Fig. 5: UBP5-mediated H2Aub deubiquitination prevents deposition of H3K27me3. | Nature Communications

Fig. 5: UBP5-mediated H2Aub deubiquitination prevents deposition of H3K27me3.

From: The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development

Fig. 5

a Motif enrichment analysis of UBP5 target genes. The sequence logos, accuracies and hits of the best motifs found by MEME-ChIP. b H3K27me3 levels in ubp5 seedlings, Histone H3 used as a loading control. Numbers above blots indicate relative H3K27me3 levels. Three independent experiments were performed. c Metagene plot of average H3K27me3 enrichment over the UBP5 target genes. d H3K27me3 ChIP seq signal in ubp5/Col-0 between UBP5 targets and non-UBP5 targets. Violin overlaid boxplots display median (middle line), first and third quartiles (Q1 and Q3), with whiskers indicating data spread (1.5*IQR from Q1 and Q3). Statistical significance was determined by two-sided Wilcoxon rank sum test. e Heatmap showing the distribution of H3K27me3 on UBP5 binding sites for Col-0 and ubp5. UBP5 binding peaks are clustered based on higher to lower enrichment (top to bottom). f Venn diagram representing the overlap between UBP5 targets, H2Aub and H3K27me3 gained genes in ubp5 (FDR < 0.05). Super exact test is performed to test the overlap (*** represents significant overlap with p < 2.2e-16). g IGV browser snapshots of representative UBP5 target genes in which H2Aub and H3K27me3 are gained in the ubp5 mutant. h Average signal of H3K27me3 at gene body for downregulated, upregulated and non-misregulated genes. Median (middle line), first and third quartiles (Q1 and Q3), with whiskers indicating data spread (1.5*IQR from Q1 and Q3). Statistical significance was determined by two-sided Wilcoxon rank sum test. i Scatter plot shows correspondence between H3K27me3 levels and gene expression changes between Col-0 and ubp5 plants. The x-axis shows Log2FC levels of H3K27me3 marked genes by DESeq2 analysis (FDR < 0.05), y-axis shows expression of misregulated genes in ubp5 (Log2FC > 1, FDR < 0.05). Blue curve shows trend-line from LOWESS smoother function, with Pearson correlation coefficient (R) and significance (p values) displayed. Quadrant IV shows significant enrichment of low expressed genes that have gained H3K27me3.

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