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Plant Cell Advance Online Publication
Published on February 24, 2009; 10.1105/tpc.108.064691

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Received December 1, 2008
Returned for revision February 2, 2009
Accepted February 9, 2009

Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis

Eunkyoo Oh 1, Hyojin Kang 2, Shinjiro Yamaguchi 3, Jeongmoo Park 1, Doheon Lee 2, Yuji Kamiya 3, and Giltsu Choi 1*

1 Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
2 Department of Bio and Brain Engineering, KAIST, Daejeon 305-701, Korea
3 RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan

* To whom correspondence should be addressed. E-mail: gchoi{at}kaist.edu.

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.




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