ArticleThe Plant cell2016
EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.
Article in The Plant cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers, 2 of them syntheses that pooled it.
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Who cites it
96 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Multi-omics revolution to promote plant breeding efficiency.Frontiers in plant science · 2022Pooled it
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- Drought and salinity stress remodel Asian rice (Oryza sativa) leaf development through cell-type-specific regulatory programs.The New phytologist · 2026Article
- Machine Learning-Guided Stress Atlases Reveal Co-Expression Rewiring and Divergent Cellular Deployment of Abiotic Stress Programs in Rice and Wheat.International journal of molecular sciences · 2026Article
- Back to the future 2: the implications of germplasm structure on the balance between short- and long-term genetic gain in a changing target population of environments.G3 (Bethesda, Md.) · 2026Article
- Shoot transcriptome and co-expression network analysis of African rice cultivars identify drought-tolerance hub genes and growth stage-dependent trade-offs.Frontiers in plant science · 2026Article
- Selection on genome-wide gene expression plasticity of rice in wet and dry field environments.Molecular ecology · 2025Article
- Unlocking gene regulatory networks for crop resilience and sustainable agriculture.Nature biotechnology · 2025Review
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Climate Adaptation Strategies for Maintaining Rice Grain Quality in Temperate Regions.Biology · 2025Review
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses.The Plant journal : for cell and molecular biology · 2025Article
- Transcriptomic Temperature Stress Responses Show Differentiation Between Biomes for Diverse Plants.Genome biology and evolution · 2025Article
- Article
- Dynamic Chromatin Accessibility and Transcriptional Regulation in the Eyes of Red Tilapia (Oreochromis sp.) in Response to Wintering Stress.Marine biotechnology (New York, N.Y.) · 2025Article
- A network-enabled pipeline for gene discovery and validation in non-model plant species.Cell reports methods · 2025Article
- Systems genomics of salinity stress response in rice.bioRxiv : the preprint server for biology · 2024Article
- Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare).Plant molecular biology · 2024Article
- Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model.Plants (Basel, Switzerland) · 2024Article
- Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
36 more citing papers are in PubMed but not listed here.
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11 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental signals. EGRINs encompass many layers of regulation, which culminate in changes in accumulated transcript levels. Here, we inferred EGRINs for the response of five tropical Asian rice (Oryza sativa) cultivars to high temperatures, water deficit, and agricultural field conditions by systematically integrating time-series transcriptome data, patterns of nucleosome-free chromatin, and the occurrence of known cis-regulatory elements. First, we identified 5447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes harboring known cis-regulatory motifs in nucleosome-free regions proximal to their transcriptional start sites. We then used network component analysis to estimate the regulatory activity for each TF based on the expression of its putative target genes. Finally, we inferred an EGRIN using the estimated transcription factor activity (TFA) as the regulator. The EGRINs include regulatory interactions between 4052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of the heat shock factor family, including a putative regulatory connection between abiotic stress and the circadian clock. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference.
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