Journal: Communications Biology
Article Title: A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean
doi: 10.1038/s42003-024-06306-2
Figure Lengend Snippet: 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).
Article Snippet: McrBC digestion of DNA samples of all dry soybean seeds was carried out in a volume of 20 μL, containing 2 μL 10 × NEB buffer, 1 μL 2 mg/mL BSA, 2 μL 10 mM GTP, 1 μL McrBC enzyme (NEB), and 400 ng DNA, brought to the final volume of 20 μL using ddH 2 O.
Techniques: Mutagenesis, Produced, DNA Methylation Assay, Expressing, Methylation, Two Tailed Test
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