Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA

We performed MeDIP assays using in vitro methylated DNA, with or without previous DNA amplification, and hybridization to a human promoter array. We observed that CpG content at gene promoters indeed correlates strongly with the MeDIP signal obtained using in vitro methylated DNA, even when lowering significantly the amount of starting material. In analyzing MeDIP products that were subjected to whole genome amplification (WGA), we also revealed a strong bias against CpG-rich promoters during this amplification procedure, which may potentially affect the significance of the resulting data.We illustrate the use of in vitro methylated DNA to assess the efficiency and accuracy of MeDIP procedures. We report that efficient and reproducible genome-wide data can be obtained via MeDIP experiments using relatively low amount of starting genomic DNA; and emphasize for the precaution that must be taken in data analysis when an additional DNA amplification step is required.DNA methylation at CpG dinucleotides is a major epigenetic modification with direct implications in many aspects of mammalian biology, including development and disease [1]. In normal tissues, most promoter-associated CpGs remain unmethylated, although DNA methylation does occur at promoters of a small set of genes where it generally leads to transcriptional silencing. On the other hand, cancer cells undergo dramatic changes in the level and distribution of DNA methylation [2]. Indeed, the DNA methylation-dependent silencing of many tumor suppressor genes is now recognized as a major mechanism of gene inactivation that complements genetic lesions. Recent technological advances have allowed the comprehensive analysis of DNA methylation profiles in normal and disease-associated cells [3-6]. In particular, the Methylated DNA ImmunoPrecipitation (MeDIP) assay appears to be an efficient, reproducible and cost-effective approach to characterize the methylome of large collections of DNA samples [7-10]. The overall