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| Status |
Public on May 06, 2014 |
| Title |
Arabidopsis phytochrome A directly targets numerous promoters for individualized modulation of genes in wide range of pathways [RNA-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Chen F, Li B, Li G, Charron J, Daie M, Shi X, Deng XW |
| Citation(s) |
24794133 |
| Submission date |
Jul 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Bosheng Li |
| E-mail(s) |
libs@sustc.edu.cn
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| Organization name |
SUSTC (current, may different with previous institution )
|
| Department |
MCDB
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| Street address |
SUStech Huiyuan #1 406
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
581055 |
| Country |
China |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE48770 |
Arabidopsis phytochrome A directly targets numerous promoters for individualized modulation of genes in wide range of pathways |
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| Relations |
| BioProject |
PRJNA211593 |
| SRA |
SRP026703 |
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