Fig. 2

EphrinA5-Fc stimulation induces changes in DNA methylation signatures, including cell adhesion-related genes. a Bar plot shows the localization of the differentially methylated CpG sites (DMS) in response to ephrinA5-Fc versus Fc stimulation detected with the Infinium Mouse Methylation BeadChip array across CpG shores, shelves, islands, and intergenic CpG sites. b A separation of DMSs based on their distribution across distinct genetic elements reveals them to be enriched in promoters, introns, and the 1–5 kb region upstream of the TSS. DMSs with upregulated methylation levels 24 h after ephrinA5-Fc are depicted in red while those with downregulated methylation levels are depicted in blue. c Volcano plot displays loci with significantly increased and decreased levels of DNA methylation, shown in red or blue, respectively, while differences below -log₁₀p-val after false discovery rate (FDR) correction are depicted in gray. Loci changed below 0.1 log₂FC (fold change) are excluded from the plot. d Venn diagram shows overlap between differentially expressed genes (DEG) and DMSs in ephrinA5-Fc-treated versus control-Fc-treated CB cells. e Gene Ontology analysis (GO) reveals enrichment for several GO terms related to cell adhesion and neuronal development; fold enrichment represented by the x-axis and -log₁₀p-val is encoded by the color gradient. f Table lists all protein-coding genes with predicted binding sites for Snhg15 that are upregulated (RNA-seq; Pensold et al. [34]) and simultaneously display DNA methylation changes 24 h after ephrinA5-Fc treatment. Genes with reduced methylation at discrete CpG sites are presented in blue font, red font indicates increased methylation at discrete CpG sites after ephrinA5-Fc treatment, while for genes with purple font CpG sites with increased as well as decreased methylation levels were detected. CB: cerebellar granule. TSS: transcription start site. UTR: untranslated region