Morris Park Avenue, Bronx, NY 10461 USA.
Epigenetics Chromatin. 2015 Jan 22;8:5. doi: 10.1186/1756-8935-8-5. eCollection 2015.
The number of different assays that has been published to study DNA methylation is extensive, complemented by recently described assays that test modifications of cytosine other than the most abundant 5-methylcytosine (5mC) variant. In this review, we describe the considerations involved in choosing how to study 5mC throughout the genome, with an emphasis on the common application of testing for epigenetic dysregulation in human disease. While microarray studies of 5mC continue to be commonly used, these lack the additional qualitative information from sequencing-based approaches that is increasingly recognized to be valuable. When we test the representation of functional elements in the human genome by several current assay types, we find that no survey approach interrogates anything more than a small minority of the nonpromoter cis-regulatory sites where DNA methylation variability is now appreciated to influence gene expression and to be associated with human disease. However, whole-genome bisulphite sequencing (WGBS) adds a substantial representation of loci at which DNA methylation changes are unlikely to be occurring with transcriptional consequences. Our assessment is that the most effective approach to DNA methylation studies in human diseases is to use targeted bisulphite sequencing of the cis-regulatory loci in a cell type of interest, using a capture-based or comparable system, and that no single design of a survey approach will be suitable for all cell types.
已发表的用于研究DNA甲基化的不同检测方法数量众多，最近描述的检测方法对其进行了补充，这些方法可检测除最常见的5-甲基胞嘧啶（5mC）变体之外的胞嘧啶修饰。在本综述中，我们描述了在选择如何研究全基因组5mC时所涉及的考虑因素，重点是在人类疾病中检测表观遗传失调的常见应用。虽然5mC的微阵列研究仍被广泛使用，但这些研究缺乏基于测序方法的额外定性信息，而这种信息越来越被认为是有价值的。当我们通过几种当前的检测类型测试人类基因组中功能元件的代表性时，我们发现没有一种调查方法能够探究超过一小部分非启动子顺式调控位点，而现在人们认识到DNA甲基化变异性会影响基因表达并与人类疾病相关。然而，全基因组亚硫酸氢盐测序（WGBS）增加了大量位点的代表性，在这些位点上DNA甲基化变化不太可能产生转录后果。我们的评估是，在人类疾病中进行DNA甲基化研究的最有效方法是使用基于捕获或类似系统，对感兴趣的细胞类型中的顺式调控位点进行靶向亚硫酸氢盐测序，而且没有一种单一的调查方法设计适用于所有细胞类型。
