Arabidopsis phytochrome A directly targets numerous promoters for individualized modulation of genes in wide range of pathways [ChIP-seq]
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. Overall design: 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 .