Transcriptomics,Multiomics

Dataset Information

133

Transcription profiling by high throughput sequencing of Arabidopsis 35S:GFP-FHY1; fhy1-1 transgenic line compared to fhy1-1 mutant


ABSTRACT: 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 following FR irradiation remains elusive. Here, by 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 developmental aspects, 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 new aspects of FHY1 function beyond its currently recognized role in phyA-dependent photomorphogenesis. The 35S: GFP-FHY1 fhy1-1 transgenic line and the fhy1-1 mutant were grown under the same light conditions used (D4d+FR3h) for RNA preparation and sequencing. Three biologically replicates were subjected to high-throughput Solexa (Illumina) sequencing.

REANALYSED by: E-GEOD-58082

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Bosheng Li  Fang Chen   Xing W Deng   Jordan Demone   Jean-Benoit Charron   bosheng Li   Xiarong Shi    

PROVIDER: E-GEOD-58082 | ArrayExpress | 2016-02-26

SECONDARY ACCESSION(S): GSE58082SRP042365PRJNA248877

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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

Chen Fang F   Li Bosheng B   Demone Jordan J   Charron Jean-Benoit JB   Shi Xiarong X   Deng Xing Wang XW  

Proceedings of the National Academy of Sciences of the United States of America 20140728 32


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 si  ...[more]

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