Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia.
Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia.
Trends Genet. 2014 Feb;30(2):75-84. doi: 10.1016/j.tig.2013.11.004. Epub 2013 Dec 21.
There are over 28 million CpG sites in the human genome. Assessing the methylation status of each of these sites will be required to understand fully the role of DNA methylation in health and disease. Genome-wide analysis, using arrays and high-throughput sequencing, has enabled assessment of large fractions of the methylome, but each protocol comes with unique advantages and disadvantages. Notably, except for whole-genome bisulfite sequencing, most commonly used genome-wide methods detect <5% of all CpG sites. Here, we discuss approaches for methylome studies and compare genome coverage of promoters, genes, and intergenic regions, and capacity to quantitate individual CpG methylation states. Finally, we examine the extent of published cancer methylomes that have been generated using genome-wide approaches.
人类基因组中有超过 2800 万个 CpG 位点。要全面了解 DNA 甲基化在健康和疾病中的作用，就需要评估每个 CpG 位点的甲基化状态。利用微阵列和高通量测序进行全基因组分析，已经能够评估甲基组的很大一部分，但每种方案都有其独特的优缺点。值得注意的是，除了全基因组亚硫酸氢盐测序外，最常用的全基因组方法只能检测到所有 CpG 位点的<5%。在这里，我们讨论了甲基组研究的方法，并比较了启动子、基因和基因间区域的基因组覆盖范围，以及定量个别 CpG 甲基化状态的能力。最后，我们研究了使用全基因组方法生成的已发表癌症甲基组的范围。
