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G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.

Capra JA, Paeschke K, Singh M, Zakian VA - PLoS Comput. Biol. (2010)

Bottom Line: We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures.We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA.The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.

ABSTRACT
G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs) across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs). Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

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The conservation of G4 DNA motifs as a function of the loop length threshold.The number of G4 DNA motifs identified in S. cerevisiae increases as maximum loop length limit is increased (blue line). More than half of the motifs are conserved in at least one other species at each loop threshold (green line). The number of motifs conserved in all sensu stricto species also increases as longer loops are tolerated (red line).
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pcbi-1000861-g003: The conservation of G4 DNA motifs as a function of the loop length threshold.The number of G4 DNA motifs identified in S. cerevisiae increases as maximum loop length limit is increased (blue line). More than half of the motifs are conserved in at least one other species at each loop threshold (green line). The number of motifs conserved in all sensu stricto species also increases as longer loops are tolerated (red line).

Mentions: The number of non-telomeric, nuclear G4 DNA motifs found in the S. cerevisiae genome increased with the maximum length allowed for the loop regions (Fig. 3). For example, there were 54 motifs with all loops less than or equal to 10 nt, and 552 G4 DNA motifs with loops less than or equal to 25 nt. This increasing pattern is similar to that observed in a previous analysis [10] that placed an explicit limit on motif length and did not constrain the loops.


G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.

Capra JA, Paeschke K, Singh M, Zakian VA - PLoS Comput. Biol. (2010)

The conservation of G4 DNA motifs as a function of the loop length threshold.The number of G4 DNA motifs identified in S. cerevisiae increases as maximum loop length limit is increased (blue line). More than half of the motifs are conserved in at least one other species at each loop threshold (green line). The number of motifs conserved in all sensu stricto species also increases as longer loops are tolerated (red line).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2908698&req=5

pcbi-1000861-g003: The conservation of G4 DNA motifs as a function of the loop length threshold.The number of G4 DNA motifs identified in S. cerevisiae increases as maximum loop length limit is increased (blue line). More than half of the motifs are conserved in at least one other species at each loop threshold (green line). The number of motifs conserved in all sensu stricto species also increases as longer loops are tolerated (red line).
Mentions: The number of non-telomeric, nuclear G4 DNA motifs found in the S. cerevisiae genome increased with the maximum length allowed for the loop regions (Fig. 3). For example, there were 54 motifs with all loops less than or equal to 10 nt, and 552 G4 DNA motifs with loops less than or equal to 25 nt. This increasing pattern is similar to that observed in a previous analysis [10] that placed an explicit limit on motif length and did not constrain the loops.

Bottom Line: We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures.We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA.The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.

ABSTRACT
G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs) across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs). Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.

Show MeSH