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Figure 3 | Genome Biology

Figure 3

From: Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse

Figure 3

A class of CpG islands gains partial methylation during development. (A) Density histograms showing the distribution of methylation in E8.5 embryos in genomic tiles (400 bp) covering CpG-poor regions and CGIs, which reveals a high prevalence of partially methylated CGIs (pmCGIs). (B) Frequency of pmCGIs in CGIs covering TSSs and exons. (C) Distribution of pmCGIs in TSSs, exons, introns and intergenic regions. (D) Comparison of the distribution of CpG ratios in unmethylated (u; <10% methylation in E8.5 embryos), partially methylated (pm; >15% and <60% methylation) and methylated (m; >60% methylation) CGIs. (E) Dynamics of DNA methylation at TSS-proximal pmCGIs (defined as >15% and <60% methylation in E8.5 embryos) across embryonic development and in adult tissues. Crb, cerebellum; Pancr, pancreas. (F) Examples of RRBS methylation scores at three TSS-associated pmCGIs in blastocysts (E3.5), post-implantation embryos (E8.5 and E10.5) and adult liver. (G) Distribution of RRBS single-allele methylation scores from E8.5 embryos in TSS-proximal pmCGIs compared with imprinted gDMRs. (H) Gene Ontology terms associated with TSS-proximal pmCGIs.

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