title: Transcriptional repressor PRR5 directly regulates clock-output pathways.
abstract: The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external daily cycles. The clock coordinates biological activities with these cycles, mainly through genome-wide gene expression. However, the exact mechanism underlying regulation of circadian gene expression is poorly understood. Here we demonstrated that an Arabidopsis PSEUDO-RESPONSE REGULATOR 5 (PRR5), which acts in the clock genetic circuit, directly regulates expression timing of key transcription factors involved in clock-output pathways. A transient expression assay and ChIP-quantitative PCR assay using mutated PRR5 indicated that PRR5 associates with target DNA through binding at the CCT motif in vivo. ChIP followed by deep sequencing coupled with genome-wide expression profiling revealed the direct-target genes of PRR5. PRR5 direct-targets include genes encoding transcription factors involved in flowering-time regulation, hypocotyl elongation, and cold-stress responses. PRR5-target gene expression followed a circadian rhythm pattern with low, basal expression from noon until midnight, when PRR9, PRR7, and PRR5 were expressed. ChIP-quantitative PCR assays indicated that PRR7 and PRR9 bind to the direct-targets of PRR5. Genome-wide expression profiling using a prr9 prr7 prr5 triple mutant suggests that PRR5, PRR7, and PRR9 repress these targets. Taken together, our results illustrate a genetic network in which PRR5, PRR7, and PRR9 directly regulate expression timing of key transcription factors to coordinate physiological processes with daily cycles.
authors.affiliation: Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan. norih1@agr.nagoya-u.ac.jp
authors.forename: Norihito
authors.initials: N
authors.lastname: Nakamichi
authors.forename: Takatoshi
authors.initials: T
authors.lastname: Kiba
authors.forename: Mari
authors.initials: M
authors.lastname: Kamioka
authors.forename: Takamasa
authors.initials: T
authors.lastname: Suzuki
authors.forename: Takafumi
authors.initials: T
authors.lastname: Yamashino
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Higashiyama
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Sakakibara
authors.forename: Takeshi
authors.initials: T
authors.lastname: Mizuno
mesh_terms: D029681:Arabidopsis Proteins / Q000235:genetics / Q000502:physiology*; D047369:Chromatin Immunoprecipitation; D057906:Circadian Clocks / Q000502:physiology; D002940:Circadian Rhythm / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation / Q000235:genetics; D016133:Polymerase Chain Reaction; D012097:Repressor Proteins / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism* / Q000502:physiology
chemical_list: D029681:Arabidopsis Proteins; C523307:PRR5 protein, Arabidopsis; C523308:PRR7 protein, Arabidopsis; C514751:PRR9 protein, Arabidopsis; D012097:Repressor Proteins; D014157:Transcription Factors