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Fig. 4 | Genome Biology

Fig. 4

From: Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis

Fig. 4

Overlap of DMRi with deregulated genes in triploid (3x) seeds. a Venn diagrams showing overlap of non-CG DMRi intersected genes and deregulated genes in Arabidopsis endosperm of 3x seeds (log2FC > 1, p < 0.05 in 3x vs 2x wt and log2FC < −1, p <0.05 in 3x nrpd1 vs 3x) [16]. b Enriched gene ontologies (GO) for biological processes (p < 0.01) of intersected CHG DMRi overlapping genes and deregulated genes in Arabidopsis endosperm of 3x seeds (log2FC > 1, p < 0.05 in 3x vs 2x wt and log2FC < −1, p <0.05 in 3x nrpd1 vs 3x). c Venn diagram showing overlap of genes downregulated (log2FC < −1, p <0.05) in 3x phe1 phe2 seeds vs 3x seeds [40] and genes downregulated (log2FC < −1, p <0.05) in endosperm of 3x nrpd1 vs 3x seeds [16]. d Heatmap showing genes downregulated (log2FC < −1, p <0.05) in 3x phe1 phe2 seeds vs 3x seeds [40] and their expression in the endosperm of 3x vs 2x seeds [16], 3x phe1 phe2 vs 3x seeds, and endosperm of 3x nrpd1 vs 3x seeds [16]. e Heatmap of type I AGLs and ARFs with CHG DMRi and upregulated (log2FC > 1, p <0.05) in the endosperm of 3x vs 2x seeds [16] and their expression in 3x vs 2x and 3x phe1 phe2 vs 3x seeds [40] and endosperm of 3x nrpd1 vs 3x seeds. For definition of DMRs, see Fig. 2a

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