title: Promoter nucleosome organization shapes the evolution of gene expression.
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.
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Dalia
authors.initials: D
authors.lastname: Rosin
authors.forename: Gil
authors.initials: G
authors.lastname: Hornung
authors.forename: Itay
authors.initials: I
authors.lastname: Tirosh
authors.forename: Ariel
authors.initials: A
authors.lastname: Gispan
authors.forename: Naama
authors.initials: N
authors.lastname: Barkai
mesh_terms: D058674:Chromosome Duplication / Q000235:genetics; D055028:Comparative Genomic Hybridization; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D009154:Mutation; D009707:Nucleosomes / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D005656:Fungal Proteins; D009707:Nucleosomes