The photoreceptor chaperone FHY1 has an independent role in gene modulation and plant development under far-red light [RNA-Seq]. Arabidopsis thaliana

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 Overall design: 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.

为将远红光（far-red light, FR）信号应用于植物生长优化策略，远红光下胚轴伸长1（FAR-RED ELONGATED HYPOCOTYL1, FHY1）可介导远红光光受体光敏色素A（phytochrome A, phyA）的核易位，并促进phyA与众多响应环境刺激的关键相关基因的启动子结合。然而，远红光照射后FHY1是否存在额外调控功能仍不明晰。本研究通过染色质免疫共沉淀测序（ChIP-seq）分析全局鉴定FHY1的染色质结合位点，并将FHY1结合位点与phyA结合位点进行比对，证实核定位的FHY1既可独立于phyA发挥调控作用，也可与phyA协同激活不同靶基因的表达。本研究同时发现，phyA在调控其特异性靶基因时可不依赖FHY1。此外，独立的FHY1核通路参与诸多关键发育过程，例如盐胁迫环境下远红光抑制种子萌发的过程。值得注意的是，共有及独有FHY1和/或phyA结合基因中顺式作用元件与转录因子的差异分布，揭示了FHY1与phyA独立及协同调控通路的复杂性。本研究揭示了FHY1除当前公认的依赖phyA的光形态建成功能之外的新作用维度。整体实验设计：将35S: GFP-FHY1 fhy1-1转基因株系与fhy1-1突变体在相同光照条件（暗培养4天+远红光照射3小时，D4d+FR3h）下培养，用于RNA提取与测序。设置3次生物学重复，开展高通量Solexa（Illumina）测序。