@article{32fda1ec623847e885c7536bc8e05c36,
title = "Gene regulatory network and its constituent transcription factors that control nitrogen-deficiency responses in rice",
abstract = "Increase in the nitrogen (N)-use efficiency and optimization of N response in crop species are urgently needed. Although transcription factor-based genetic engineering is a promising approach for achieving these goals, transcription factors that play key roles in the response to N deficiency have not been studied extensively. Here, we performed RNA-seq analysis of root samples of 20 Asian rice (Oryza sativa) accessions with differential nutrient uptake. Data obtained from plants exposed to N-replete and N-deficient conditions were subjected to coexpression analysis and machine learning-based pathway inference to dissect the gene regulatory network required for the response to N deficiency. Four transcription factors, including members of the G2-like and bZIP families, were predicted to function as key regulators of gene transcription within the network in response to N deficiency. Cotransfection assays validated inferred novel regulatory pathways, and further analyses using genome-edited knockout lines suggested that these transcription factors are important for N-deficiency responses in planta. Many of the N deficiency-responsive genes, including those encoding key regulators within the network, were coordinately regulated by transcription factors belonging to different families. Transcription factors identified in this study could be valuable for the modification of N response and metabolism.",
keywords = "coexpression, gene regulatory network, genome editing, machine learning, nitrogen, rice, systems biology, transcription factor",
author = "Yoshiaki Ueda and Namie Ohtsuki and Koji Kadota and Ayumi Tezuka and Nagano, {Atsushi J.} and Taro Kadowaki and Yonghyun Kim and Mitsue Miyao and Shuichi Yanagisawa",
note = "Funding Information: We thank the National Agriculture and Food Research Organization (Japan) for providing rice seeds, and the Stable Isotope Facility at the University of California, Davis, for performing the N analysis. We thank Drs M. Endo, H. Saika, and S. Toki (National Agriculture and Foot Research Organization, Japan) for provision of vectors for genome editing and valuable advice for rice transformation. We also thank M. Tsumura for technical assistance during plant cultivation. This study was partially funded by the CREST, JST (grant no. JPMJCR15O5 to SY; grant no. JPMJCR15O2 to AJN) and JSPS KAKENHI (grant number 18H03940 to SY; grant no. 18J01554 to YU). 15 Funding Information: We thank the National Agriculture and Food Research Organization (Japan) for providing rice seeds, and the Stable Isotope Facility at the University of California, Davis, for performing the 15N analysis. We thank Drs M. Endo, H. Saika, and S. Toki (National Agriculture and Foot Research Organization, Japan) for provision of vectors for genome editing and valuable advice for rice transformation. We also thank M. Tsumura for technical assistance during plant cultivation. This study was partially funded by the CREST, JST (grant no. JPMJCR15O5 to SY; grant no. JPMJCR15O2 to AJN) and JSPS KAKENHI (grant number 18H03940 to SY; grant no. 18J01554 to YU). Publisher Copyright: {\textcopyright} 2020 The Authors. New Phytologist {\textcopyright} 2020 New Phytologist Trust",
year = "2020",
month = sep,
day = "1",
doi = "10.1111/nph.16627",
language = "English",
volume = "227",
pages = "1434--1452",
journal = "New Phytologist",
issn = "0028-646X",
publisher = "Wiley-Blackwell",
number = "5",
}