ArticleProceedings of the National Academy of Sciences of the United States of America2008
Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Enzyme kinetics shapes the growth response of metabolic networks.PLoS computational biology · 2026Article
- Mount Fuji's stubby peak: the genotypic density of additive landscapes near maximal fitness.bioRxiv : the preprint server for biology · 2026Article
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- Concepts and Methods for Predicting Viral Evolution.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Concepts and methods for predicting viral evolution.bioRxiv : the preprint server for biology · 2024Article
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- Energy landscapes of peptide-MHC binding.PLoS computational biology · 2024Article
- Position-specific evolution in transcription factor binding sites, and a fast likelihood calculation for the F81 model.Royal Society open science · 2024Article
- Cis-Regulatory Elements in Mammals.International journal of molecular sciences · 2023Review
- On the incongruence of genotype-phenotype and fitness landscapes.PLoS computational biology · 2022Article
- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
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- Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing.eLife · 2021Article
- Predicting in vivo escape dynamics of HIV-1 from a broadly neutralizing antibody.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Adaptive gene misregulation.Genetics · 2021Article
- Promoter Architecture and Promoter Engineering inMetabolites · 2020Review
- Minimum epistasis interpolation for sequence-function relationships.Nature communications · 2020Article
- Recent insights into the genotype-phenotype relationship from massively parallel genetic assays.Evolutionary applications · 2019Review
- From biophysics to 'omics and systems biology.European biophysics journal : EBJ · 2019Review
9 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
We present a genomewide cross-species analysis of regulation for broad-acting transcription factors in yeast. Our model for binding site evolution is founded on biophysics: the binding energy between transcription factor and site is a quantitative phenotype of regulatory function, and selection is given by a fitness landscape that depends on this phenotype. The model quantifies conservation, as well as loss and gain, of functional binding sites in a coherent way. Its predictions are supported by direct cross-species comparison between four yeast species. We find ubiquitous compensatory mutations within functional sites, such that the energy phenotype and the function of a site evolve in a significantly more constrained way than does its sequence. We also find evidence for substantial evolution of regulatory function involving point mutations as well as sequence insertions and deletions within binding sites. Genes lose their regulatory link to a given transcription factor at a rate similar to the neutral point mutation rate, from which we infer a moderate average fitness advantage of functional over nonfunctional sites. In a wider context, this study provides an example of inference of selection acting on a quantitative molecular trait.
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