@article{c4301d6fa62245edaa023170c31545f4,
title = "Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate",
abstract = "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.",
keywords = "Cell-specific, Nitrate signaling, Transcriptional regulation",
author = "Orlando Contreras-L{\'o}pez and Vidal, {Elena A.} and Eleodoro Riveras and Alvarez, {Jos{\'e} M.} and Moyano, {Tom{\'a}s C.} and Sparks, {Erin E.} and Joaqu{\'i}n Medina and Angelo Pasquino and Benfey, {Philip N.} and Coruzzi, {Gloria M.} and Guti{\'e}rrez, {Rodrigo A.}",
note = "Funding Information: ACKNOWLEDGMENTS. We thank Dr. Matthew D. Brooks for the helpful discussion of area under the precision recall analyses. This work is funded by Agencia Nacional de Investigaci{\'o}n y Desarrollo (ANID) National Fund for Scientific and Technological Development Grants 1180759 (to R.A.G.), 1210389 (to J.M.A.), and 1170926 and 1211130 (to E.A.V.); ANID–Millennium Science Initiative Program, Millennium Institute for Integrative Biology Grant ICN17_022 (to R.A.G., E.A.V., and J.M.A.); ANID PCI Redes entre Centros de Investigaci{\'o}n Grant REDES180097 (to E.A.V.); ANID Fondo de Desarrollo de Areas Prioritarias Grant 15090007 (to R.A.G.); EvoNet Project Grant DE-SC0014377 (to R.A.G. and G.M.C.); Comisi{\'o}n Nacional de Investigaci{\'o}n Cient{\'i}fica y Tecnol{\'o}gica (CONICYT)-MPG 2019 Grant MPG190013 (to R.A.G.); HHMI and NIH Maximizing Investigator{\textquoteright}s Research Award 1R35GM131725 (to P.N.B.); NIH National Institute of General Medical Sciences Grant R01GM121753 (to G.M.C.); NSF Plant Genome Grant NSF-PGRP: IOS-1840761 (to G.M.C. and J.M.A.); Zegar Family Foundation Grant A16-0051 (to G.M.C.); and National Institute for Agriculture and Food Research and Technology Grant RTA2015-00014-c02-01 (to J.M.). Publisher Copyright: {\textcopyright} 2022 National Academy of Sciences. All rights reserved.",
year = "2022",
month = jan,
day = "25",
doi = "10.1073/pnas.2107879119",
language = "English (US)",
volume = "119",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
publisher = "National Academy of Sciences",
number = "4",
}