High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array
High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array
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DOI：
10.1007/s00439-006-0254-6
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发表时间：
2007-01-01
期刊：
影响因子：
5.3
通讯作者：
Aburatani, Hiroyuki
中科院分区：
文献类型：
--
作者：
Hayashi, Hiroshi;Nagae, Genta;Aburatani, Hiroyuki
DNA甲基化是一种表观遗传标记，在基因表达调控中起关键作用。在人类癌症中，异常的DNA甲基化导致肿瘤抑制基因的沉默并促进染色体的不稳定。以前对DNA甲基化的研究大多集中在有限的基因组区域，如选择的基因或包含甲基化敏感限制性内切酶识别位点的启动子CpG岛(CGI)。在这里，我们描述了一种使用寡核苷酸平铺阵列对DNA甲基化进行高分辨率分析的方法。输入材料是用抗甲基胞嘧啶抗体免疫沉淀的甲基化DNA。我们检测了三个人结直肠癌细胞系的ENCODE区域(类似于人类基因组的1%)，并确定了700多个候选甲基化位点(CMS)，其中随机选择的25个CMS中的24个随后通过亚硫酸氢盐测序进行了验证。CMS主要集中在基因的5‘调控区和3’区。我们还比较了Hoxa簇区的DNA甲基化模式与组蛋白H3和H4乙酰化模式。我们的分析显示，在高甲基化区域没有乙酰化组蛋白，这表明DNA甲基化与组蛋白H3和H4乙酰化之间存在相互关系。我们的方法通过基因组定位识别DNA甲基化，偏差很小，因此，对于在表观基因组学中提供新发现的DNA甲基化的全面高分辨率分析是有用的。
DNA methylation is an epigenetic mark crucial in regulation of gene expression. Aberrant DNA methylation causes silencing of tumor suppressor genes and promotes chromosomal instability in human cancers. Most of previous studies for DNA methylation have focused on limited genomic regions, such as selected genes or promoter CpG islands (CGIs) containing recognition sites of methylation-sensitive restriction enzymes. Here, we describe a method for high-resolution analysis of DNA methylation using oligonucleotide tiling arrays. The input material is methylated DNA immunoprecipitated with anti-methylcytosine antibodies. We examined the ENCODE region (similar to 1% of human genome) in three human colorectal cancer cell lines and identified over 700 candidate methylated sites (CMS), where 24 of 25 CMS selected randomly were subsequently verified by bisulfite sequencing. CMS were enriched in the 5' regulatory regions and the 3' regions of genes. We also compared DNA methylation patterns with histone H3 and H4 acetylation patterns in the HOXA cluster region. Our analysis revealed no acetylated histones in the hypermethylated region, demonstrating reciprocal relationship between DNA methylation and histone H3 and H4 acetylation. Our method recognizes DNA methylation with little bias by genomic location and, therefore, is useful for comprehensive high-resolution analysis of DNA methylation providing new findings in the epigenomics.