Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development
Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development
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DOI：
10.1105/tpc.111.085126
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发表时间：
2011-07-01
期刊：
影响因子：
11.6
通讯作者：
Deng, Xing Wang
中科院分区：
文献类型：
--
作者：
Ouyang, Xinhao;Li, Jigang;Deng, Xing Wang
FHY 3及其同源物FAR 1是两个转座酶衍生的转录因子，是光敏色素A信号传导和生物钟的关键组分。在这里，我们使用基于染色质免疫沉淀的测序（ChIP-seq）在拟南芥基因组中分别在黑暗（D）和远红光（FR）条件下识别1559和1009个FHY 3直接靶基因。FHY 3通过FHY 3/FAR 1结合基序（CACGCGC）优先结合启动子。有趣的是，FHY 3也结合到178 bp的拟南芥着丝粒重复序列中的两个基序。ChIP-seq和微阵列数据之间的比较表明，FHY 3分别快速调节D和FR中197和86个基因的表达。FHY 3还与植物色素相互作用因子3样5和伸长下胚轴5共调节许多共同的靶基因。此外，我们发现了FHY 3在控制叶绿体发育中的作用，通过直接激活叶绿体的积累和复制5，其产物是拟南芥叶绿体分裂后期的结构组成部分的表达。综上所述，我们的数据表明，FHY 3调节植物发育的多个方面，从而提供了对它在光和昼夜节律途径之外的功能的见解。
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.