Transcriptional regulation,determined by the chromatin structure and regulatory elements interacting at pro-moter 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 regula-tory 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.