ArticleeLife2013
Evolutionary principles of modular gene regulation in yeasts.
Article in eLife, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 54 papers.
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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
54 citing papers in PubMed, 90 citations in OpenAlex.
- The Origin and Early Evolution of Fungi: Challenges, Inferences, and Principles.Annual review of cell and developmental biology · 2026Review
- Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts.Molecular biology and evolution · 2026Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Natural trait variation across Saccharomycotina species.FEMS yeast research · 2024Review
- The ensemble of gene regulatory networks at mutation-selection balance.Journal of the Royal Society, Interface · 2023Article
- Functional Divergence in a Multi-gene Family Is a Key Evolutionary Innovation for Anaerobic Growth in Saccharomyces cerevisiae.Molecular biology and evolution · 2022Article
- Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.Molecular biology and evolution · 2022Article
- Genome doubling enabled the expansion of yeast vesicle traffic pathways.Scientific reports · 2022Article
- Article
- Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience.Plant, cell & environment · 2021Review
- A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.Nucleic acids research · 2021Article
- Evolution of regulatory networks associated with traits under selection in cichlids.Genome biology · 2021Article
- Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast.Frontiers in fungal biology · 2021Article
- Computational animal welfare: towards cognitive architecture models of animal sentience, emotion and wellbeing.Royal Society open science · 2020Review
- Functional Constitutional Dynamic Networks Revealing Evolutionary Reproduction/Variation/Selection Principles.Journal of the American Chemical Society · 2020Article
- Independent evolution of transcript abundance and gene regulatory dynamics.Genome research · 2020Article
- Performance, genomic rearrangements, and signatures of adaptive evolution: Lessons from fermentative yeasts.Ecology and evolution · 2020Article
- Resolving noise-control conflict by gene duplication.PLoS biology · 2019Article
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
14 authors at 3 institutions in 1 country.
Funding
Abstract
Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years [corrected]. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles. DOI:http://dx.doi.org/10.7554/eLife.00603.001.
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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.