Fig. 3

Genome-wide DNA methylation analysis in the retina of 21-day-old mice. A Mtr deficiency does not change global CpG methylation. B Volcano plot highlighting Mtr deficiency-induced differentially methylated CpGs (methylation difference > 25 and q < 0.01). Among the differentially methylated CpGs the decreased methylated CpGs are represented in green (HypoCpG) and increased methylated in red (HyperCpG). C Genomic enrichment of differentially methylated CpGs. HypoCpG and hyperCpG are mainly located at CpG islands. D Top 10 most significantly enriched Gene Ontology (GO) biological process terms for hypo- and hypermethylated CpG sites in the retina of Mtr-cKO mice, respectively represented in green and red (FDR < 0.05). E Volcano plot highlighting Mtr deficiency-induced differentially methylated regions (methylation difference > 15 and q < 0.01). Among the differentially methylated regions the decreased methylated are represented in green (HypoM Genes) and increased methylated in red (HyperM Genes). D Genomic enrichment of differentially methylated regions. HypoM and HyperM genes are mainly located at the promoter. G Top 10 most significantly enriched Reactome Pathways Database terms for DMRs in the retina of Mtr-cKO mice (FDR < 0.05). E Venn diagram highlighting differentially methylated genes involved in eye development and their corresponding methylation fold change. F Venn diagram illustrating differentially methylated genes associated with retinoid metabolism and their corresponding methylation fold change