Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts

• Published in: PLoS genetics Vol. 4; no. 11; p. e1000247
• Main Authors: Teytelman, Leonid, Eisen, Michael B., Rine, Jasper
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.11.2008; Public Library of Science (PLoS)
• Subjects: Base Sequence; Chromatin; Chromatin - genetics; Chromosomes; Computational Biology; Computational Biology/Comparative Sequence Analysis; Computational Biology/Genomics; Conserved Sequence; DNA, Fungal - genetics; DNA, Intergenic - genetics; Evolutionary Biology/Evolutionary and Comparative Genetics; Evolutionary Biology/Genomics; Fungal Proteins - genetics; Gene Silencing; Genetic aspects; Genetics and Genomics; Genetics and Genomics/Chromosome Biology; Genetics and Genomics/Comparative Genomics; Metazoa; Molecular Sequence Data; Mutation; Physiological aspects; Point Mutation; Polymorphism, Single Nucleotide; Proteins; Saccharomyces; Saccharomyces - genetics; Saccharomyces cerevisiae; Single nucleotide polymorphisms; Telomere - genetics; Transcription, Genetic; Yeast; United States
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1000247

Subtelomeric DNA in budding yeasts, like metazoan heterochromatin, is gene poor, repetitive, transiently silenced, and highly dynamic. The rapid evolution of subtelomeric regions is commonly thought to arise from transposon activity and increased recombination between repetitive elements. However, we found evidence of an additional factor in this diversification. We observed a surprising level of nucleotide divergence in transcriptionally silenced regions in inter-species comparisons of Saccharomyces yeasts. Likewise, intra-species analysis of polymorphisms also revealed increased SNP frequencies in both intergenic and synonymous coding positions of silenced DNA. This analysis suggested that silenced DNA in Saccharomyces cerevisiae and closely related species had increased single base-pair substitution that was likely due to the effects of the silencing machinery on DNA replication or repair.