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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 S. paradoxus and S. cerevisiae intergenic regions flanking HML and HMR.Average percent of SNPs per indicated region in 37 sequenced S. cerevisiae and in 27 sequenced S. paradoxus strains. The average intergenic SNP frequency in S. cerevisiae was 4.5%, and in S. paradoxus 7% (blue horizontal lines).
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pgen-1000247-g005: High SNP frequency in S. paradoxus and S. cerevisiae intergenic regions flanking HML and HMR.Average percent of SNPs per indicated region in 37 sequenced S. cerevisiae and in 27 sequenced S. paradoxus strains. The average intergenic SNP frequency in S. cerevisiae was 4.5%, and in S. paradoxus 7% (blue horizontal lines).

Mentions: If rapid divergence were an inherent property of silenced DNA, more intra-species polymorphisms in these regions would also be expected. We measured genome-wide average intergenic SNP frequencies in S. cerevisiae and S. paradoxus[19] and compared them to the frequencies in sequences flanking HML and HMR. Although the HML and HMR loci, per se, and the four neighboring genes exhibited SNP frequencies typical of genome-wide averages, the intergenic silenced DNA around HML or HMR had SNP frequencies two to three times higher than average in both species (Figure 5).


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 S. paradoxus and S. cerevisiae intergenic regions flanking HML and HMR.Average percent of SNPs per indicated region in 37 sequenced S. cerevisiae and in 27 sequenced S. paradoxus strains. The average intergenic SNP frequency in S. cerevisiae was 4.5%, and in S. paradoxus 7% (blue horizontal lines).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000247-g005: High SNP frequency in S. paradoxus and S. cerevisiae intergenic regions flanking HML and HMR.Average percent of SNPs per indicated region in 37 sequenced S. cerevisiae and in 27 sequenced S. paradoxus strains. The average intergenic SNP frequency in S. cerevisiae was 4.5%, and in S. paradoxus 7% (blue horizontal lines).
Mentions: If rapid divergence were an inherent property of silenced DNA, more intra-species polymorphisms in these regions would also be expected. We measured genome-wide average intergenic SNP frequencies in S. cerevisiae and S. paradoxus[19] and compared them to the frequencies in sequences flanking HML and HMR. Although the HML and HMR loci, per se, and the four neighboring genes exhibited SNP frequencies typical of genome-wide averages, the intergenic silenced DNA around HML or HMR had SNP frequencies two to three times higher than average in both species (Figure 5).

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