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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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High SNP frequency in subtelomeric S. cerevisiae regions.Boxplots of SNP frequencies for intergenic regions and fourfold-degenerate synonymous positions of genes, as a function of distance from telomeres. Only single-copy intergenic and coding regions were included. For codons, only verified genes were considered. Wilcoxon–Mann–Whitney p-values for each distance interval, comparing SNP frequencies against the genome-wide distribution, are indicated within each boxplot.
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pgen-1000247-g006: High SNP frequency in subtelomeric S. cerevisiae regions.Boxplots of SNP frequencies for intergenic regions and fourfold-degenerate synonymous positions of genes, as a function of distance from telomeres. Only single-copy intergenic and coding regions were included. For codons, only verified genes were considered. Wilcoxon–Mann–Whitney p-values for each distance interval, comparing SNP frequencies against the genome-wide distribution, are indicated within each boxplot.

Mentions: A similar pattern of SNP frequencies to that observed at the HM loci was also detected for telomere-proximal intergenic regions among S. cerevisiae isolates. To avoid counting polymorphisms arising from recombination between repetitive DNA sequences, only SNPs in single-copy intergenic regions were considered. SNPs were significantly more frequent in subtelomeric regions, within 0–20 and 20–40 kilobases of telomere edges, than in the rest of the genome (Figure 6, upper panel). The subtelomeric regions were the only ones that deviated strongly from the genome-wide frequencies.


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

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

High SNP frequency in subtelomeric S. cerevisiae regions.Boxplots of SNP frequencies for intergenic regions and fourfold-degenerate synonymous positions of genes, as a function of distance from telomeres. Only single-copy intergenic and coding regions were included. For codons, only verified genes were considered. Wilcoxon–Mann–Whitney p-values for each distance interval, comparing SNP frequencies against the genome-wide distribution, are indicated within each boxplot.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000247-g006: High SNP frequency in subtelomeric S. cerevisiae regions.Boxplots of SNP frequencies for intergenic regions and fourfold-degenerate synonymous positions of genes, as a function of distance from telomeres. Only single-copy intergenic and coding regions were included. For codons, only verified genes were considered. Wilcoxon–Mann–Whitney p-values for each distance interval, comparing SNP frequencies against the genome-wide distribution, are indicated within each boxplot.
Mentions: A similar pattern of SNP frequencies to that observed at the HM loci was also detected for telomere-proximal intergenic regions among S. cerevisiae isolates. To avoid counting polymorphisms arising from recombination between repetitive DNA sequences, only SNPs in single-copy intergenic regions were considered. SNPs were significantly more frequent in subtelomeric regions, within 0–20 and 20–40 kilobases of telomere edges, than in the rest of the genome (Figure 6, upper panel). The subtelomeric regions were the only ones that deviated strongly from the genome-wide frequencies.

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