title: Methylation analysis by DNA immunoprecipitation.
abstract: DNA methylation regulates gene expression primarily through modification of chromatin structure. Global methylation studies have revealed biologically relevant patterns of DNA methylation in the human genome affecting sequences such as gene promoters, gene bodies, and repetitive elements. Disruption of normal methylation patterns and subsequent gene expression changes have been observed in several diseases especially in human cancers. Immunoprecipitation (IP)-based methods to evaluate methylation status of DNA have been instrumental in such genome-wide methylation studies. This review describes techniques commonly used to identify and quantify methylated DNA with emphasis on IP based platforms. In an effort to consolidate the wealth of information and highlight critical aspects of methylated DNA analysis, sample considerations, experimental and bioinformatic approaches for analyzing genome-wide methylation profiles, and the benefit of integrating DNA methylation data with complementary dimensions of genomic data are discussed.
authors.affiliation: Department of Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada. kthu@bccrc.ca
authors.forename: Kelsie L
authors.initials: KL
authors.lastname: Thu
authors.forename: Larissa A
authors.initials: LA
authors.lastname: Pikor
authors.forename: Jennifer Y
authors.initials: JY
authors.lastname: Kennett
authors.forename: Carlos E
authors.initials: CE
authors.lastname: Alvarez
authors.forename: Wan L
authors.initials: WL
authors.lastname: Lam
mesh_terms: D019295:Computational Biology; D018899:CpG Islands; D004247:DNA / Q000032:analysis*; D019175:DNA Methylation; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA