Fig. 4: UBP5 mediates transcriptional de-repression.

a Volcano plot representing the UBP5 target genes which were downregulated and upregulated in ubp5. Up- and down-regulated DEGs are shown in orange and blue color dots respectively. Non-significant genes are shown as grey dots and UBP5 target genes as red dots. FDR < 0.05 and FDR values are derived from DESeq2 package by adjusting p-values using Benjamini-Hochberg method. b & c Venn diagrams showing overlap between UBP5 targets, H2Aub gained genes (hypermarked + de-novo) in ubp5 and (b) downregulated or (c) upregulated genes in ubp5 mutant. Super exact test was performed to check the statistical significance (*** represents significance with the p value = 3.4e-114, ns signifies non-significance). d Scatter plot showing the correlation between H2Aub and gene expression changes between Col-0 and ubp5 plants. The x-axis shows Log2FC levels of H2Aub marked genes (FDR < 0.05) and y-axis shows expression in Log2FC of misregulated genes in ubp5 as determined by DESeq2 (>1 fold variation, FDR < 0.05). For each quadrant, the correlation coefficient (R) along with the significance (p-values) are shown. The blue curve shows trend-line from LOWESS smoother function. Quadrant IV shows higher correlation between low expressed genes and hyper-marking of H2Aub. e Violin cum box plots represents the average signal of H2Aub at gene body for downregulated, upregulated genes and non-misregulated genes in Col-0 and ubp5. The violin plots show the distribution pattern of data and are overlaid with boxplots. For box and whiskers plots the middle line represents the median; the upper and lower lines are the first and third quartile (Q1 and Q3); the whiskers indicate the upper and lower limits of data spread by subtracting 1.5* interquartile range (IQR) from Q1 and adding 1.5* IQR toQ3. Statistical significance was calculated with two-sided Wilcoxon rank sum test, p-values are indicated above the plot.