Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome
Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome
复制标题
DOI：
10.4161/epi.6.6.16196
复制
发表时间：
2011-06-01
期刊：
影响因子：
3.7
通讯作者：
Esteller, Manel
中科院分区：
文献类型：
--
作者：
Sandoval, Juan;Heyn, Holger A.;Esteller, Manel
DNA甲基化是研究最多的表观遗传标记，CpG甲基化在许多生物学过程和人类疾病中至关重要。由于癌症凸显了异常DNA甲基化模式对疾病的影响，例如肿瘤抑制基因启动子CpG岛高甲基化相关的沉默以及全基因组DNA低甲基化缺陷，它们在其他疾病中的重要性肯定也会显现出来。然而，目前用于全基因组DNA甲基化分析的单核苷酸方法成本高且耗时，这阻碍了获取全面DNA甲基化组的进展。继针对1505个CpG位点和27000个CpG位点的标准CpG甲基化微阵列取得成功之后，我们在体内验证了新开发的450000（450K）胞嘧啶微阵列（Illumina）。450K微阵列包括CpG和CNG位点、CpG岛/岸/架/开阔海域、非编码RNA（微小RNA和长链非编码RNA）以及编码基因转录起始位点周围（-200bp至-1500bp、5' - 非翻译区和外显子1）的位点，此外还包括相应的基因体和3' - 非翻译区，以及来自全基因组关联研究（GWAS）的基因间区域。在此，我们证明与正常结肠黏膜或DNA甲基转移酶缺陷（DKO）的HCT - 116细胞相比，450K DNA甲基化阵列能够一致且显著地检测HCT - 116结直肠癌细胞系中CpG甲基化的变化。所提供的验证凸显了450K DNA甲基化微阵列作为正在进行和新设计的表观基因组项目的有用工具的潜在用途。
DNA methylation is the most studied epigenetic mark and CpG methylation is central to many biological processes and human diseases. Since cancer has highlighted the contribution to disease of aberrant DNA methylation patterns, such as the presence of promoter CpG island hypermethylation-associated silencing of tumor suppressor genes and global DNA hypomethylation defects, their importance will surely become apparent in other pathologies. However, advances in obtaining comprehensive DNA methylomes are hampered by the high cost and time-consuming aspects of the single nucleotide methods currently available for whole genome DNA methylation analyses. Following the success of the standard CpG methylation microarrays for 1,505 CpG sites and 27,000 CpG sites, we have validated in vivo thenewly developed 450,000 (450K) cytosine microarray (Illumina). The 450K microarray includes CpG and CNG sites, CpG islands/shores/shelves/open sea, non-coding RNA (microRNAs and long non-coding RNAs) and sites surrounding the transcription start sites (-200 bp to -1,500 bp, 5'-UTRs and exons 1) for coding genes, but also for the corresponding gene bodies and 3'-UTRs, in addition to intergenic regions derived from GWAS studies. Herein, we demonstrate that the 450K DNA methylation array can consistently and significantly detect CpG methylation changes in the HCT-116 colorectal cancer cell line in comparison with normal colon mucosa or HCT-116 cells with defective DNA methyltransferases (DKO). The provided validation highlights the potential use of the 450K DNA methylation microarray as a useful tool for ongoing and newly designed epigenome projects.