Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in <i>Arabidopsis</i> Development

Ouyang, Xinhao; Li, Jigang; Li, Gang; Li, Bosheng; Chen, Beibei; Shen, Huangxuan; Huang, Xi; Mo, Xiaoning; Wan, Xiangyuan; Lin, Rongcheng; Li, Shigui; Wang, Haiyang; Deng, Xing Wang

doi:10.1105/tpc.111.085126

Cited by 120 publications

(153 citation statements)

References 82 publications

(120 reference statements)

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“…Consequently, FHY1 associated with either the promoter or 5′ UTR on 79% of its associated genes (Fig. 1B), whereas the transcription factor FHY3 only binds the promoter or 5′ UTR on 55% of its target genes (14). Last, the precise locations of FHY1 chromatin association sites further revealed that 46.9% of FHY1 association specifically occurs within a 400-bp region upstream of the transcription start site (Fig.…”

Section: Resultsmentioning

confidence: 98%

“…We thus compared the common associated genes, phyA unique associated genes, and FHY1 unique associated genes with the target genes of several transcription factors known to be involved in light signaling (14,(22)(23)(24)(25)(26). Each of these transcription factors was required for both coordinate and unique associations, but with different degrees of participation (Fig.…”

Section: (E) Rt-pcrmentioning

confidence: 99%

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Photoreceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light

Chen

Demone

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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To incorporate the far-red light (FR) signal into a strategy for optimizing plant growth, FAR-RED ELONGATED HYPOCOTYL1 (FHY1) mediates the nuclear translocation of the FR photoreceptor phytochrome A (phyA) and facilitates the association of phyA with the promoters of numerous associated genes crucial for the response to environmental stimuli. However, whether FHY1 plays additional roles after FR irradiation remains elusive. Here, through the global identification of FHY1 chromatin association sites through ChIP-seq analysis and by the comparison of FHY1-associated sites with phyA-associated sites, we demonstrated that nuclear FHY1 can either act independently of phyA or act in association with phyA to activate the expression of distinct target genes. We also determined that phyA can act independently of FHY1 in regulating phyA-specific target genes. Furthermore, we determined that the independent FHY1 nuclear pathway is involved in crucial aspects of plant development, as in the case of inhibited seed germination under FR during salt stress. Notably, the differential presence of cis-elements and transcription factors in common and unique FHY1-and/or phyA-associated genes are indicative of the complexity of the independent and coordinated FHY1 and phyA pathways. Our study uncovers previously unidentified aspects of FHY1 function beyond its currently recognized role in phyA-dependent photomorphogenesis.L ight is one of the most important environmental cues in plant growth and development. Arabidopsis has thus evolved several photoreceptors to perceive different wavelengths in the visible light spectrum (1). Among them, phytochrome A (phyA) is the primary photoreceptor to mediate the far-red light (FR) and early red light (R) responses (2, 3). PhyA therefore plays a predominant role in plant adaptation to a shade environment where the R/FR ratio decreases. Upon FR and R irradiation phyA will shuttle between the inactive R-absorbing Pr form and the active FR-absorbing Pfr form. These two forms display distinct biological activities, nuclear translocation rates, degradation rates, and affinities for various signaling intermediates (2, 4, 5).Both FR and R trigger the localization of cytosolic phyA to the nucleus (6), albeit through different mechanisms. Two essential partners for phyA nuclear translocation, FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and its less abundant homolog FHY1-LIKE (FHL), influence this process at two levels; first, after the initial burst of phyA nuclear importation under R, FHY1 is gradually phosphorylated by action of the Pfr form of phyA (7). This event inhibits the nuclear translocation of FHY1 and consequently prevents further nuclear accumulation of phyA. Under FR, however, persistent phyA nuclear translocation is observed with nonphosphorylated FHY1 (8); second, the nucleo-cytoplasmic shuttling of FHY1/FHL is also reduced under R owing to the low dissociation rate of the Pfr-FHY1/ FHL complex. The FR-driven phyA conversion to its Pr form benefits the recycling of FHY1/FHL for continuous phyA n...

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Section: Resultsmentioning

confidence: 98%

Section: (E) Rt-pcrmentioning

confidence: 99%

Photoreceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light

Chen

Demone

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Thus, it will be a substantial undertaking to map all of the regulatory proteins using ChIPseq and ChIP-chip approaches. Thus far, only a limited number of genome-wide transcription factor binding maps have been reported in plant species, all in Arabidopsis (Thibaud-Nissen et al, 2006;Lee et al, 2007;Kaufmann et al, 2009;Morohashi and Grotewold, 2009;Oh et al, 2009;Zheng et al, 2009;Kaufmann et al, 2010;Yant et al, 2010;Ouyang et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

et al. 2012

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Gene expression and regulation in eukaryotes is controlled by orchestrated binding of regulatory proteins, including both activators and repressors, to promoters and other cis-regulatory DNA elements. An increasing number of plant genomes have been sequenced; however, a similar effort to the ENCODE project, which aimed to identify all functional elements in the human genome, has yet to be initiated in plants. Here we report genome-wide high-resolution mapping of DNase I hypersensitive (DH) sites in the model plant Arabidopsis thaliana. We identified 38,290 and 41,193 DH sites in leaf and flower tissues, respectively. The DH sites were depleted of bulk nucleosomes and were tightly associated with RNA polymerase II binding sites. Approximately 90% of the binding sites of two well-characterized MADS domain transcription factors, APETALA1 and SEPALLATA3, were covered by the DH sites. We demonstrate that protein binding footprints within a specific genomic region can be revealed using the DH site data sets in combination with known or putative protein binding motifs and gene expression data sets. Thus, genome-wide DH site mapping will be an important tool for systematic identification of all cis-regulatory DNA elements in plants.

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“…In addition, several other proteins were reported to affect chloroplast division, but most of them showed no direct interactions with the chloroplast division machinery or the mechanisms of regulation were not clear (Basak and Møller, 2013). FHY3, a key regulator of far-red light signaling, and its homolog FRS4 were recently reported to bind the promoter region of DRP5B and activate its expression (Ouyang et al, 2011;Gao et al, 2013). These results showed that transcription factors are also involved in the regulation of chloroplast division, although a relationship between far-red light signaling and chloroplast division was not demonstrated.…”

Section: Introductionmentioning

confidence: 99%

Phosphatidylinositol 4-Phosphate Negatively Regulates Chloroplast Division in Arabidopsis

2015

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Chloroplast division is performed by the constriction of envelope membranes at the division site. Although constriction of a ring-like protein complex has been shown to be involved in chloroplast division, it remains unknown how membrane lipids participate in the process. Here, we show that phosphoinositides with unknown function in envelope membranes are involved in the regulation of chloroplast division in Arabidopsis thaliana. PLASTID DIVISION1 (PDV1) and PDV2 proteins interacted specifically with phosphatidylinositol 4-phosphate (PI4P). Inhibition of phosphatidylinositol 4-kinase (PI4K) decreased the level of PI4P in chloroplasts and accelerated chloroplast division. Knockout of PI4Kb2 expression or downregulation of PI4Ka1 expression resulted in decreased levels of PI4P in chloroplasts and increased chloroplast numbers. PI4Ka1 is the main contributor to PI4P synthesis in chloroplasts, and the effect of PI4K inhibition was largely abolished in the pdv1 mutant. Overexpression of DYNAMIN-RELATED PROTEIN5B (DRP5B), another component of the chloroplast division machinery, which is recruited to chloroplasts by PDV1 and PDV2, enhanced the effect of PI4K inhibition, whereas overexpression of PDV1 and PDV2 had additive effects. The amount of DRP5B that associated with chloroplasts increased upon PI4K inhibition. These findings suggest that PI4P is a regulator of chloroplast division in a PDV1-and DRP5B-dependent manner.

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Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development

Cited by 120 publications

References 82 publications

Photoreceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light

Photoreceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

Phosphatidylinositol 4-Phosphate Negatively Regulates Chloroplast Division in Arabidopsis

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