title: Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters.
abstract: The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays. This technique allowed us to simultaneously determine the methylation status of 6,177 genes, 92% of which include dense CpG islands. Among these 5,549 autosomal genes with dense CpG island promoters, we have identified 4.0% genes that are nearly completely methylated in normal blood, providing another exception to the general rule that CpG island methylation in normal tissue is limited to X inactivation and imprinted genes. We examined seven genes in detail, including ANKRD30A, FLJ40201, INSL6, SOHLH2, FTMT, C12orf12, and DPPA5. Dense promoter CpG island methylation and gene silencing were found in normal tissues studied except testis and sperm. In both tissues, bisulfite cloning and sequencing identified cells carrying unmethylated alleles. Interestingly, hypomethylation of several genes was associated with gene activation in cancer. Furthermore, reactivation of silenced genes could be induced after treatment with a DNA demethylating agent or in a cell line lacking DNMT1 and/or DNMT3b. Sequence analysis identified five motifs significantly enriched in this class of genes, suggesting that cis-regulatory elements may facilitate preferential methylation at these promoter CpG islands. We have identified a group of non-X-linked bona fide promoter CpG islands that are densely methylated in normal somatic tissues, escape methylation in germline cells, and for which DNA methylation is a primary mechanism of tissue-specific gene silencing.
authors.affiliation: Department of Leukemia, The University of Texas at M. D. Anderson Cancer Center, Houston, Texas, USA. lshen@mdanderson.org
authors.forename: Lanlan
authors.initials: L
authors.lastname: Shen
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Kondo
authors.forename: Yi
authors.initials: Y
authors.lastname: Guo
authors.forename: Jiexin
authors.initials: J
authors.lastname: Zhang
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.forename: Saira
authors.initials: S
authors.lastname: Ahmed
authors.forename: Jingmin
authors.initials: J
authors.lastname: Shu
authors.forename: Xinli
authors.initials: X
authors.lastname: Chen
authors.forename: Robert A
authors.initials: RA
authors.lastname: Waterland
authors.forename: Jean-Pierre J
authors.initials: JP
authors.lastname: Issa
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D018899:CpG Islands / Q000235:genetics*; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000172:deficiency / Q000378:metabolism; D019175:DNA Methylation / Q000187:drug effects; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D020868:Gene Silencing; D052138:Genes, Neoplasm; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D006877:Hydroxamic Acids / Q000494:pharmacology; D008214:Lymphocytes / Q000378:metabolism; D008297:Male; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000201:enzymology / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic / Q000187:drug effects; D015533:Transcriptional Activation
chemical_list: D006877:Hydroxamic Acids; C012589:trichostatin A; D004248:DNA (Cytosine-5-)-Methyltransferases