SIZ1 promotes the timing and amplitude of the expression of thermosensitive genes, including genomic targets of the transcription factors PIF4/BZR1.
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(A) Heat maps representing thermosensitive genes, i.e. differentially expressed genes in pad4 in response to the shift to 28°C and their expression profiles in the siz1 pad4 and sumo1/2KD pad4 mutants (blue-to-red diagrams). Gene clustering was based on Pearson correlation of the expression profiles in pad4 (shown on the left). To reveal gene expression dynamics over time in the mutants versus pad4, the expression values were standardized (zero mean, unit variance per profile). Of note, the expression profiles of the thermosensitive genes were largely similar for the three genotypes. In addition, the relative difference-in-expression (log2 fold change, non-standardized) is shown for the thermosensitive genes in ‘siz1 pad 4 versus pad4’ and ‘sumo1/2KD versus pad4’ (brown-to-cyan depicting less expressed-to-more expressed in the mutant). (B) Venn diagrams showing the total number of differentially expressed genes (#DEGs, q≤0.01) in siz1 pad4 (green), sumo1/2KD pad4 (red) and their overlap (yellow) in comparison to pad4 at the three time points. The largest change in global gene induction/repression occurs at day 1 in both two mutants. (C) Scatter plot depicting the change-in-expression at day 1 or 4 with respect to the expression at day 0 (day 1–0; day 4–0) for all the DEGs in siz1 pad4 (y-axis) in comparison to their change in expression in pad4 (x-axis). The DEGs are the same as panel (B). For each DEG is shown the log2-fold change-in-expression. The density plots at the right and top depict the global change in expression for these DEGs in the mutant and the wild type, respectively. The black lines depict a Pearson linear regression analysis for all the DEGs with the 95% confidence interval indicated by the grey zone. The red line depicts an equal change in expression for all genes in siz1 pad4 versus pad4. (D) Similar to (C), but the scatter plot depicts the change in expression for the DEGs in sumo1/2KD pad4 in comparison to pad4. (E) Pie diagrams depicting the total number of direct genomic targets of PIF4, BZR1 and ARF6, retrieved from published chromatin immuno-precipitation (ChIP) datasets (Adapted from ), and the number these targets that are differentially expressed (DE) in siz1 pad4 (green+yellow) or sumo1/2KD pad4 (red+yellow). These two sets are a combination of the DEGs from panel B. The overlap between the genomic targets of these three TFs and the DEGs in siz1 pad4 and sumo1/2KD pad4 was significant (p-values for siz1 pad4: PIF4, 3.1e-24; BZR1, 2.1e-8; ARF6, 9.2e-11; p-values for sumo1/2KD pad4: PIF4, 1.2e-6; BZR1, 6.9e-4; ARF6, 1.5e-4; hypergeometric test). (F) Venn diagram depicting the overlap between the genomics targets of PIF4, BZR1 and ARF6 that are differentially expressed in siz1 pad4 over the course of the experiment. Most DEGs are a target of PIF4 and/or BZR1. (G) Venn diagram depicting the overlap between the genomics targets of PIF4, BZR1 and ARF6 that are differentially expressed in sumo1/2 KD pad4 over the course of the experiment.