ArticleGenetics2016
Buffering of Genetic Regulatory Networks in Drosophila melanogaster.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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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
36 citing papers in PubMed.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Article
- Transcriptome dynamics and allele-specific regulation underlie wheat heterosis at the anthesis and grain-filling stages.BMC genomics · 2025Article
- The regulatory architecture of gene expression variation in Caenorhabditis elegans revealed by multi-strain allele-specific analysis.Genetics · 2025Article
- The regulatory architecture of gene expression variation inbioRxiv : the preprint server for biology · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Pervasive tissue-, genetic background-, and allele-specific gene expression effects in Drosophila melanogaster.PLoS genetics · 2024Article
- Viruses in LaboratoryViruses · 2023Article
- Review
- Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.G3 (Bethesda, Md.) · 2023Article
- Transcriptional misexpression in hybrids between species linked by gene flow is associated with patterns of sequence divergence.Genome biology and evolution · 2023Article
- Allele-specific regulatory effects on the pig transcriptome.GigaScience · 2022Article
- Power calculator for detecting allelic imbalance using hierarchical Bayesian model.BMC research notes · 2021Article
- Parallel and population-specific gene regulatory evolution in cold-adapted fly populations.Genetics · 2021Article
- Testcrosses are an efficient strategy for identifying cis-regulatory variation: Bayesian analysis of allele-specific expression (BayesASE).G3 (Bethesda, Md.) · 2021Article
- Variation in Pleiotropic Hub Gene Expression Is Associated with Interspecific Differences in Head Shape and Eye Size in Drosophila.Molecular biology and evolution · 2021Article
- Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT.Scientific reports · 2021Article
- Trajectories of Homoeolog-Specific Expression in AllotetraploidFrontiers in plant science · 2021Article
- Parental legacy and regulatory novelty inNAR genomics and bioinformatics · 2020Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Regulatory variation in gene expression can be described by cis- and trans-genetic components. Here we used RNA-seq data from a population panel of Drosophila melanogaster test crosses to compare allelic imbalance (AI) in female head tissue between mated and virgin flies, an environmental change known to affect transcription. Indeed, 3048 exons (1610 genes) are differentially expressed in this study. A Bayesian model for AI, with an intersection test, controls type I error. There are ∼200 genes with AI exclusively in mated or virgin flies, indicating an environmental component of expression regulation. On average 34% of genes within a cross and 54% of all genes show evidence for genetic regulation of transcription. Nearly all differentially regulated genes are affected in cis, with an average of 63% of expression variation explained by the cis-effects. Trans-effects explain 8% of the variance in AI on average and the interaction between cis and trans explains an average of 11% of the total variance in AI. In both environments cis- and trans-effects are compensatory in their overall effect, with a negative association between cis- and trans-effects in 85% of the exons examined. We hypothesize that the gene expression level perturbed by cis-regulatory mutations is compensated through trans-regulatory mechanisms, e.g., trans and cis by trans-factors buffering cis-mutations. In addition, when AI is detected in both environments, cis-mated, cis-virgin, and trans-mated-trans-virgin estimates are highly concordant with 99% of all exons positively correlated with a median correlation of 0.83 for cis and 0.95 for trans We conclude that the gene regulatory networks (GRNs) are robust and that trans-buffering explains robustness.
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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.