ArticlePLoS genetics2012
Promoter nucleosome organization shapes the evolution of gene expression.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 16 citations in OpenAlex.
- Gene expression is stable despite widespread cis and trans regulatory divergence inbioRxiv : the preprint server for biology · 2026Article
- Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding.Nucleic acids research · 2023Article
- Evolution-guided engineering of small-molecule biosensors.Nucleic acids research · 2020Article
- Pervasive and dynamic transcription initiation inGenome research · 2019Article
- Invisible cities: segregated domains in the yeast genome with distinct structural and functional attributes.Current genetics · 2018Article
- Neighboring Genes Show Correlated Evolution in Gene Expression.Molecular biology and evolution · 2015Article
- Silencing is noisy: population and cell level noise in telomere-adjacent genes is dependent on telomere position and sir2.PLoS genetics · 2014Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Understanding why genes evolve at different rates is fundamental to evolutionary thinking. In species of the budding yeast, the rate at which genes diverge in expression correlates with the organization of their promoter nucleosomes: genes lacking a nucleosome-free region (denoted OPN for "Occupied Proximal Nucleosomes") vary widely between the species, while the expression of those containing NFR (denoted DPN for "Depleted Proximal Nucleosomes") remains largely conserved. To examine if early evolutionary dynamics contributes to this difference in divergence, we artificially selected for high expression of GFP-fused proteins. Surprisingly, selection was equally successful for OPN and DPN genes, with -80% of genes in each group stably increasing in expression by a similar amount. Notably, the two groups adapted by distinct mechanisms: DPN-selected strains duplicated large genomic regions, while OPN-selected strains favored trans mutations not involving duplications. When selection was removed, DPN (but not OPN) genes reverted rapidly to wild-type expression levels, consistent with their lower diversity between species. Our results suggest that promoter organization constrains the early evolutionary dynamics and in this way biases the path of long-term evolution.
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Registered trials
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