Limits...
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.

Show MeSH
Conservation of the HMR-E silencer in five sensu stricto species.Multiple alignment of the putative HMR-E silencer in the five sensu stricto species. There was strong conservation among all of the species of the Rap1 and Abf1 binding sites (shaded) and the spacing between them, with diverged intervening sequence from the Rap1 site to the Abf1 site. Similarly, even though the distance from the Abf1 site to HMR was identical in S. cerevisiae and S. paradoxus, DNA-level pairwise alignment of the region gave only 55% identity (Figure S1).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2570616&req=5

pgen-1000247-g003: Conservation of the HMR-E silencer in five sensu stricto species.Multiple alignment of the putative HMR-E silencer in the five sensu stricto species. There was strong conservation among all of the species of the Rap1 and Abf1 binding sites (shaded) and the spacing between them, with diverged intervening sequence from the Rap1 site to the Abf1 site. Similarly, even though the distance from the Abf1 site to HMR was identical in S. cerevisiae and S. paradoxus, DNA-level pairwise alignment of the region gave only 55% identity (Figure S1).

Mentions: We determined that the flanking sequences in the five species were indeed orthologous by analyzing conservation of the silencers that have been identified in S. cerevisiae. In three of the four cases (HMR-E, HMR-I, HML-I), there was clear conservation of the known functional binding sites in the silencers, despite the low sequence similarity throughout the intergenic regions. To the right of HML, an Abf1 binding site was present 319–321 base pairs past the HMLα1 stop codon in all five species. At HMR-I, the sequence of the Rap1 and Abf1 binding sites, their orientation, distance to HMR, and spacing between the binding sites were conserved between S. cerevisiae and S. paradoxus. Similarly, the Abf1 and Rap1 binding sites in HMR-E were conserved in all five species, with virtually the same spacing between the sites (39–43 bp), and the distance to HMR was identical in S. paradoxus and S. cerevisiae (Figure 3, Figure S2).


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

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

Conservation of the HMR-E silencer in five sensu stricto species.Multiple alignment of the putative HMR-E silencer in the five sensu stricto species. There was strong conservation among all of the species of the Rap1 and Abf1 binding sites (shaded) and the spacing between them, with diverged intervening sequence from the Rap1 site to the Abf1 site. Similarly, even though the distance from the Abf1 site to HMR was identical in S. cerevisiae and S. paradoxus, DNA-level pairwise alignment of the region gave only 55% identity (Figure S1).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000247-g003: Conservation of the HMR-E silencer in five sensu stricto species.Multiple alignment of the putative HMR-E silencer in the five sensu stricto species. There was strong conservation among all of the species of the Rap1 and Abf1 binding sites (shaded) and the spacing between them, with diverged intervening sequence from the Rap1 site to the Abf1 site. Similarly, even though the distance from the Abf1 site to HMR was identical in S. cerevisiae and S. paradoxus, DNA-level pairwise alignment of the region gave only 55% identity (Figure S1).
Mentions: We determined that the flanking sequences in the five species were indeed orthologous by analyzing conservation of the silencers that have been identified in S. cerevisiae. In three of the four cases (HMR-E, HMR-I, HML-I), there was clear conservation of the known functional binding sites in the silencers, despite the low sequence similarity throughout the intergenic regions. To the right of HML, an Abf1 binding site was present 319–321 base pairs past the HMLα1 stop codon in all five species. At HMR-I, the sequence of the Rap1 and Abf1 binding sites, their orientation, distance to HMR, and spacing between the binding sites were conserved between S. cerevisiae and S. paradoxus. Similarly, the Abf1 and Rap1 binding sites in HMR-E were conserved in all five species, with virtually the same spacing between the sites (39–43 bp), and the distance to HMR was identical in S. paradoxus and S. cerevisiae (Figure 3, Figure S2).

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