Methylation analysis by DNA immunoprecipitation

• Published in: Journal of cellular physiology Vol. 222; no. 3; pp. 522 - 531
• Main Authors: Thu, Kelsie L., Pikor, Larissa A., Kennett, Jennifer Y., Alvarez, Carlos E., Lam, Wan L.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.03.2010
• Subjects: Computational Biology; CpG Islands; DNA - analysis; DNA Methylation; Gene Expression Regulation; Genomics - methods; Humans; Immunoprecipitation; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Promoter Regions, Genetic; Reproducibility of Results; Sequence Analysis, DNA
• ISSN: 0021-9541; 1097-4652
• DOI: 10.1002/jcp.22009

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. J. Cell. Physiol. 222: 522–531, 2010. © 2009 Wiley‐Liss, Inc.