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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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Deletion of the S. bayanus HMR-E resulted in loss of silencing.Mating test of MATα strains to MATa tester strain (JRY2726). Disruption of silencing changed the mating type of the MATa strains to nonmating phenotype of a/α diploid. Two independently constructed S. bayanus hmr-e deletion strains (JRY8785, JRY8786) lost silencing to the same extent as the S. bayanus sir2Δ strain. The parental HMR-E strains (JRY8781, JRY8782) mated as efficiently as the S. cerevisiae control (JRY2728).
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pgen-1000247-g004: Deletion of the S. bayanus HMR-E resulted in loss of silencing.Mating test of MATα strains to MATa tester strain (JRY2726). Disruption of silencing changed the mating type of the MATa strains to nonmating phenotype of a/α diploid. Two independently constructed S. bayanus hmr-e deletion strains (JRY8785, JRY8786) lost silencing to the same extent as the S. bayanus sir2Δ strain. The parental HMR-E strains (JRY8781, JRY8782) mated as efficiently as the S. cerevisiae control (JRY2728).

Mentions: To test if the observed sequence conservation reflected functional conservation, we deleted a 140-bp fragment containing known Abf1p and Rap1p binding sites from the presumptive HMR-E in haploid S. bayanus. The deletion abolished silencing at the HMR locus to the same extent as did deletion of the SIR2 gene (Figure 4). This experiment, together with the in silico observations of the conservation of binding sites and silencer architectures in the HML and HMR silencers, established that the regions from the five species were orthologous and suggested that the DNA flanking the HM loci evolved more rapidly than other intergenic DNA.


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

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

Deletion of the S. bayanus HMR-E resulted in loss of silencing.Mating test of MATα strains to MATa tester strain (JRY2726). Disruption of silencing changed the mating type of the MATa strains to nonmating phenotype of a/α diploid. Two independently constructed S. bayanus hmr-e deletion strains (JRY8785, JRY8786) lost silencing to the same extent as the S. bayanus sir2Δ strain. The parental HMR-E strains (JRY8781, JRY8782) mated as efficiently as the S. cerevisiae control (JRY2728).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000247-g004: Deletion of the S. bayanus HMR-E resulted in loss of silencing.Mating test of MATα strains to MATa tester strain (JRY2726). Disruption of silencing changed the mating type of the MATa strains to nonmating phenotype of a/α diploid. Two independently constructed S. bayanus hmr-e deletion strains (JRY8785, JRY8786) lost silencing to the same extent as the S. bayanus sir2Δ strain. The parental HMR-E strains (JRY8781, JRY8782) mated as efficiently as the S. cerevisiae control (JRY2728).
Mentions: To test if the observed sequence conservation reflected functional conservation, we deleted a 140-bp fragment containing known Abf1p and Rap1p binding sites from the presumptive HMR-E in haploid S. bayanus. The deletion abolished silencing at the HMR locus to the same extent as did deletion of the SIR2 gene (Figure 4). This experiment, together with the in silico observations of the conservation of binding sites and silencer architectures in the HML and HMR silencers, established that the regions from the five species were orthologous and suggested that the DNA flanking the HM loci evolved more rapidly than other intergenic DNA.

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