and compared with unprocessed DNA samples using Nimblegen arrays focusing on CpG islands and promoter regions. The authors categorized all available RefSeq promoters based on GC content within a defined region of 1,300 bp upstream and 500 bp downstream of the transcription start site (TSS) into three groups: high, low, and intermediate CpG density (labeled as HCP, LCP, and ICP in their results). Initial analysis averaged methylation levels from multiple probes over each promoter region. Over all ethanol-treated embryos, the ratios of hypermethylated regions in each of the three promoter categories (HCP, LCP, and ICP) were significantly increased compared with control (Liu et al. 2009). The ICP group exhibited an inverse relationship between promoter DNA methylation and adjacent mRNA expression levels, as determined by Affymetrix expression microarrays.
