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

Orlando Contreras-López, Elena A. Vidal, Eleodoro Riveras, José M. Alvarez, Tomás C. Moyano, Erin E. Sparks, Joaquín Medina, Angelo Pasquino, Philip N. Benfey, Gloria M. Coruzzi, Rodrigo A. Gutiérrez

Research output: Contribution to journalArticlepeer-review


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 sequencing 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 components of cell-specific gene regulatory networks.

Original languageEnglish (US)
Article numbere2107879119
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number4
StatePublished - Jan 25 2022


  • Cell-specific
  • Nitrate signaling
  • Transcriptional regulation

ASJC Scopus subject areas

  • General


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