ArticleGenome biology and evolution2017
Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species.
Article in Genome biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed, 94 citations in OpenAlex.
- Haplotype-resolved genome assembly of femaleHorticulture research · 2026Article
- Rising from the fragments: a multi-factorial regulatory framework of DNA damage response in Deinococcus radiodurans.Extremophiles : life under extreme conditions · 2026Review
- Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Gene expression is stable despite widespread cis and trans regulatory divergence 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
- Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen.Microbial genomics · 2026Article
- 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
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- Read mismapping from segmental duplications drives spuriousbioRxiv : the preprint server for biology · 2025Article
- Predicting Gene Expression Responses to Cold inGenes · 2025Article
- Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.Genetics · 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
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- Gene-by-environment Interactions and Adaptive Body Size Variation in Mice From the Americas.Molecular biology and evolution · 2025Article
- The genetic architecture of gene expression regulation in aFrontiers in plant science · 2025Article
- cis- and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation.Communications biology · 2024Article
- Cis-regulatory Variation in Relation to Sex and Sexual Dimorphism in Drosophila melanogaster.Genome biology and evolution · 2024Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. Although previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical restrictions to closely related species and limited comparisons have made this observation difficult to test. To address this problem, we used allele-specific RNA-seq data from Saccharomyces species and hybrids to expand both the evolutionary timescale and number of species in which the evolution of regulatory divergence has been investigated. We find that as sequence divergence increases, cis-regulatory differences do indeed become the dominant type of regulatory difference between species, ultimately becoming a better predictor of expression divergence than trans-regulatory divergence. When both cis- and trans-regulatory differences accumulate for the same gene, they more often have effects in opposite directions than in the same direction, indicating widespread compensatory changes underlying the evolution of gene expression. The frequency of compensatory changes within and between species and the magnitude of effect for the underlying cis- and trans-regulatory differences suggests that compensatory changes accumulate primarily due to selection against divergence in gene expression as a result of weak stabilizing selection on gene expression levels. These results show that cis-regulatory differences and compensatory changes in regulation play increasingly important roles in the evolution of gene expression as time increases.
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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.