The present study represents the first genome-wide methylation pattern analysis at the mouse neurulation stage. Differences in DNA methylation patterns for three classes of CpG islands—HCP, LCP and ICP—were observed during early development. Furthermore, by comparing our data with recently published studies on CpG distribution patterns around promoter regions, we found that the promoter CpG landscape was remarkably conserved among mouse embryonic stem cells,53 mouse developing embryos (current study), and differentiated human fibroblast cells,54 allowing DNA methylation profiles to be compared in various stages across species, supporting the belief that CpG island patterns are evolutionally conserved and biologically significant. Among CpG island distribution categories, many HCP genes are known to be associated with ubiquitous housekeeping genes and highly regulated, key developmental genes, while LCP genes are generally associated with tissue-specific genes55,56 suggesting that analyzing methylation changes according to CpG density profiles may provide additional functional insight, as discussed below.
