School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
Genes (Basel). 2010 Jun 4;1(1):85-101. doi: 10.3390/genes1010085.
DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly variable among cells types and developmental stages and influenced by disease processes and genetic factors, which brings considerable theoretical and technological challenges for its comprehensive mapping. Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states.
DNA 甲基化是一种主要的表观遗传修饰形式，在生理和疾病过程中发挥着重要作用。在人类基因组中，大约 80%的 CpG 位点中的胞嘧啶被甲基化为 5-甲基胞嘧啶。DNA 的甲基化模式在细胞类型和发育阶段之间具有高度的可变性，并受疾病过程和遗传因素的影响，这给其全面图谱绘制带来了相当大的理论和技术挑战。最近，基于亚硫酸氢盐转化结合下一代测序的各种高通量方法已经被开发出来，并应用于全基因组 DNA 甲基化分析。这些方法提供了具有全基因组覆盖的单碱基分辨率、定量的 DNA 甲基化数据。我们在这里综述了这些方法，并讨论了一些特别感兴趣的技术要点，如达到结论所需的测序深度、亚硫酸氢盐转化后克隆性 DNA 扩增的鉴定以及非 CpG 甲基化的检测。这些方法的未来应用将极大地促进不同物种、个体和细胞类型在健康和疾病状态下的基因组 DNA 甲基化谱的分析。
