ArticleProceedings of the National Academy of Sciences of the United States of America2015
Genetic basis of transcriptome diversity in Drosophila melanogaster.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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Who cites it
93 citing papers in PubMed.
- From bench to farm: leveragingFly · 2027Review
- Mapping the regulatory architecture of circadian clock adaptation: A genome-wide eQTL analysis in Drosophila melanogaster.Heredity · 2026Article
- Female genetic variation controlling timing of mating plug ejection inbioRxiv : the preprint server for biology · 2026Article
- Stabilizing and directional selection shape the genetic variation of gene expression in the transcriptome of Chlamydomonas.Molecular biology and evolution · 2026Article
- Genome-wide association studies identify new candidate genes and tissues underlying resistance to a natural toxin in drosophilids.G3 (Bethesda, Md.) · 2026Article
- Environmental perturbation increases gene expression variability and unmasks genetic regulation for transcriptional robustness.bioRxiv : the preprint server for biology · 2026Article
- Article
- Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations.Cell genomics · 2025Article
- A basic framework to explain splice-site choice in eukaryotes.Nature communications · 2025Article
- Adaptive gene expression parallelism in the male reproductive tract of two Drosophila species.Genetics · 2025Article
- Phylogenetic Relatedness Does not Predict Patterns of Parallel Transcriptome Adaptation in Drosophila.Genome biology and evolution · 2025Article
- Expression Divergence in Response to Sex-biased Selection.Molecular biology and evolution · 2025Article
- Genetic and Pharmacological Inhibition of Metabotropic Glutamate Receptor Signalling Extends Lifespan in Drosophila.Aging cell · 2025Article
- Crossbreeding Simmental with Mongolian, and Holstein cattle can improve feed efficiency and energy metabolism by upregulating COX3 and downregulating PRSS2 gene expression.Frontiers in nutrition · 2025Article
- Acute exposure to mercury drives changes in gene expression in Drosophila melanogaster.BMC research notes · 2024Article
- Pleiotropy, epistasis and the genetic architecture of quantitative traits.Nature reviews. Genetics · 2024Review
- DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs.Genome biology and evolution · 2024Article
- Reference genes to study the sex-biased expression of genes regulating Drosophila metabolism.Scientific reports · 2024Article
- Genetic, Environmental, and Stochastic Components of Lifespan Variability: TheInternational journal of molecular sciences · 2024Review
- Genetic variation for sexual dimorphism in developmental traits in Drosophila melanogaster.G3 (Bethesda, Md.) · 2024Article
33 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.
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