ArticleGenome research2022
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 27 citations in OpenAlex.
- Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune Cells.bioRxiv : the preprint server for biology · 2026Article
- Developmental signaling reveals functionally enriched human-specific gene regulation in telencephalic progenitors.bioRxiv : the preprint server for biology · 2026Article
- Evidence for genetically-based sperm discrimination in the vaginal tract of a primate species.PLoS biology · 2026Article
- Choice of phenotype scale is critical in biobank-based G×E tests.bioRxiv : the preprint server for biology · 2026Article
- Article
- Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.Nature communications · 2025Article
- Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque.Molecular ecology · 2025Article
- Addressing missing context in regulatory variation across primate evolution.Current opinion in genetics & development · 2025Review
- Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster.G3 (Bethesda, Md.) · 2025Article
- Fusion of spatiotemporal and network models to prioritize multiscale effects in single-cell perturbations.Briefings in bioinformatics · 2025Article
- Article
- Sphenoid sinus hyperpneumatization: anatomical variants, molecular blueprints, and AI-augmented roadmaps for skull base surgery.Frontiers in endocrinology · 2025Review
- Pathogen stimulations and immune cells synergistically affect the gene expression profile characteristics of porcine peripheral blood mononuclear cells.BMC genomics · 2024Article
- Genotype × environment interactions in gene regulation and complex traits.Nature genetics · 2024Review
- Cell-type-specific and disease-associated expression quantitative trait loci in the human lung.Nature genetics · 2024Article
- Gene expression variation underlying tissue-specific responses to copper stress in Drosophila melanogaster.G3 (Bethesda, Md.) · 2024Article
- Chromatin activity identifies differential gene regulation across human ancestries.Genome biology · 2024Article
- Integrating the Thrifty Genotype and Evolutionary Mismatch Hypotheses to understand variation in cardiometabolic disease risk.Evolution, medicine, and public health · 2024Review
- Gene expression variation underlying tissue-specific responses to copper stress inbioRxiv : the preprint server for biology · 2023Article
- Characterizing the landscape of gene expression variance in humans.PLoS genetics · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
There is increasing appreciation that, in addition to being shaped by an individual's genotype and environment, most complex traits are also determined by poorly understood interactions between these two factors. So-called "genotype × environment" (G×E) interactions remain difficult to map at the organismal level but can be uncovered using molecular phenotypes. To do so at large scale, we used TM3'seq to profile transcriptomes across 12 cellular environments in 544 immortalized B cell lines from the 1000 Genomes Project. We mapped the genetic basis of gene expression levels across environments and revealed a context-dependent genetic architecture: The average heritability of gene expression levels increased in treatment relative to control conditions, and on average, each treatment revealed new expression quantitative trait loci (eQTLs) at 11% of genes. Across our experiments, 22% of all identified eQTLs were context-dependent, and this group was enriched for trait- and disease-associated loci. Further, evolutionary analyses suggested that positive selection has shaped G×E loci involved in responding to immune challenges and hormones but not to man-made chemicals. We hypothesize that this reflects a reduced opportunity for selection to act on responses to molecules recently introduced into human environments. Together, our work highlights the importance of considering an exposure's evolutionary history when studying and interpreting G×E interactions, and provides new insight into the evolutionary mechanisms that maintain G×E loci in human populations.
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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.