title: A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis.
abstract: PSEUDO-RESPONSE REGULATORs (PRRs) play overlapping and distinct roles in maintaining circadian rhythms and regulating diverse biological processes, including the photoperiodic control of flowering, growth, and abiotic stress responses. PRRs act as transcriptional repressors and associate with chromatin via their conserved C-terminal CCT (CONSTANS, CONSTANS-like, and TIMING OF CAB EXPRESSION 1 [TOC1/PRR1]) domains by a still-poorly understood mechanism. Here, we identified genome-wide targets of PRR9 using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and compared them with PRR7, PRR5, and TOC1/PRR1 ChIP-seq data. We found that PRR binding sites are located within genomic regions of low nucleosome occupancy and high DNase I hypersensitivity. Moreover, conserved noncoding regions among Brassicaceae species are enriched around PRR binding sites, indicating that PRRs associate with functionally relevant cis-regulatory regions. The PRRs shared a significant number of binding regions, and our results indicate that they coordinately restrict the expression of target genes to around dawn. A G-box-like motif was overrepresented at PRR binding regions, and we showed that this motif is necessary for mediating transcriptional regulation of CIRCADIAN CLOCK ASSOCIATED 1 and PRR9 by the PRRs. Our results further our understanding of how PRRs target specific promoters and provide an extensive resource for studying circadian regulatory networks in plants.
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Tiffany L
authors.identifier: http://orcid.org/0000-0002-3427-6430
authors.initials: TL
authors.lastname: Liu
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Linsey
authors.initials: L
authors.lastname: Newton
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Ming-Jung
authors.initials: MJ
authors.lastname: Liu
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Shin-Han
authors.identifier: http://orcid.org/0000-0001-6470-235X
authors.initials: SH
authors.lastname: Shiu
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 farre@msu.edu.
authors.forename: Eva M
authors.identifier: http://orcid.org/0000-0003-1566-7572
authors.initials: EM
authors.lastname: Farré
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D002940:Circadian Rhythm / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059372:Nucleotide Motifs; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012097:Repressor Proteins / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; C523307:PRR5 protein, Arabidopsis; C523308:PRR7 protein, Arabidopsis; C514751:PRR9 protein, Arabidopsis; D012097:Repressor Proteins; C411822:TOC1 protein, Arabidopsis; D014157:Transcription Factors