Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type- specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequenc-ing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important compo-nents of cell-specific gene regulatory networks.

Automated summary

Nitrate, a nutrient and signaling molecule, affects global gene expression in plants. This study investigated the temporal and cell type-specific responses to nitrate in major root cell types of Arabidopsis thaliana. The gene expression response to nitrate was found to be dynamic and highly localized, and specific transcription factor (TF)-target interactions were predicted. The endodermis cell layer exhibited the largest and most connected nitrate-regulatory gene network, with ABF2 and ABF3 identified as major hubs for transcriptional responses. Experimental validation confirmed TF-target interactions for ABF2 and ABF3, which accounted for over 50% of the nitrate-responsive transcriptome in the endodermis. Additionally, ABF2 and ABF3 were found to play a role in nitrate-induced lateral root growth. This study provides unprecedented spatiotemporal resolution of root response to nitrate and identifies important components of cell-specific gene regulatory networks.