ArticleThe Plant cell2014
Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 81 citations in OpenAlex.
- Article
- Article
- Predicting Gene Expression Responses to Cold inGenes · 2025Article
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- Cis-regulatory Variation in Relation to Sex and Sexual Dimorphism in Drosophila melanogaster.Genome biology and evolution · 2024Article
- Molecular mechanisms underlying gene regulatory variation of maize metabolic traits.The Plant cell · 2024Article
- Natural variation in response to combined water and nitrogen deficiencies in Arabidopsis.The Plant cell · 2024Article
- Plasticity of maternal environment-dependent expression-QTLs of tomato seeds.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Article
- Heterosis of fitness and phenotypic variance in the evolution of a diploid gene regulatory network.PNAS nexus · 2022Article
- Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information.The Plant cell · 2022Article
- Transcriptomic Variations and Network Hubs Controlling Seed Size and Weight During Maize Seed Development.Frontiers in plant science · 2022Article
- The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population.G3 (Bethesda, Md.) · 2021Article
- Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity.mSystems · 2021Article
- Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress.Scientific reports · 2021Article
- Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity.Nature communications · 2021Article
- Testcrosses are an efficient strategy for identifying cis-regulatory variation: Bayesian analysis of allele-specific expression (BayesASE).G3 (Bethesda, Md.) · 2021Article
- Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects.Journal of experimental botany · 2020Article
- The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions.Journal of experimental botany · 2020Article
- Genetic Analysis of the Transition from Wild to Domesticated Cotton (G3 (Bethesda, Md.) · 2020Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.
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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.