title: Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast.
abstract: Evolution maintains organismal fitness by preserving genomic information. This is widely assumed to involve conservation of specific genomic loci among species. Many genomic encodings are now recognized to integrate small contributions from multiple genomic positions into quantitative dispersed codes, but the evolutionary dynamics of such codes are still poorly understood. Here we show that in yeast, sequences that quantitatively affect nucleosome occupancy evolve under compensatory dynamics that maintain heterogeneous levels of A+T content through spatially coupled A/T-losing and A/T-gaining substitutions. Evolutionary modeling combined with data on yeast polymorphisms supports the idea that these substitution dynamics are a consequence of weak selection. This shows that compensatory evolution, so far believed to affect specific groups of epistatically linked loci like paired RNA bases, is a widespread phenomenon in the yeast genome, affecting the majority of intergenic sequences in it. The model thus derived suggests that compensation is inevitable when evolution conserves quantitative and dispersed genomic functions.
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Ephraim
authors.initials: E
authors.lastname: Kenigsberg
authors.forename: Amir
authors.initials: A
authors.lastname: Bar
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
authors.forename: Amos
authors.initials: A
authors.lastname: Tanay
mesh_terms: D001482:Base Composition / Q000235:genetics; D019295:Computational Biology; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency; D008957:Models, Genetic; D009154:Mutation; D009707:Nucleosomes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes