title: Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development.
abstract: FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), two transposase-derived transcription factors, are key components in phytochrome A signaling and the circadian clock. Here, we use chromatin immunoprecipitation-based sequencing (ChIP-seq) to identify 1559 and 1009 FHY3 direct target genes in darkness (D) and far-red (FR) light conditions, respectively, in the Arabidopsis thaliana genome. FHY3 preferentially binds to promoters through the FHY3/FAR1 binding motif (CACGCGC). Interestingly, FHY3 also binds to two motifs in the 178-bp Arabidopsis centromeric repeats. Comparison between the ChIP-seq and microarray data indicates that FHY3 quickly regulates the expression of 197 and 86 genes in D and FR, respectively. FHY3 also coregulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE5 and ELONGATED HYPOCOTYL5. Moreover, we uncover a role for FHY3 in controlling chloroplast development by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5, whose product is a structural component of the latter stages of chloroplast division in Arabidopsis. Taken together, our data suggest that FHY3 regulates multiple facets of plant development, thus providing insights into its functions beyond light and circadian pathways.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520-8104, USA.
authors.forename: Xinhao
authors.initials: X
authors.lastname: Ouyang
authors.forename: Jigang
authors.initials: J
authors.lastname: Li
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.forename: Bosheng
authors.initials: B
authors.lastname: Li
authors.forename: Beibei
authors.initials: B
authors.lastname: Chen
authors.forename: Huaishun
authors.initials: H
authors.lastname: Shen
authors.forename: Xi
authors.initials: X
authors.lastname: Huang
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Mo
authors.forename: Xiangyuan
authors.initials: X
authors.lastname: Wan
authors.forename: Rongcheng
authors.initials: R
authors.lastname: Lin
authors.forename: Shigui
authors.initials: S
authors.lastname: Li
authors.forename: Haiyang
authors.initials: H
authors.lastname: Wang
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000235:genetics* / Q000254:growth & development*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics*; D002736:Chloroplasts / Q000502:physiology; D047369:Chromatin Immunoprecipitation; D003624:Darkness; D034281:Dynamins / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D008027:Light; D046228:Microarray Analysis; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D010834:Phytochrome / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D020798:Two-Hybrid System Techniques
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D034281:Dynamins; D009687:Nuclear Proteins; D010834:Phytochrome; C120919:FAR1 protein, Arabidopsis; C452847:FHY3 protein, Arabidopsis; C109254:HY5 protein, Arabidopsis; C473942:ARC5 protein, Arabidopsis; C508068:At2g20180 protein, Arabidopsis