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Fig. 3 | Genome Biology

Fig. 3

From: Downregulation of RdDM during strawberry fruit ripening

Fig. 3

Characterization of ripening-induced DNA hypomethylation. a Pictures of DNA methylation inhibitor 5-azacytidine-treated fruits. Fruits treated with water served as control (mock). b McrBC-qPCR analysis of DNA methylation levels (upper panel) and qPCR analysis of gene expression levels (lower panel) of two genes in mock and 5-azacytidine-treated fruits. In McrBC-qPCR analysis, a higher qPCR signal indicates lower mC level. Error bars indicate SD, n = 3 (*P value < 0.05, two-tailed t test). c Distribution of genomic elements within ripening-induced hypo-DMRs, hyper-DMRs, and the whole genome. Gene, gene body; TSS up 2 kb, 2 kb upstream of TSS; TES down 2 kb, 2 kb downstream of TES; Intergenic, intergenic regions. d Hypo-DMRs are significantly associated with regions 2 kb upstream of TSS as compared to random genomic regions (***P value < 0.01, as determined using Fisher’s exact test). e Heatmaps showing DNA methylation changes (Fa3-Fa1) across hypo-DMR-associated genes. Methylation changes in mC, mCG, mCHG, and mCHH contexts are shown. f Distributions of hypo-DMRs (blue line in upper panel) and hyper-DMRs (red line in lower panel) around genes as compared to that of randomly selected genomic regions (light-blue line and light-red line)

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