Figure 5.

LUH Regulates a Subset of Genes Both Directly Activated and Directly Repressed by PIF1.

(A) Venn diagram identifying 31 PIF1 targets whose expression is regulated by LUH and PIF1. The significance of the overlap was determined with a hypergeometric test (P < 1.29 × 10⁻⁸).

(B) Dot plot comparing the log₂-transformed expression levels of these 31 genes in pif1 and luh mutant seeds.

(C) and (D) Validation of the expression patterns for 10 PIF1-repressed targets (C) and 8 PIF1-activated targets (D) in luh and pif1 mutant seeds exposed to the phyB_off condition (sd, n = 3 biological replicates).

(E) Dot plot comparing the log₂-transformed expression levels of 188 PIF1-regulated targets in luh and pif1 mutant seeds. Empty circles indicate genes significantly regulated (FDR < 0.05) by both PIF1 and LUH.

(F) Venn diagram identifying 84 PIF1 targets whose expression is also regulated by LUH (P = 0.004627, hypergeometric test).

(G) Dot plot comparing the log₂-transformed expression levels in the luh and the pif1 mutant seeds of the 84 PIF1 targets whose expression is also regulated by LUH. Empty circles indicate genes significantly regulated (FDR < 0.05) by both PIF1 and LUH.