Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Ruberti A.thaliana Shade Avoidance Response wt and phyA

ABSTRACT: Aim of the experiment is the identification of genes differentially regulated in phyA seedlings relative to wild type after prolonged exposure to low R/FR. To this end, gene expression changes were analysed in Arabidopsis wild-type and phyA knock-out mutant seedlings exposed to low R/FR light. The experiment was designed to enable comparison between the different genotypes exposed or not exposed to low R/FR light.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Ida Ruberti

PROVIDER: E-MEXP-3267 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamics of the shade-avoidance response in Arabidopsis.

Ciolfi Andrea A Sessa Giovanna G Sassi Massimiliano M Possenti Marco M Salvucci Samanta S Carabelli Monica M Morelli Giorgio G Ruberti Ida I

Plant physiology 20130726 1

Shade-intolerant plants perceive the reduction in the ratio of red light (R) to far-red light (FR) as a warning of competition with neighboring vegetation and display a suite of developmental responses known as shade avoidance. In recent years, major progress has been made in understanding the molecular mechanisms underlying shade avoidance. Despite this, little is known about the dynamics of this response and the cascade of molecular events leading to plant adaptation to a low-R/FR environment. ...[more]

PMID: 23893169

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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 .

Dataset Information

Ruberti A.thaliana Shade Avoidance Response wt and phyA

Publications

Dynamics of the shade-avoidance response in Arabidopsis.

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