Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
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DOI：
10.1101/gr.110601.110
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发表时间：
2010-12-01
期刊：
影响因子：
7
通讯作者：
Clark, Susan J.
中科院分区：
文献类型：
--
作者：
Robinson, Mark D.;Stirzaker, Clare;Clark, Susan J.
DNA甲基化是一种重要的表观遗传修饰，在分化过程中与基因表达的调控相关，但在癌症等疾病状态下，DNA甲基化景观往往是失调的。现在有许多技术可用于以靶向或全基因组方式询问CpG位点的DNA甲基化状态，但由于固有的偏差，每种方法都可能询问基因组的不同部分。在这项研究中，我们比较了两种流行的全基因组技术，甲基化DNA免疫沉淀（MeDIP）和甲基-CpG结合域为基础的捕获（MBDCap）之间的甲基化DNA的亲和纯化，并表明，每种技术在不同的域的CpG密度景观。我们探讨了全基因组扩增的效果，并说明它可以降低检测基因组富含GC区域DNA甲基化的灵敏度。通过使用MBDCap，我们比较和对比基于微阵列和测序的读数，并强调拷贝数变异（CNV）可以在甲基化组的差异比较中产生的影响。这些研究表明，DNA甲基化数据和基因组覆盖率的分析高度依赖于所采用的方法，并且必须根据GC含量、DNA扩增的程度和拷贝数进行考虑。
DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation, but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate the DNA methylation status of CpG sites in a targeted or genome-wide fashion, but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, we compare the affinity-purification of methylated DNA between two popular genome-wide techniques, methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap), and show that each technique operates in a different domain of the CpG density landscape. We explored the effect of whole-genome amplification and illustrate that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. By using MBDCap, we compare and contrast microarray- and sequencing-based readouts and highlight the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed, and consideration must be made in light of the GC content, the extent of DNA amplification, and the copy number.