E-GEOD-48767 - Transcription profiling by high throughput sequencing of Arabidopsis phyA-1 mutants

Released on 6 May 2014, last updated on 9 November 2015
Arabidopsis thaliana
Samples (6)
Protocols (4)
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.
Experiment type
RNA-seq of coding RNA 
bosheng Li <leoleooel@163.com>, Bosheng Li, Fang Chen, Gang Li, Jean-Benoit Charron, Mingqiu Daie, Xiarong Shi, Xing W Deng
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-48767.idf.txt
Sample and data relationshipE-GEOD-48767.sdrf.txt
Additional data (1)E-GEOD-48767.additional.1.zip