Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development

Lee, Jung-Eun; He, Kongwang; Štolc, Viktor; Lee, Horim; Figueroa, Pablo; Gao, Ying; Tongprasit, Waraporn; Zhao, Hongyu; Lee, Ilha; Deng, Xing Wang

doi:10.1105/tpc.106.047688

Cited by 828 publications

(1,011 citation statements)

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“…The pleiotropic response observed in the hy5 mutant suggests that there are many genes regulated by HY5. This is in agreement with the finding of a large number (approximately 3,900) of in vivo HY5 targets in the Arabidopsis genome (Lee et al, 2007). From the EMSA, the high-affinity binding site for homodimeric STF1 and HY5 was defined as 5#-( G / A )( G / A )TGACGT( C /G/ A )( A /T/ G )-3#.…”

Section: Analysis Of Target Genes Of Stf1 and Hy5supporting

confidence: 76%

“…The in vitro analysis corresponds with earlier in vivo and functional analyses that identified the predicted locations of the HY5 binding sites in the promoters of anthocyanin biosynthetic genes (Hartmann et al, 2005;Shin et al, 2007). It also helps explain the abundance (approximately 3,900) of in vivo HY5 targets in the Arabidopsis genome identified by coupled chromatin immunoprecipitation and DNA chip hybridization (ChIP-chip; Lee et al, 2007). By identifying the HY5/STF1 recognition elements and the parameters associated with target genes, this study extends our understanding of the roles of HY5 and related bZIP proteins in the regulation of gene expression during plant development.…”

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confidence: 99%

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DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins

et al. 2008

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LONG HYPOCOTYL5 (HY5) is a bZIP (basic leucine zipper) transcription factor that activates photomorphogenesis and root development in Arabidopsis (Arabidopsis thaliana). Previously, STF1 (soybean [Glycine max] TGACG-motif binding factor 1), a homologous legume protein with a RING-finger motif and a bZIP domain, was reported in soybean. To investigate the role of STF1, the phenotypes of transgenic Arabidopsis plants overexpressing STF1 and HY5 were compared. In addition, the DNA-binding properties of STF1 and HY5 were extensively studied using random binding site selection and electrophoretic mobility shift assay. Overexpression of STF1 in the hy5 mutant of Arabidopsis restored wild-type photomorphogenic and root development phenotypes of short hypocotyl, accumulation of chlorophyll, and root gravitropism with partial restoration of anthocyanin accumulation. This supports that STF1 is a homolog of HY5 with a role in light and hormone signaling. The DNA-binding properties of STF1 and HY5 are shown to be similar to each other in recognizing many ACGT-containing elements with a consensus sequence motif of 5#-( G / A )( G / A ) TGACGT( C /G/ A )( A /T/ G )-3#. The motif represents a characteristically strong preference for flanking sequence to TGACGT and a larger sequence than the sequences recognized by the G-box binding factor and TGA protein families. The finding of C-box, hybrid C/G-, and C/A-boxes as high-affinity binding sites over the G-box and parameters associated with HY5 recognition define the criteria of HY5/STF1 protein-DNA interaction in the promoter regions. This study helps to predict the precise in vivo binding sites of the HY5 protein from the vast number of putative HY5 genomic binding sites analyzed by chromatin immunoprecipitation on chip.

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Section: Analysis Of Target Genes Of Stf1 and Hy5supporting

confidence: 76%

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confidence: 99%

DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins

et al. 2008

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“…Chromatin immunoprecipitation (ChIP) was performed as described 29 . PIF4-HA seedlings and an anti-HA antibody (Santa Cruz) were used in these assays.…”

Section: Methods Summarymentioning

confidence: 99%

A molecular framework for light and gibberellin control of cell elongation

Lucas

Davière

Rodríguez-Falcón

et al. 2008

Nature

1,064

1,072

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Cell elongation during seedling development is antagonistically regulated by light and gibberellins (GAs) 1,2 . Light induces photomorphogenesis, leading to inhibition of hypocotyl growth, whereas GAs promote etiolated growth, characterized by increased hypocotyl elongation. The mechanism underlying this antagonistic interaction remains unclear. Here we report on the central role of the Arabidopsis thaliana nuclear transcription factor PIF4 (encoded by PHYTOCHROME INTERACTING FACTOR 4) 3 in the positive control of genes mediating cell elongation and show that this factor is negatively regulated by the light photoreceptor phyB (ref. 4) and by DELLA proteins that have a key repressor function in GA signalling 5 . Our results demonstrate that PIF4 is destabilized by phyB in the light and that DELLAs block PIF4 transcriptional activity by binding the DNA-recognition domain of this factor. We show that GAs abrogate such repression by promoting DELLA destabilization, and therefore cause a concomitant accumulation of free PIF4 in the nucleus. Consistent with this model, intermediate hypocotyl lengths were observed in transgenic plants over-accumulating both DELLAs and PIF4. Destabilization of this factor by phyB, together with its inactivation by DELLAs, constitutes a protein interaction framework that explains how plants integrate both light and GA signals to optimize growth and development in response to changing environments.Seedlings undergo alternative developmental programmes depending on whether they are germinated in the dark or in the light. Dark-grown seedlings exhibit etiolated growth, characterized by long hypocotyls, small and closed cotyledons with undifferentiated chloroplasts, and the repression of light-regulated genes 1 . During photomorphogenesis, light inhibits hypocotyl growth and promotes cotyledon opening and expansion, chloroplast differentiation and the activation of light-regulated genes. phyB is the main photoreceptor mediating de-etiolation in red light 4,6 . Absorption of red light converts this photoreceptor into a Pfr active form that is translocated into the nucleus 7,8 ; Pfr interacts there with members of the bHLH family of phytochrome-interacting factors (PIFs), involved in modulation of light-regulated genes with a role in photomorphogenesis 1,4 . Gibberellins (GAs) exert an opposite effect to light on photomorphogenesis 2 . GAs promote etiolated growth, whereas GA-deficiency induces a partially de-etiolated phenotype in the dark, which is reverted by a lack of DELLA function 2,9 . DELLAs function as key repressors of GA-responsive growth, by inhibiting GA-regulated gene expression 5 . These repressors accumulate in the nucleus and are rapidly degraded in response to GA 10,11 . In Arabidopsis, RGA (encoded by repressor of ga1-3) and GAI (encoded by GA insensitive) are the main repressors controlling hypocotyl growth and stem elongation 12,13 . Mutations within the DELLA domain render these proteins resistant to degradation, and result in a GA-insensitive dwarf phenotype 12,14 . This ...

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“…From a practical point of view, modules are typically identified as highly connected subgraphs within the network (Barabási and Oltvai, 2004). Depending on the type of interaction data, different types of modules are defined, and examples in Arabidopsis include coexpression modules (Lisso et al, 2005;Horan et al, 2008;Atias et al, 2009), protein complexes (Geisler- Lee et al, 2007;Boruc et al, 2010;De Bodt et al, 2010;Arabidopsis Interactome Mapping Consortium, 2011), and modules grouping genes that are regulated by the same transcription factor (TF; Ferrier et al, 2011). Genes can be part of different (sometimes overlapping) modules, while modules can be involved in different biological processes.…”

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confidence: 99%

Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

2012

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A major challenge is to unravel how genes interact and are regulated to exert specific biological functions. The integration of genome-wide functional genomics data, followed by the construction of gene networks, provides a powerful approach to identify functional gene modules. Large-scale expression data, functional gene annotations, experimental protein-protein interactions, and transcription factor-target interactions were integrated to delineate modules in Arabidopsis (Arabidopsis thaliana). The different experimental input data sets showed little overlap, demonstrating the advantage of combining multiple data types to study gene function and regulation. In the set of 1,563 modules covering 13,142 genes, most modules displayed strong coexpression, but functional and cis-regulatory coherence was less prevalent. Highly connected hub genes showed a significant enrichment toward embryo lethality and evidence for cross talk between different biological processes. Comparative analysis revealed that 58% of the modules showed conserved coexpression across multiple plants. Using modulebased functional predictions, 5,562 genes were annotated, and an evaluation experiment disclosed that, based on 197 recently experimentally characterized genes, 38.1% of these functions could be inferred through the module context. Examples of confirmed genes of unknown function related to cell wall biogenesis, xylem and phloem pattern formation, cell cycle, hormone stimulus, and circadian rhythm highlight the potential to identify new gene functions. The module-based predictions offer new biological hypotheses for functionally unknown genes in Arabidopsis (1,701 genes) and six other plant species (43,621 genes). Furthermore, the inferred modules provide new insights into the conservation of coexpression and coregulation as well as a starting point for comparative functional annotation.

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Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development

Cited by 828 publications

References 66 publications

DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins

DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins

A molecular framework for light and gibberellin control of cell elongation

Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

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