MBD2 enrichment by MeKL-chip enables detection of differential methylation over a range of CpG densities and CpGO/Es. (A) CpG density and (B) CpGO/E at each T-DMR was calculated over a 300 bp window. A range of CpG densities was observed, but the majority of T-DMRs were within low-CpG density regions. (C) Three T-DMRs (black boxes) associated with the retina-specific gene Rbp3 for the retina (red, solid) and brain (blue, dashed) are shown. The TSS (arrow) and a portion of Exon 1 are shown in grey. The three T-DMRs had varying CpGO/Es: 0.31 (left box), 0.38 (central box) and 0.47 (right box), and local CpG densities: 4.6 (left box), 9.4 (center box) and 13.2 (right box). CpGO/E: observed-to-expected CpG ratio; MeKL: MBD2b/MBD3L1 enrichment of DNA followed by KLM-PCR; T-DMR: tissue-specific differentially methylated region; TSS: transcription start site.