Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity

Our previous studies using restriction landmark genomic scanning (RLGS) defined tissue- or cell-specific DNA methylation profiles. It remains to be determined whether the DNA sequence compositions in the genomic contexts of the Not I loci tested by RLGS influence their tendency to change with differentiation. We carried out 3834 methylation measurements consisting of 213 Not I loci in the mouse genome in 18 different tissues and cell types, using quantitative real-time PCR based on a V irtual image rlgs database. Loci were categorized as CpG islands or other, and as unique or repetitive sequences, each category being associated with a variety of methylation categories. Strikingly, the tissue-dependently and differentially methylated regions (T-DMRs) were disproportionately distributed in the non-CpG island loci. These loci were located not only in 5′-upstream regions of genes but also in intronic and non-genic regions. Hierarchical clustering of the methylation profiles could be used to define developmental similarity and cellular phenotypes. The results show that distinctive tissue- and cell type-specific methylation profiles by RLGS occur mostly at Not I sites located at non-CpG island sequences, which delineate developmental similarity of different cell types. The finding indicates the power of Not I methylation profiles in evaluating the relatedness of different cell types.