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Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts.

Teytelman L, Eisen MB, Rine J - PLoS Genet. (2008)

Bottom Line: However, we found evidence of an additional factor in this diversification.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California, United States of America.

ABSTRACT
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.

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Chromosome III mating loci.MAT and the cryptic mating loci on chromosome III of S. cerevisiae. The genes in the mating loci, HML- and HMR-neighboring genes, the E and I silencers, and the binding sites for ORC, Rap1, and Abf1 in the silencers are shown. The boxes around the mating-type genes represent the sequences shared between the MAT and the HML and HMR loci. The Saccharomyces cerevisiae genome feature coordinates are in Table S2.
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pgen-1000247-g001: Chromosome III mating loci.MAT and the cryptic mating loci on chromosome III of S. cerevisiae. The genes in the mating loci, HML- and HMR-neighboring genes, the E and I silencers, and the binding sites for ORC, Rap1, and Abf1 in the silencers are shown. The boxes around the mating-type genes represent the sequences shared between the MAT and the HML and HMR loci. The Saccharomyces cerevisiae genome feature coordinates are in Table S2.

Mentions: In S. cerevisiae, the best characterized silenced regions are the HML and HMR transcriptionally inactive mating loci of chromosome III. They contain non-expressed copies of the MATa and MATα mating-type genes. During mating type interconversion, HML or HMR is copied into the MAT locus, also on chromosome III, where the resident allele is transcribed. Since haploid cells that express both MATa and MATα behave as non-mating diploids, it is crucial that HML and HMR are silenced. This is achieved through the E and I silencers that flank both of the silenced loci (Figure 1) and recruit Silent Information Regulator (Sir) proteins which then spread throughout the regions. The Sir proteins bind to and deacetylate the tails of histones H3 and H4, leading to silencing of HML and HMR[7].


Silent but not static: accelerated base-pair substitution in silenced chromatin of budding yeasts.

Teytelman L, Eisen MB, Rine J - PLoS Genet. (2008)

Chromosome III mating loci.MAT and the cryptic mating loci on chromosome III of S. cerevisiae. The genes in the mating loci, HML- and HMR-neighboring genes, the E and I silencers, and the binding sites for ORC, Rap1, and Abf1 in the silencers are shown. The boxes around the mating-type genes represent the sequences shared between the MAT and the HML and HMR loci. The Saccharomyces cerevisiae genome feature coordinates are in Table S2.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570616&req=5

pgen-1000247-g001: Chromosome III mating loci.MAT and the cryptic mating loci on chromosome III of S. cerevisiae. The genes in the mating loci, HML- and HMR-neighboring genes, the E and I silencers, and the binding sites for ORC, Rap1, and Abf1 in the silencers are shown. The boxes around the mating-type genes represent the sequences shared between the MAT and the HML and HMR loci. The Saccharomyces cerevisiae genome feature coordinates are in Table S2.
Mentions: In S. cerevisiae, the best characterized silenced regions are the HML and HMR transcriptionally inactive mating loci of chromosome III. They contain non-expressed copies of the MATa and MATα mating-type genes. During mating type interconversion, HML or HMR is copied into the MAT locus, also on chromosome III, where the resident allele is transcribed. Since haploid cells that express both MATa and MATα behave as non-mating diploids, it is crucial that HML and HMR are silenced. This is achieved through the E and I silencers that flank both of the silenced loci (Figure 1) and recruit Silent Information Regulator (Sir) proteins which then spread throughout the regions. The Sir proteins bind to and deacetylate the tails of histones H3 and H4, leading to silencing of HML and HMR[7].

Bottom Line: However, we found evidence of an additional factor in this diversification.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus