title: Analysis of methylation microarray for tissue specific detection.
abstract: The role of human DNA methylation has been extensively studied in genomic imprinting, X-inactivation, and disease. However, studies of tissue-specific methylation remain limited. In this study, we use bioinformatics methods to analyze methylation data and reveal loci that are exclusively methylated or unmethylated in individual tissues. We collect 39 previously published DNA methylation profiles using an Illumina® HumanMethylation 27 BeadChip Kit containing 22 common tissues and involving 27,578 CpG loci across the human genome. We found 86 positions of tissue specific methylation CpG (TSM) that encompass 34 hypermethylated TSMs (31 genes) and 52 hypomethylated TSMs (47 genes). Tissues were found to contain 1 to 25 TSM loci, with the majority in the liver (25), testis (18), and brain (16). Fewer TSM loci were found in the muscle (8), ovary (7), adrenal gland (3), pancreas (2-4), kidney, spleen, and stomach (1 each). TSMs are predominantly located 0-300 base pairs in the 3' direction after the transcription start site. Similar to known promoters of methylation, hypermethylated TSM genes suppress transcription, while hypomethylated TSMs allow gene transcription. The majority of hypermethylated TSM genes encode membrane proteins and receptors, while hypomethylated TSM genes primarily encode signal peptides and tissue-specific proteins. In summary, the database of TSM loci produced herein is useful for the selection of tissue-specific DNA markers as diagnostic tools, as well as for the further study of the mechanisms and roles of TSM.
authors.affiliation: Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
authors.forename: Tachapol
authors.initials: T
authors.lastname: Muangsub
authors.affiliation: Department of Forensic Biochemistry, Institute of Forensic Medicine, Police General Hospital, Royal Thai Police, Bangkok 10330, Thailand.
authors.forename: Jarunya
authors.initials: J
authors.lastname: Samsuwan
authors.affiliation: Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.
authors.forename: Pumipat
authors.initials: P
authors.lastname: Tongyoo
authors.affiliation: Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand. Electronic address: Nakarinkit@gmail.com.
authors.forename: Nakarin
authors.initials: N
authors.lastname: Kitkumthorn
authors.affiliation: Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
authors.forename: Apiwat
authors.initials: A
authors.lastname: Mutirangura
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D019175:DNA Methylation; D006801:Humans; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis
keywords: CpG loci; GPL8490; Methylation microarray; Tissue specific methylation