Figure 4.

Genome-Wide Patterns of Rapidly Rc Light–Responsive and PIF-Regulated Gene Expression Reveal Pathway Convergence on Potential Target Genes.

Three-way comparison of SSTF genes responding to 1 h Rc (WT-D versus WT-R1), long-term (2d)-Rc (WT-D versus WT-Rc), and to the pifq mutations in darkness (WT-D versus pifq-D). Classification of the genes as induced (B) or repressed (C) is based on the direction of the response, relative to WT-D, elicited by each genotype treatment combination. A small group of 25 genes in Classes 4 to 7 were designated as ambiguous as the direction of the response relative to WT-D differed between WT-R1, WT-Rc, and/or pifqD. These genes are listed in Supplemental Data Set 5 online and were excluded from the analysis shown in (B) and (C). The mean fold change in expression relative to WT-D (set at unity) for all genes in each class is shown in the bar graphs in (B) and (C). Error bars represent the mean standard error for the genes averaged for each genotype treatment combination. Percentage of genes having a G-box in the 3-kb upstream regulatory sequence is indicated in parenthesis.

(A) Venn diagram showing comparison among all genes in the three different sets of SSTF differentially regulated genes (left panel). This comparison between genes responding to WT-R1, WT-Rc, and pifq-D resulted in the definition of seven classes of responsive genes (right panel) corresponding to the sectors of the diagram (circled numbers in red). The number of genes in each sector/class is indicated in black.

(B) Induced genes. The number of induced genes in each class is indicated by the black numbers in each sector of the Venn diagram. The gene lists are in Supplemental Data Set 3 online.

(C) Repressed genes. The number of repressed genes in each class is indicated by the black numbers in each sector of the Venn diagram. The gene lists are in Supplemental Data Set 4 online.