ArticleGenome research2007
Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 50 citations in OpenAlex.
- Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents.Cell proliferation · 2026Article
- Non-additive genetic components contribute significantly to population-wide gene expression variation.Cell genomics · 2024Article
- Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention.RNA biology · 2024Review
- Parallel and population-specific gene regulatory evolution in cold-adapted fly populations.Genetics · 2021Article
- Molecular and evolutionary processes generating variation in gene expression.Nature reviews. Genetics · 2021Review
- CompensatoryEvolution letters · 2019Article
- Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids.BMC genomics · 2018Article
- Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.Nature communications · 2017Article
- Article
- Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species.Genome biology and evolution · 2017Article
- Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape.BMC genomics · 2013Article
- Evolution of cichlid vision via trans-regulatory divergence.BMC evolutionary biology · 2012Article
- Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression.BMC genomics · 2012Article
- Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines.Proceedings of the National Academy of Sciences of the United States of America · 2012Review
- Gene expression divergence is coupled to evolution of DNA structure in coding regions.PLoS computational biology · 2011Article
- Chromatin regulators as capacitors of interspecies variations in gene expression.Molecular systems biology · 2010Article
- Natural selection on cis and trans regulation in yeasts.Genome research · 2010Article
- The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution.The New phytologist · 2010Review
- Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes.Genome biology · 2010Article
- Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae.Genome biology and evolution · 2010Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Both cis- and trans-regulatory mutations contribute to gene expression divergence within and between species. To estimate their relative contributions, we examined two yeast strains, BY (a laboratory strain) and RM (a wild strain), for their gene-expression divergence by microarray. Using these data and published ChIP-chip data, we obtained a set of single-regulator-regulated genes that showed expression divergence between BY and RM. We randomly selected 50 of these genes for further study. We developed a step-by-step approach to assess the relative contributions of cis- and trans-variations to expression divergence by using pyrosequencing to quantify the mRNA levels of the BY and RM alleles in the same culture (co-culture) and in hybrid diploids. Forty genes showed expression divergence between the two strains in co-culture, and pyrosequencing of the BY/RM hybrid diploids showed that 45% (18/40) can be attributed to differences in trans-acting factors alone, 17.5% (7/40) mainly to trans-variations, 20% (8/40) to both cis- and trans-acting factors, 7.5% (3/40) mainly to cis-variations, and 10% (4/40) to cis-acting factors alone. In addition, we replaced the BY promoter by the RM promoter in each of 10 BY genes that were found from our microarray data to have expression divergence between BY and RM, and in each case our quantitative PCR analysis revealed a cis effect of the promoter replacement on gene expression. In summary, our study suggests that trans-acting factors play the major role in expression evolution between yeast strains, but the role of cis variation is also important.
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