Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis
Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis
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DOI：
10.1105/tpc.108.064691
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发表时间：
2009-02-01
期刊：
影响因子：
11.6
通讯作者：
Choi, Giltsu
中科院分区：
文献类型：
--
作者：
Oh, Eunkyoo;Kang, Hyojin;Choi, Giltsu
植物色素相互作用因子3样5（Phytochrome Interacting Factor 3-Like 5，PIL 5）是一种碱性螺旋-环-螺旋转录因子，通过直接或间接调控赤霉素（GA）和脱落酸（阿坝）相关基因的表达来抑制种子萌发。然而，目前尚不清楚PIL 5是否仅通过GA和阿坝调节种子萌发。在这里，我们使用染色质免疫沉淀芯片（ChIP芯片）分析，以确定748个新的PIL 5结合位点在拟南芥基因组。与PIL 5作为转录调节因子的分子功能一致，大多数鉴定的结合位点位于基因启动子区。结合位点分析表明，PIL 5在体内主要通过G-box基序与其靶位点结合。基因芯片分析表明，光敏色素在种子萌发过程中主要通过PIL 5对大量基因进行调控。ChIP芯片和微阵列数据之间的比较表明，PIL 5通过直接结合到它们的启动子来调节166个基因。许多已识别的基因编码参与激素信号传导的转录调节因子，而一些基因编码参与细胞壁修饰的酶。有趣的是，PIL 5直接调节激素信号传导的许多转录调节因子，并间接调节参与激素代谢的许多基因。总之，我们的数据表明，PIL 5抑制种子萌发不仅通过GA和阿坝，但也通过协调激素信号和调节细胞壁的吸胀种子的性质。
PHYTOCHROME INTERACTING FACTOR 3-LIKE5 (PIL5) is a basic helix-loop-helix transcription factor that inhibits seed germination by regulating the expression of gibberellin (GA)- and abscisic acid (ABA)-related genes either directly or indirectly. It is not yet known, however, whether PIL5 regulates seed germination solely through GA and ABA. Here, we used Chromatin immunoprecipitation-chip (ChIP-chip) analysis to identify 748 novel PIL5 binding sites in the Arabidopsis thaliana genome. Consistent with the molecular function of PIL5 as a transcription regulator, most of the identified binding sites are located in gene promoter regions. Binding site analysis shows that PIL5 binds to its target sites mainly through the G-box motif in vivo. Microarray analysis reveals that phytochromes regulate a large number of genes mainly through PIL5 during seed germination. Comparison between the ChIP-chip and microarray data indicates that PIL5 regulates 166 genes by directly binding to their promoters. Many of the identified genes encode transcription regulators involved in hormone signaling, while some encode enzymes involved in cell wall modification. Interestingly, PIL5 directly regulates many transcription regulators of hormone signaling and indirectly regulates many genes involved in hormone metabolism. Taken together, our data indicate that PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds.