title: Isolation and enrichment of human genomic CpG islands by methylation-sensitive mirror orientation selection.
abstract: CpG islands (CGIs) in human genomic DNA are GC-rich fragments whose aberrant methylation is associated with human disease development. In the current study, methylation-sensitive mirror orientation selection (MS-MOS) was developed to efficiently isolate and enrich unmethylated CGIs from human genomic DNA. The unmethylated CGIs prepared by the MS-MOS procedure subsequently were used to construct a CGI library. Then the sequence characteristics of cloned inserts of the library were analyzed by bioinformatics tools, and the methylation status of CGI clones was analyzed by HpaII PCR. The results showed that the MS-MOS method could be used to isolate up to 0.001% of differentially existed unmethylated DNA fragments in two complex genomic DNA. In the CGI library, 34.1% of clones had insert sequences satisfying the minimal criteria for CGIs. Excluding duplicates, 22.0% of the 80,000 clones were unique CGI clones, representing 60% of all the predicted CGIs (about 29,000) in human genomic DNA, and most or all of the CGI clones were unmethylated in human normal cell DNA based on the HpaII PCR analysis results of randomly selected CGI clones. In conclusion, MS-MOS was an efficient way to isolate and enrich human genomic CGIs. The method has powerful potential application in the comprehensive identification of aberrantly methylated CGIs associated with human tumorigenesis to improve understanding of the epigenetic mechanisms involved.
authors.affiliation: Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, People's Republic of China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Huang
authors.forename: Larry
authors.initials: L
authors.lastname: Baum
authors.forename: Jun-Fu
authors.initials: JF
authors.lastname: Huang
authors.forename: Jian-Ping
authors.initials: JP
authors.lastname: You
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.forename: Jue
authors.initials: J
authors.lastname: Wang
authors.forename: Jiang
authors.initials: J
authors.lastname: Zheng
authors.forename: Xiao-Chu
authors.initials: XC
authors.lastname: Yan
authors.forename: Han
authors.initials: H
authors.lastname: Xia
authors.forename: Yu-Hui
authors.initials: YH
authors.lastname: Zhao
authors.forename: Hong
authors.initials: H
authors.lastname: Kuang
authors.forename: Wei-Ling
authors.initials: WL
authors.lastname: Fu
mesh_terms: D018899:CpG Islands / Q000235:genetics*; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification*; D019175:DNA Methylation; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008297:Male
chemical_list: D004247:DNA