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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Contreras-López, O; Vidal, EA; Riveras, E; Alvarez, JM; Moyano, TC; Sparks, EE; Medina, J; Pasquino, A; Benfey, PN; Coruzzi, GM; Gutiérrez, RA

Published Date

  • January 2022

Published In

Volume / Issue

  • 119 / 4

Start / End Page

  • e2107879119 -

PubMed ID

  • 35046022

Pubmed Central ID

  • PMC8794810

Electronic International Standard Serial Number (EISSN)

  • 1091-6490

International Standard Serial Number (ISSN)

  • 0027-8424

Digital Object Identifier (DOI)

  • 10.1073/pnas.2107879119

Language

  • eng