Arabidopsis thaliana
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-48767
PROVIDER: PRJNA211593 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Arabidopsis phytochrome A directly targets numerous promoters for individualized modulation of genes in wide range of pathways
| PRJNA211582 | ENA
Project description:Arabidopsis phytochrome A directly targets numerous promoters for individualized modulation of genes in wide range of pathways [ChIP-seq]
| PRJNA211591 | ENA
Project description:The far-red light (FR) photoreceptor phytochrome A (phyA) contains no DNA binding domain but associates with CHS promoter through its chaperon FHY1 and transcription factors to regulate transcription. Here, we performed a genome-wide identification of phyA targets using a combination of phyA ChIP- and RNA-sequencing methods. Our results indicate that the phyA signaling widely impact gene promoters involved in multiple FR-modulated aspects of plant growth. Furthermore, there was an enrichment of hormones- and stresses-responsive elements in the phyA direct target promoters, indicating that a much broader than expected range of transcription factors are involved in the phyA signaling. To verify our hypothesis that phyA regulates genes other than light-responsive ones through interaction with corresponding transcription factors, we examined the phyA action on one of its direct target gene NAC019, encoding an ABAdependent transcription factor. The phyA signaling cascade, consisting of FHY1 and HY5, not only targets two G-boxes on NAC019 promoter for subsequent transcriptional regulation, but also positively coordinates with ABA response for the root elongation inhibition under FR. Our study provides new insights into how plants rapidly fine-tune their growth strategy upon dynamic light environment by escorting photoreceptors to the promoters of hormones- or stresses-responsive genes for individualized modulation. The wild-type seedlings and the phyA-1 mutant (both of the Landsberger ecta [Ler] ecotype) were grown in the same conditions used for the phyA ChIP-seq analysis (D4d+FR3h) prior to RNA isolation. Three independent biological replicates were subjected to RNA-seq analysis.
2014-05-06 | E-GEOD-48767 | biostudies-arrayexpress
Project description:The far-red light (FR) photoreceptor phytochrome A (phyA) contains no DNA binding domain but associates with CHS promoter through its chaperon FHY1 and transcription factors to regulate transcription. Here, we performed a genome-wide identification of phyA targets using a combination of phyA ChIP- and RNA-sequencing methods. Our results indicate that the phyA signaling widely impact gene promoters involved in multiple FR-modulated aspects of plant growth. Furthermore, there was an enrichment of hormones- and stresses-responsive elements in the phyA direct target promoters, indicating that a much broader than expected range of transcription factors are involved in the phyA signaling. To verify our hypothesis that phyA regulates genes other than light-responsive ones through interaction with corresponding transcription factors, we examined the phyA action on one of its direct target gene NAC019, encoding an ABAdependent transcription factor. The phyA signaling cascade, consisting of FHY1 and HY5, not only targets two G-boxes on NAC019 promoter for subsequent transcriptional regulation, but also positively coordinates with ABA response for the root elongation inhibition under FR. Our study provides new insights into how plants rapidly fine-tune their growth strategy upon dynamic light environment by escorting photoreceptors to the promoters of hormones- or stresses-responsive genes for individualized modulation.
2014-05-06 | GSE48769 | GEO
Project description:The far-red light (FR) photoreceptor phytochrome A (phyA) contains no DNA binding domain but associates with CHS promoter through its chaperon FHY1 and transcription factors to regulate transcription. Here, we performed a genome-wide identification of phyA targets using a combination of phyA ChIP- and RNA-sequencing methods. Our results indicate that the phyA signaling widely impact gene promoters involved in multiple FR-modulated aspects of plant growth. Furthermore, there was an enrichment of hormones- and stresses-responsive elements in the phyA direct target promoters, indicating that a much broader than expected range of transcription factors are involved in the phyA signaling. To verify our hypothesis that phyA regulates genes other than light-responsive ones through interaction with corresponding transcription factors, we examined the phyA action on one of its direct target gene NAC019, encoding an ABAdependent transcription factor. The phyA signaling cascade, consisting of FHY1 and HY5, not only targets two G-boxes on NAC019 promoter for subsequent transcriptional regulation, but also positively coordinates with ABA response for the root elongation inhibition under FR. Our study provides new insights into how plants rapidly fine-tune their growth strategy upon dynamic light environment by escorting photoreceptors to the promoters of hormones- or stresses-responsive genes for individualized modulation.
2014-05-06 | GSE48767 | GEO
Project description:The far-red light (FR) photoreceptor phytochrome A (phyA) contains no DNA binding domain but associates with CHS promoter through its chaperon FHY1 and transcription factors to regulate transcription. Here, we performed a genome-wide identification of phyA targets using a combination of phyA ChIP- and RNA-sequencing methods. Our results indicate that the phyA signaling widely impact gene promoters involved in multiple FR-modulated aspects of plant growth. Furthermore, there was an enrichment of hormones- and stresses-responsive elements in the phyA direct target promoters, indicating that a much broader than expected range of transcription factors are involved in the phyA signaling. To verify our hypothesis that phyA regulates genes other than light-responsive ones through interaction with corresponding transcription factors, we examined the phyA action on one of its direct target gene NAC019, encoding an ABAdependent transcription factor. The phyA signaling cascade, consisting of FHY1 and HY5, not only targets two G-boxes on NAC019 promoter for subsequent transcriptional regulation, but also positively coordinates with ABA response for the root elongation inhibition under FR. Our study provides new insights into how plants rapidly fine-tune their growth strategy upon dynamic light environment by escorting photoreceptors to the promoters of hormones- or stresses-responsive genes for individualized modulation. Four day-old PphyA: phyA-GFP phyA201 transgenic seedlings were irradiated with 3h FR for ChIP with an anti-GFP antibody, which was previously used to detect phyA-GFP upon FR irradiation . Three biologically distinct phyA associated-DNA samples were subjected to library construction and high-throughput Solexa (Illumina) sequencing. An input DNA sample (genomic DNA before antibody immunoprecipitation in ChIP) was sequenced in parallel to exclude false positive signals caused by preferential PCR on certain genomic regions in the process of library construction .
2014-05-06 | E-GEOD-48769 | biostudies-arrayexpress
Project description:PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The ChIP-chip analysis aimed to find various PIL5 direct targets in the Arabidopsis genome.
2010-01-12 | GSE14450 | GEO
Project description:In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. Three biological replicates for 4-d-old seedlings grown under dark or red-light and long-day (0.5 ?mole m-2 sec-1) contitions.
2013-07-22 | E-GEOD-30910 | biostudies-arrayexpress
Project description:PIL5 is a key negative regulator of phytochrome mediated seed germination and PIL5 protein is degraded by red light irradiation through phytochrome. The ChIP-chip analysis aimed to find various PIL5 direct targets in the Arabidopsis genome. PIL5-myc over-expressed seeds were used for ChIP-chip analysis. Conventional ChIP DNA was amplified by using LM-PCR method. Input DNA (before immuno-precipitation) was used as control DNA.Total three biological replicates were used for the ChIP-chip analysis.
2010-05-16 | E-GEOD-14450 | biostudies-arrayexpress
Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis.
2013-02-01 | GSE39215 | GEO