assessing the efficiency and significance of methylated dna immunoprecipitation (medip) assays in using in vitro methylated genomic dna评估的效率和意义甲基化dna免疫沉淀反应(medip)化验使用体外基因组dna甲基化.pdfVIP

Jia et al. BMC Research Notes 2010, 3:240 /1756-0500/3/240 SHORT REPORT Open Access Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA Jinsong Jia 1,2,3†, Aleksandra Pekowska1,2,3†, Sebastien Jaeger1,2,3, Touati Benoukraf1,2,3, Pierre Ferrier1,2,3*, Salvatore Spicuglia1,2,3* Abstract Background: DNA methylation contributes to the regulation of gene expression during development and cellular differentiation. The recently developed Methylated DNA ImmunoPrecipitation (MeDIP) assay allows a comprehensive analysis of this epigenetic mark at the genomic level in normal and disease-derived cells. However, estimating the efficiency of the MeDIP technique is difficult without previous knowledge of the methylation status of a given cell population. Attempts to circumvent this problem have involved the use of in vitro methylated DNA in parallel to the investigated samples. Taking advantage of this stratagem, we sought to improve the sensitivity of the approach and to assess potential biases resulting from DNA amplification and hybridization procedures using MeDIP samples. Findings: 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. Conclusion: We illustrate the use of in vitro methylated DNA to as