Fig. 4: In the MuDR transposon, CHH methylation suppresses gene expression. | Communications Biology

Fig. 4: In the MuDR transposon, CHH methylation suppresses gene expression.

From: A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean

Fig. 4

a Circos plot indicating the genome-wide distribution of genes, all TEs, Gypsy, Copia, MuDR, and CHH-DMRs in wild type (DN50) and the mutant (gmdmea-3). b Methylation levels within gene, TE and 1 kb flanking (upstream and downstream) regions in CG, CHG and CHH sequence contexts of DN50 (green) and gmdmea-3 (red). c Number of hypermethylated (red bar) or hypomethylated (green bar) differentially methylated regions (hyper-DMRs and hypo-DMRs) in CG, CHG and CHH sequence contexts. d CHH methylation level changes in the three major (Copia, Gypsy and MuDR) and other types of transposons, where transposons that did not show methylation changes (0.0) were removed. e AT ratios of different transposon types throughout the soybean whole genome. f Distances of MuDR, Copia, Gypsy and the other transposons from genes. The X-axis represents the distance to the gene, and the Y-axis represents the density of TEs. g Four-way Venn diagram indicating the number of DEGs and genes associated with CHH-DMR (hypergene and hypogene). h Distribution of transposons located upstream of DME-regulated DEGs (upper) and all genes of the soybean genome (lower).

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