title: High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array.
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 ( approximately 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.
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Hayashi
authors.forename: Genta
authors.initials: G
authors.lastname: Nagae
authors.forename: Shuichi
authors.initials: S
authors.lastname: Tsutsumi
authors.forename: Kiyofumi
authors.initials: K
authors.lastname: Kaneshiro
authors.forename: Takazumi
authors.initials: T
authors.lastname: Kozaki
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kaneda
authors.forename: Hajime
authors.initials: H
authors.lastname: Sugisaki
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Aburatani
mesh_terms: D000107:Acetylation; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D001665:Binding Sites / Q000235:genetics; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000235:genetics / Q000473:pathology; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D000077209:Decitabine; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D045325:HCT116 Cells; D006657:Histones / Q000235:genetics / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D046228:Microarray Analysis / Q000379:methods; D015345:Oligonucleotide Probes; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D006657:Histones; D018398:Homeodomain Proteins; D015345:Oligonucleotide Probes; C088144:HoxA protein; D000077209:Decitabine; D001374:Azacitidine