title: Arabidopsis Phytochrome A Directly Targets Numerous Promoters for Individualized Modulation of Genes in a Wide Range of Pathways.
abstract: The far-red light (FR) photoreceptor phytochrome A (phyA) contains no DNA binding domain but associates with the CHALCONE SYNTHASE promoter through its chaperone FAR-RED ELONGATED HYPOCOTYL1 and transcription factors. Here, we performed a genome-wide identification of phyA targets using a combination of phyA chromatin immunoprecipitation and RNA sequencing methods in Arabidopsis thaliana. Our results indicate that phyA signaling widely affects gene promoters involved in multiple FR-modulated aspects of plant growth. Furthermore, we observed an enrichment of hormone- and stress-responsive elements in the phyA direct target promoters, indicating that a much broader than expected range of transcription factors is involved in the phyA signaling pathway. To verify our hypothesis that phyA regulates genes other than light-responsive ones through the interaction with corresponding transcription factors, we examined the action of phyA on one of its direct target genes, NAC019, which encodes an abscisic acid-dependent transcription factor. The phyA signaling cascade not only targets two G-boxes on the NAC019 promoter for subsequent transcriptional regulation but also positively coordinates with the abscisic acid signaling response for root elongation inhibition under FR. Our study provides new insight into how plants rapidly fine-tune their growth strategy upon changes in the light environment by escorting photoreceptors to the promoters of hormone- or stress-responsive genes for individualized modulation.
authors.affiliation: Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520.
authors.forename: Fang
authors.identifier: http://orcid.org/0000-0002-2938-1770
authors.initials: F
authors.lastname: Chen
authors.affiliation: Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520.
authors.forename: Bosheng
authors.identifier: http://orcid.org/0000-0002-1816-7007
authors.initials: B
authors.lastname: Li
authors.affiliation: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.affiliation: Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada H9X 3V9.
authors.forename: Jean-Benoit
authors.initials: JB
authors.lastname: Charron
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
authors.forename: Mingqiu
authors.initials: M
authors.lastname: Dai
authors.affiliation: Department of Pharmacology, Yale University, New Haven, Connecticut 06520.
authors.forename: Xiarong
authors.initials: X
authors.lastname: Shi
authors.affiliation: Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520 xingwang.deng@yale.edu.
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng