The transition from skotomorphogenesis to photomorphogenesis is regulated in part by COP1/SPA complex and PIFs in Arabidopsis. The constitutive photomorphogenic (cop) phenotypes of the cop1 and spaQ mutants were shown to be due to a high abundance of the positively acting transcription factors. Here we show that the four major PIF proteins are unstable in cop1 mutant, and overexpression of PIF1, PIF3, PIF4 and PIF5 suppresses the cop1 phenotypes in the dark. Comparison of the transcriptome data among cop1, spaQ and pifQ reveal remarkably overlapping gene expression profiles with preferential regulation of the PIF direct target genes. Additionally, HFR1 strongly inhibits the in vivo binding and transcriptional activation activity of PIF1 in the dark. Taken together, these data suggest that the cop phenotype of the cop1 and spaQ mutants might be due to a combination of the reduced level of PIFs, increased level of positive factors (e.g., HY5/HFR1 and others), and the HFR1-mediated inhibition of PIF targeted gene expression in the dark.
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