Fig. 4: Decreased DNA methylation associated with Dnmt1 deficiency enhances expression of genes related to energy metabolism.
From: Dnmt1 determines bone length by regulating energy metabolism of growth plate chondrocytes
A, B Volcano plot for RNA-seq data (A) without and (B) with BMP2 differentiation stimulus. The plots were generated automatically using RaNA-seq. The tables show the number of differentially expressed genes. Red dots correspond to genes that had significant differential expression (Padj <0.05) between Dnmt1ΔPrx1 chondrocytes and Dnmt1flox chondrocytes. C Percentage of MBD2-mediated enrichment in methylated DNA in 1 µg total DNA from Dnmt1flox (n = 6) and Dnmt1ΔPrx1 (n = 6) chondrocytes. Data is mean ± s.d. Significance of mean differences was assessed using unpaired two-sided t-tests. D Peak count frequency of MBD-Seq. E Venn diagram highlights the number of genes with increased expression accompanying decreases in methylated DNA due to Dnmt1 deficiency. F Enrichment analysis of genes (n = 123) having increased expression that accompanied decreases in methylated DNA due to Dnmt1 deficiency, with P values calculated using Metascape. G Schematic diagram of genes related to energy metabolism. H log2 fold-change of in vitro and in vivo RNA-seq data for energy metabolism-related genes shown in (G). I Methylated DNA signals for selected genes as illustrated with the Integrative Genome Viewer (IGV). Source data are provided as a Source Data file.
