Summary: Epigenetic changes in DNA methylation patterns and chromatin structure play key roles in the development of disease. Examples include Angelman and Prader-Willi syndromes, where epigenetic silencing is one factor in the development of these diseases. Therefore, understanding epigenetics is critical to our future understanding of many important diseases. Methods exist to analyze DNA methylation patterns in higher eukaryotes including methylated DNA immunoprecipitation-on-chip (MeDIP-chip), an affinity based approach to enrich methylated DNA regions from genomic DNA followed by microarray analysis. Similarly, chromatin structure and DNA-binding proteins can be mapped using chromatin immunoprecipitation-on-chip (ChIP-chip) using target protein specific antibodies and microarrays. Here we introduce our new Human, Mouse and Rat 3x720K ChIP-chip and DNA Methylation Arrays which offer comprehensive coverage of gene promoters and CpG islands in a multiplex platform. These arrays offer high resolution, 100bp probe spacing through all covered regions for highly sensitive and reproducible detection of DNA methylation and target protein DNA binding. In addition, the DNA methylation arrays also include probes covering positive, negative and nonCpG control regions to aid in assessment of the overall array performance. In this presentation, we will (1) describe the array designs and content in more detail, (2) demonstrate the sensitive and reproducible detection capabilities of these new arrays, and (3) compare the performance of these multiplex arrays with the single-plex 2.1M Deluxe Promoter arrays.
