PT  - JOURNAL ARTICLE
AU  - Ouyang, Xinhao
AU  - Li, Jigang
AU  - Li, Gang
AU  - Li, Bosheng
AU  - Chen, Beibei
AU  - Shen, Huaishun
AU  - Huang, Xi
AU  - Mo, Xiaorong
AU  - Wan, Xiangyuan
AU  - Lin, Rongcheng
AU  - Li, Shigui
AU  - Wang, Haiyang
AU  - Deng, Xing Wang
TI  - Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in <em>Arabidopsis</em> Development
AID  - 10.1105/tpc.111.085126
DP  - 2011 Jul 01
TA  - The Plant Cell
PG  - 2514--2535
VI  - 23
IP  - 7
4099  - http://www.plantcell.org/content/23/7/2514.short
4100  - http://www.plantcell.org/content/23/7/2514.full
SO  - Plant Cell2011 Jul 01; 23
AB  - 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.