Fig. 5: ABA response genes, transcription factors, and ubiquitin pathway genes are downregulated due to GmDMEa mutation-induced hypermethylation. | Communications Biology

Fig. 5: ABA response genes, transcription factors, and ubiquitin pathway genes are downregulated due to GmDMEa mutation-induced hypermethylation.

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

Fig. 5

a GO enrichment analysis of the DEGs between DN50 and the gmdmea-3 mutant. The bars show the -log10 values. The threshold for DEGs was set at a fold change ≥2 and p adjusted <0.05. b The interactions among CHH-hyper-DEGs (dark green), and GO-enriched TFs (light red) and ABA response genes (light green) were revealed by the PPI network produced with STRING. c Snapshots from the Integrative Genomics Viewer (IGV) showing DNA methylation and gene expression levels of SAMBA (Glyma.01g015700), BLH3 (Glyma.06G029100)and GoLS1 (Glyma.20G094500)in DN50 and gmdmea-3. Dashed frames indicated as the CHH-DMRs located in upstream of the three genes. The height of each column represents the methylation level at each cytosine. The lower part indicates the transcript level of SAMBA, BLH3 and GoLS1. d McrBC-qRT‒PCR (left) was used to measure the methylation levels of CHH-DMRs in the SAMBA, BLH3 and GoLS1 genes. Expression levels (right) of the above genes in gmdmea-3 revealed by qRT‒PCR. Data are shown as the mean ± SD (n = 3). Statistical disparities between means were evaluated using unpaired two-tailed t-tests, signifying significance with *p < 0.05 (significant), **p < 0.01 (highly significant).

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