ArticleGenome research2010
Natural selection on cis and trans regulation in yeasts.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 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
115 citing papers in PubMed, 176 citations in OpenAlex.
- Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents.Cell proliferation · 2026Article
- Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses.Nature communications · 2026Article
- Read mismapping from segmental duplications drives spuriousbioRxiv : the preprint server for biology · 2025Article
- RNA-sequencing Analysis of Hybrid Females Reveals a Dominance of Expression of Alleles From Outcrossing Species Over Those From Selfing Species.Genome biology and evolution · 2025Article
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- Article
- The genetic architecture of gene expression regulation in aFrontiers in plant science · 2025Article
- Systems genomics of salinity stress response in rice.bioRxiv : the preprint server for biology · 2024Article
- Unifying framework explaining how parental regulatory divergence can drive gene expression in hybrids and allopolyploids.Nature communications · 2024Article
- Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans.Cell genomics · 2024Article
- Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice.PLoS genetics · 2024Article
- Non-additive genetic components contribute significantly to population-wide gene expression variation.Cell genomics · 2024Article
- Gene regulation and speciation in a migratory divide between songbirds.Nature communications · 2024Article
- A predominant role of genotypic variation in both expression of sperm competition genes and paternity success inProceedings. Biological sciences · 2023Article
- Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.G3 (Bethesda, Md.) · 2023Article
- Non-additive genetic components contribute significantly to population-wide gene expression variation.bioRxiv : the preprint server for biology · 2023Article
- Impact of the acquired subgenome on the transcriptional landscape in Brettanomyces bruxellensis allopolyploids.G3 (Bethesda, Md.) · 2023Article
- Contributions of mutation and selection to regulatory variation: lessons from thePhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Review
- Maternal patterns of inheritance alter transcript expression in eggs.BMC genomics · 2023Article
- Long-read genome assemblies reveal aZoological research · 2023Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 6 institutions in 2 countries.
Funding
Abstract
Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we measure genome-wide allele-specific expression by deep sequencing to investigate the patterns of cis and trans expression variation between two strains of Saccharomyces cerevisiae. We propose a statistical modeling framework based on the binomial distribution that simultaneously addresses normalization of read counts derived from different parents and estimating the cis and trans expression variation parameters. We find that expression polymorphism in yeast is common for both cis and trans, though trans variation is more common. Constraint in expression evolution is correlated with other hallmarks of constraint, including gene essentiality, number of protein interaction partners, and constraint in amino acid substitution, indicating that both cis and trans polymorphism are clearly under purifying selection, though trans variation appears to be more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests a significant departure from a neutral model of molecular evolution. A further examination of correlation between polymorphism and divergence within each category suggests that cis divergence is more frequently mediated by positive Darwinian selection than is trans divergence.
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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.