Cancer Epigenetics and Biology Program (PEBC), Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Spain.
Epigenetics. 2011 Jun;6(6):692-702. doi: 10.4161/epi.6.6.16196. Epub 2011 Jun 1.
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 the newly 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.
DNA 甲基化是研究最多的表观遗传标记，而 CpG 甲基化是许多生物过程和人类疾病的核心。由于癌症突出了异常 DNA 甲基化模式（如启动子 CpG 岛 hypermethylation 相关的肿瘤抑制基因沉默和全基因组 DNA 低甲基化缺陷）对疾病的贡献，因此它们在其他病理学中的重要性肯定会变得明显。然而，获得全面 DNA 甲基组的进展受到当前用于全基因组 DNA 甲基化分析的单核苷酸方法成本高和耗时的限制。在标准 CpG 甲基化微阵列成功用于 1505 个 CpG 位点和 27000 个 CpG 位点之后，我们已经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（microRNAs 和长非编码 RNA）以及转录起始位点（-200bp 至-1500bp、5'-UTR 和外显子 1）周围的位点，用于编码基因，还包括对应基因体和 3'-UTR，以及来自 GWAS 研究的基因间区。在此，我们证明与正常结肠黏膜或具有缺陷 DNA 甲基转移酶的 HCT-116 细胞（DKO）相比，450K DNA 甲基化阵列可以一致且显著地检测到 HCT-116 结直肠癌细胞系中的 CpG 甲基化变化。所提供的验证突出了 450K DNA 甲基化微阵列作为用于正在进行和新设计的表观基因组项目的有用工具的潜力。
