We first categorized 19,044 annotated RefSeq promoters (including 18,342 autosomal chromosomes and 702 promoters on sex chromosomes) into three categories based upon GC content: High (HCP), Low (LCP) and Intermediate (ICP) CpG density (defined in Methods, see Fig. 2A). Among the 18,342 autosomal promoters, more genes were classified as HCP (60%) than ICP (24%) and LCP (16%) (Fig. 2B1). In addition, a contrast between the methylation level profile and CpG density was apparent. Of 1725 hypermethylated promoters (higher than 1.3-fold of the genome-wide median methylation level, see Methods) in the untreated (control) embryos, the number of hypermethylated HCP and LCP genes was significantly lower (22% and 24% respectively), compared to the ICP group (54%) (Fig. 2B2), and a similar distribution was observed in the alcohol-treated group (Fig. 2B2). By plotting the distribution of genome-wide methylation profiles of untreated embryos against the CpG density within each promoter category (Fig. 2C), we observed that DNA methylation levels of the three promoter categories were markedly different during early embryo development (at neurulation stage) chi-square p-value <2.2 × 10−16 against the CpG density (Fig.
