ArticleMolecular biology and evolution2016
Contrasting Frequencies and Effects of cis- and trans-Regulatory Mutations Affecting Gene Expression.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 127 citations in OpenAlex.
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.Nature ecology & evolution · 2026Article
- Epistatic impacts of cis- and trans-regulatory mutations on the distribution of mutational effects for gene expression in Saccharomyces cerevisiae.Molecular biology and evolution · 2026Article
- Cis- and trans-regulatory factors contributing to divergent activity of the TDH3 promoter in Saccharomyces yeast.Molecular biology and evolution · 2026Article
- LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq.Plant methods · 2026Article
- Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation.bioRxiv : 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
- Environmental impacts on gene expression noise and its relationship with fitness.bioRxiv : the preprint server for biology · 2026Article
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- Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents.Cell proliferation · 2026Article
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- TOPK promotes immune suppression in kidney renal clear cell carcinoma and emerges as a prognostic and therapeutic target.BMC cancer · 2025Article
- Disentangling cell-intrinsic and cell-extrinsic factors underlying evolution.Cell genomics · 2025Article
- Improved sampling of genotypes and species reveals new insights on de novo gene history and regulatory origins.Genetics · 2025Article
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- Systems genomics of salinity stress response in rice.bioRxiv : the preprint server for biology · 2024Article
- The emergence and evolution of gene expression in genome regions replete with regulatory motifs.eLife · 2024Article
- Genetic Variants Affecting FADS2 Enzyme Dynamics and Gene Expression in Cogenetic Oysters with Different PUFA Levels Provide New Tools to Improve Unsaturated Fatty Acids.International journal of molecular sciences · 2024Article
- Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae.Nature ecology & evolution · 2024Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Heritable differences in gene expression are caused by mutations in DNA sequences encoding cis-regulatory elements and trans-regulatory factors. These two classes of regulatory change differ in their relative contributions to expression differences in natural populations because of the combined effects of mutation and natural selection. Here, we investigate how new mutations create the regulatory variation upon which natural selection acts by quantifying the frequencies and effects of hundreds of new cis- and trans-acting mutations altering activity of the TDH3 promoter in the yeast Saccharomyces cerevisiae in the absence of natural selection. We find that cis-regulatory mutations have larger effects on expression than trans-regulatory mutations and that while trans-regulatory mutations are more common overall, cis- and trans-regulatory changes in expression are equally abundant when only the largest changes in expression are considered. In addition, we find that cis-regulatory mutations are skewed toward decreased expression while trans-regulatory mutations are skewed toward increased expression. We also measure the effects of cis- and trans-regulatory mutations on the variability in gene expression among genetically identical cells, a property of gene expression known as expression noise, finding that trans-regulatory mutations are much more likely to decrease expression noise than cis-regulatory mutations. Because new mutations are the raw material upon which natural selection acts, these differences in the frequencies and effects of cis- and trans-regulatory mutations should be considered in models of regulatory evolution.
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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.