Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate
Orlando Contreras‐López, Elena A. Vidal, Eleodoro Riveras, José M. Álvarez, Tomás C. Moyano, Erin E. Sparks, Joaquı́n Medina, Angelo Pasquino, Philip N. Benfey, Gloria M. Coruzzi, Rodrigo A. Gutiérrez
Abstract
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.