Figure 4.

LUH and PIF1 Coregulate Genes in Imbibed Seeds.

(A) A Venn diagram summarizing the overlap of differentially expressed genes from imbibed pif1, luh, and red light-treated seeds. X(D) and Y(R) indicate 12-h dark-incubated X seeds and 12-h red light-incubated Y seeds, respectively. X(D)/Z(D) indicates the transcriptome comparison between 12-h dark-incubated seeds of the X and Z genotypes. Numbers indicate the numbers of DEGs.

(B) and (C) Dot plots comparing the log₂-transformed expression levels of 207 LUH and PIF1 coregulated genes (B) or 279 LUH and red light coregulated genes (C) in luh mutant, pif1 mutant, and red light-treated wild-type seeds.

(D) GSEA plotted as a heat map of NESs. All LUH-, PIF1-, or red light-regulated genes (All DEGs) were divided into activated (X-Act) and repressed (X-Rep) gene sets. Alternatively, only DEGs appearing uniquely in the list of LUH-regulated genes or in the union of PIF1- or red light-regulated genes (Non-overlapping DEGs) were divided into activated and repressed gene sets. An NES for each gene set was determined in the luh(D)/Col-0(D), pif1(D)/Col-0(D), and Col-0(R)/Col-0(D) transcriptome data sets and plotted on the heat map.

(E) GSEA plotted as a heat map of NESs. Various hormone-responsive genes were divided into hormone-activated (X-Act) and -repressed (X-Rep) gene sets. Cell wall loosening genes (EXPs and XTHs) were also used as gene sets. An NES for each gene set was determined in the luh(D)/Col-0(D), pif1(D)/Col-0(D), and Col-0(R)/Col-0(D) transcriptome data sets and plotted on the heat map. The gray cells have an FDR > 0.05 and are thus nonsignificant. Germination-promoting hormones are labeled “Promotion,” while germination-inhibiting hormones are labeled “Inhibition.” BL, brassinolide; ACC, 1-amino-cyclopropane-1-carboxylic acid; CK, zeatin; IAA, indole-3-acetic acid; MJ, methyl jasmonate.

(F) and (G) Dot plots comparing the log₂-transformed expression levels of 36 EXP (open diamonds) and 33 XTH (open circles) genes in luh and pif1 mutant seeds (F) or in luh mutant and red light-treated wild-type seeds (G).