Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Tokyo 160-8582, Japan.
Biochem Biophys Res Commun. 2012 Sep 14;426(1):33-7. doi: 10.1016/j.bbrc.2012.08.012. Epub 2012 Aug 11.
To gain a global view of epigenetic alterations around microRNA (miRNA) promoter regions, and to identify epigenetically regulated miRNAs, we developed a novel miRNA promoter microarray for chromatin immunoprecipitation (ChIP)-on-chip assay. We designed a custom oligo microarray covering regions spanning -10 to +2.5 kb of precursor miRNAs in the human genome. This microarray covers 541 miRNAs, each of which is covered by approximately 100 probes (60-mer) over its 12.5-kb genomic position, that includes predicted transcription start sites. Using this custom-made miRNA promoter microarray, we successfully performed ChIP-on-chip assay to identify miRNAs regulated by histone modification. Fifty-three miRNAs (9.8%) showed increased levels of both histone H3 acetylation and histone H3-K4 methylation in AGS gastric cancer cells treated with the DNA-methylation inhibitor 5-aza-2'-deoxycytidine and the histone deacetylase inhibitor 4-phenylbutyric acid. One of these miRNAs, miR-9, is downregulated in gastric cancer tissues and is activated by chromatin-modifying drugs, suggesting that it may be a potential target for epigenetic therapy of gastric cancer.
为了全面了解 microRNA（miRNA）启动子区域的表观遗传改变，并鉴定受表观遗传调控的 miRNA，我们开发了一种新型 miRNA 启动子芯片，用于染色质免疫沉淀（ChIP）-芯片分析。我们设计了一个定制的寡核苷酸微阵列，覆盖了人类基因组中 miRNA 前体的 -10 至 +2.5 kb 区域。该微阵列覆盖了 541 个 miRNA，每个 miRNA 大约有 100 个探针（60 个碱基）覆盖其 12.5 kb 的基因组位置，包括预测的转录起始位点。使用这种定制的 miRNA 启动子微阵列，我们成功地进行了 ChIP-on-chip 分析，以鉴定受组蛋白修饰调控的 miRNA。在接受 DNA 甲基化抑制剂 5-氮杂-2'-脱氧胞苷和组蛋白去乙酰化酶抑制剂 4-苯基丁酸处理的 AGS 胃癌细胞中，有 53 个 miRNA（9.8%）显示出组蛋白 H3 乙酰化和组蛋白 H3-K4 甲基化水平的升高。其中一个 miRNA，miR-9，在胃癌组织中下调，并被染色质修饰药物激活，提示其可能是胃癌表观遗传治疗的潜在靶点。
