ArticlePlant physiology2015
Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice.
Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- HHO5 orchestrates dose-dependent feedback regulation of organic versus inorganic nitrogen signaling in Arabidopsis.The Plant cell · 2026Article
- Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen.The Plant cell · 2025Article
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- Nitrogen sensing and regulatory networks: it's about time and space.The Plant cell · 2024Review
- Nitrate and ammonium, the yin and yang of nitrogen uptake: a time-course transcriptomic study in rice.Frontiers in plant science · 2024Article
- A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation.Plants (Basel, Switzerland) · 2023Review
- Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions.International journal of molecular sciences · 2023Article
- Interspecific comparison of gene expression profiles using machine learning.PLoS computational biology · 2023Article
- Identification of growth regulators using cross-species network analysis in plants.Plant physiology · 2022Article
- Genome-Scale Investigation ofInternational journal of molecular sciences · 2022Article
- Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.).Scientific reports · 2022Article
- Article
- Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice.Frontiers in plant science · 2022Article
- R2R3-MYBs in Durum Wheat: Genome-Wide Identification, Poaceae-Specific Clusters, Expression, and Regulatory Dynamics Under Abiotic Stresses.Frontiers in plant science · 2022Article
- Plant NIGT1/HRS1/HHO Transcription Factors: Key Regulators with Multiple Roles in Plant Growth, Development, and Stress Responses.International journal of molecular sciences · 2021Review
- Transcriptomic Characterization of Nitrate-Enhanced Stevioside Glycoside Synthesis in Stevia (International journal of molecular sciences · 2021Article
- Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice.Frontiers in plant science · 2021Article
- Transcriptomic and network analyses reveal distinct nitrate responses in light and dark in rice leaves (Oryza sativa Indica var. Panvel1).Scientific reports · 2020Article
- Nitrogen-responsive transcription factor kinetics meter plant growth.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A Tripartite Interaction among the BasidiomyceteThe Plant cell · 2020Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana) to a crop, rice (Oryza sativa), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants. To uncover such conserved N-regulatory network modules, we first generated an N-regulatory network based solely on rice transcriptome and gene interaction data. Next, we enhanced the network knowledge in the rice N-regulatory network using transcriptome and gene interaction data from Arabidopsis and new data from Arabidopsis and rice plants exposed to the same N treatment conditions. This cross-species network analysis uncovered a set of N-regulated transcription factors (TFs) predicted to target the same genes and network modules in both species. Supernode analysis of the TFs and their targets in these conserved network modules uncovered genes directly related to N use (e.g. N assimilation) and to other shared biological processes indirectly related to N. This cross-species network approach was validated with members of two TF families in the supernode network, BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTOR1-TGA and HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT SHORTENING1 (HRS1)/HRS1 Homolog family, which have recently been experimentally validated to mediate the N response in Arabidopsis.
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