Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO₃⁻) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO₃⁻ treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO₃⁻ treatments. NO₃⁻-modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO₃⁻ transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.

由染色质结构和启动子区域相互作用的调控元件决定的转录调控，是植物对环境信号响应的关键步骤。硝酸盐（NO ₃ ^- ）是调节数百个基因的表达的养分信号拟南芥。在这里，我们整合基因测序，基因组范围的RNA聚合酶II（RNPII），染色质免疫沉淀测序和DNA酶测序数据集建立RNPII占用和染色质辅助功能之间的关系响应NO ₃ ^-处理在拟南芥根。基因组足迹使我们能够识别体内响应NO调控基因表达的调控元件₃ ^-治疗。NO ₃ ^- -modulated转录因子（TF）的足迹是随着时间的推移RNPII占用和成绩单积累的快速增长很重要。我们映射的关键TF调控的相互作用和功能验证的NAP，含有TF的NAC域的作用，在没有出现新的调控因子₃ ^-运输。综上所述，我们的研究提供了对拟南芥根中营养信号响应的转录网络的全面视图。