High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array |
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Authors: | Hiroshi Hayashi Genta Nagae Shuichi Tsutsumi Kiyofumi Kaneshiro Takazumi Kozaki Atsushi Kaneda Hajime Sugisaki Hiroyuki Aburatani |
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Institution: | (1) Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan;(2) Department of Technology Development and Assessment, IVD, SRL Inc., Tokyo 191-0002, Japan |
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Abstract: | 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 (∼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.
Electronic supplementary material Supplementary material is available in the online version of this article at
and is accessible for authorized users. |
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