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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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Lack of correlation between expression level and SNP frequency in S. cerevisiae.(A) Median expression for intergenic regions and transcripts, as a function of distance from telomeres. (B) Boxplots of SNP frequencies for intergenic regions, as a function of median expression level. (C) Boxplots of SNP frequencies in fourfold-degenerate synonymous positions of genes, as a function of median expression level. Wilcoxon–Mann–Whitney p-values for each expression level, comparing SNP frequencies against the genome-wide distribution, are indicated within each boxplot.
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pgen-1000247-g007: Lack of correlation between expression level and SNP frequency in S. cerevisiae.(A) Median expression for intergenic regions and transcripts, as a function of distance from telomeres. (B) Boxplots of SNP frequencies for intergenic regions, as a function of median expression level. (C) Boxplots of SNP frequencies in fourfold-degenerate synonymous positions of genes, as a function of median expression level. Wilcoxon–Mann–Whitney p-values for each expression level, comparing SNP frequencies against the genome-wide distribution, are indicated within each boxplot.

Mentions: A genome-wide RNA-sequencing dataset [21] was used to assign median expression level for each gene and intergenic region. The extent of expression of intergenic DNA was indistinguishable between the most telomere-proximal and non-subtelomeric regions (Figure 7A). As would be expected from the observation, there was no correlation between intergenic expression and SNP density (Figure 7B). For genes, there was a definite decrease in median expression of subtelomeric genes (Figure 7A). However, as for the intergenic regions, there was no increase in SNP frequencies for highly expressed genes (Figure 7C).


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

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

Lack of correlation between expression level and SNP frequency in S. cerevisiae.(A) Median expression for intergenic regions and transcripts, as a function of distance from telomeres. (B) Boxplots of SNP frequencies for intergenic regions, as a function of median expression level. (C) Boxplots of SNP frequencies in fourfold-degenerate synonymous positions of genes, as a function of median expression level. Wilcoxon–Mann–Whitney p-values for each expression level, 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-g007: Lack of correlation between expression level and SNP frequency in S. cerevisiae.(A) Median expression for intergenic regions and transcripts, as a function of distance from telomeres. (B) Boxplots of SNP frequencies for intergenic regions, as a function of median expression level. (C) Boxplots of SNP frequencies in fourfold-degenerate synonymous positions of genes, as a function of median expression level. Wilcoxon–Mann–Whitney p-values for each expression level, comparing SNP frequencies against the genome-wide distribution, are indicated within each boxplot.
Mentions: A genome-wide RNA-sequencing dataset [21] was used to assign median expression level for each gene and intergenic region. The extent of expression of intergenic DNA was indistinguishable between the most telomere-proximal and non-subtelomeric regions (Figure 7A). As would be expected from the observation, there was no correlation between intergenic expression and SNP density (Figure 7B). For genes, there was a definite decrease in median expression of subtelomeric genes (Figure 7A). However, as for the intergenic regions, there was no increase in SNP frequencies for highly expressed genes (Figure 7C).

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