Detection of CpG methylation patterns by affinity capture methods

Introduction The 29 million CpG dinucleotides in the mammalian genome have long piqued biologists’ interest because they encode a blueprint both of the cell’s past as well as its future. Cytosine nucleotides within these CpG dinucleotide pairs exist in one of two distinct states whose conversion is accomplished via a highly evolved enzymatic machinery. The default state is unmodified cytosine, while modification with a methyl group on the 5th carbon of the pyrimidine ring unleashes a variety of biological effects. Since no change in the primary genetic structure of DNA is observed during this transition, the conversion from unmethylated to methylated state has been coined an epigenetic or “above genetic” transition. Broadly speaking there are two categories of CpG dinucleotides – clustered and unclustered – with the clustered CpG dinucleotides found primarily within and near gene loci. The methylation state of CpG dinucleotides in clustered regions of the mammalian genome – termed CpG islands (CGI) – mediates a variety of biological processes such as gene expression, X-chromosome inactivation, imprinting, cellular differentiation, aging, and chromatin structure (Ferguson-Smith and Surani, 2001; Issa, 2003; Lee, 2003; Robertson, 2005). Cellular roles for aberrant DNA methylation are now well established in disease states such as in the initiation and progression of cancer (Jones and Baylin, 2007) and clues are beginning to emerge for a potential role of DNA methylation in neuropsychiatric disorders (Plazas-Mayorca and Vrana, 2011). Central to these studies has been the emergence of methodologies that permit accurate discrimination between the unmethylated and methylated states. Thus, these methods may have useful applications during both discovery and validation phases of an experimental study. Here we describe one way to monitor these states that may promise to render deep mechanistic insight into the cellular transcriptome and lead to new and important discoveries in human diseases.