ArticleThe Plant cell2022
Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information.
Article in The Plant cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 52 citations in OpenAlex.
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Design and Testing of Root-Specific Synthetic Promoters by Machine Learning.International journal of molecular sciences · 2026Article
- Stress-responsive transcription factor families are key components of the core abiotic stress response in maize.G3 (Bethesda, Md.) · 2025Article
- Translational regulation plasticity shapes wheat grain adaptation to heat stress.Genome biology · 2025Article
- Predicting Gene Expression Responses to Cold inGenes · 2025Article
- Designing a nitrogen-efficient cold-tolerant maize for modern agricultural systems.The Plant cell · 2025Review
- The genetic architecture of gene expression regulation in aFrontiers in plant science · 2025Article
- Requirement of two simultaneous environmental signals for activation of ArabidopsisPlant signaling & behavior · 2024Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Omics-Driven Strategies for Developing Saline-Smart Lentils: A Comprehensive Review.International journal of molecular sciences · 2024Review
- MaHsf24, a novel negative modulator, regulates cold tolerance in banana fruits by repressing the expression of HSPs and antioxidant enzyme genes.Plant biotechnology journal · 2024Article
- The Role of MaWRKY70 in Regulating Lipoxygenase Gene Transcription during Chilling Injury Development in Banana Fruit.Foods (Basel, Switzerland) · 2024Article
- A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions.Frontiers in plant science · 2024Review
- Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research.The Plant journal : for cell and molecular biology · 2023Review
- Review
- Conserved and variable heat stress responses of the Heat Shock Factor transcription factor family in maize andPlant direct · 2023Article
- Advances of Apetala2/Ethylene Response Factors in Regulating Development and Stress Response in Maize.International journal of molecular sciences · 2023Review
- Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice.Frontiers in plant science · 2023Article
- Conserved hierarchical gene regulatory networks for drought and cold stress response inFrontiers in plant science · 2023Article
- A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species.Methods in molecular biology (Clifton, N.J.) · 2023Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Changes in gene expression are important for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes identifies many changes in transcript abundance. We used comparisons of expression responses in multiple genotypes to identify alleles with variable responses to heat or cold stress and to distinguish examples of cis- or trans-regulatory variation for stress-responsive expression changes. We used motifs enriched near the transcription start sites (TSSs) for thermal stress-responsive genes to develop predictive models of gene expression responses. Prediction accuracies can be improved by focusing only on motifs within unmethylated regions near the TSS and vary for genes with different dynamic responses to stress. Models trained on expression responses in a single genotype and promoter sequences provided lower performance when applied to other genotypes but this could be improved by using models trained on data from all three genotypes tested. The analysis of genes with cis-regulatory variation provides evidence for structural variants that result in presence/absence of transcription factor binding sites in creating variable responses. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and defines a framework for developing models to predict expression responses across multiple genotypes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.