Figure 1.
The G4 DNA structure and motif.
(A) Structure of a G-quartet. The planar ring of four hydrogen-bonded guanines is formed by guanines from different G-tracts, which are separated by intervening loop regions in the intra-molecular G4 DNA structure. (B) Schematic of an intra-molecular G4 DNA structure consisting of three G-quartets. Inter-molecular G4 DNA structures can also form from two or four strands. (C) The G4 DNA motif sequence used in this study with four G-tracts of three guanines separated by loop regions.
Figure 2.
The evolutionary conservation of G4 DNA motifs between S. cerevisiae and six related yeast species.
(A) The phylogenetic tree for the seven yeast species considered in this study (not to scale). The four sensu stricto species (S. paradoxus, S. mikatae, S. kudriavzevii, S. bayanus) diverged from S. cerevisiae within the last ∼20 million years. S. castelli and S. kluyveri are considerably more distant [21]. The percent sequence identity to S. cerevisiae over the alignable regions is given in parentheses. (B) The evolutionary conservation of the 507 non-telomeric, nuclear S. cerevisiae G4 DNA motifs in sequence regions that could be aligned to at least one other genome. Significantly more G4 DNA motifs were conserved than expected by chance between S. cerevisiae and five of the six species considered. The one exception was S. kluyveri, which is the most distant and GC-rich species among the seven yeasts.
Table 1.
Number of G4 DNA motifs found in each species.
Figure 3.
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).
Table 2.
Conservation of G4 DNA Motif Nucleotides.
Figure 4.
The distribution of G4 DNA motifs across the S. cerevisiae nuclear genome.
Each small circle represents the location of a G4 DNA motif in a chromosome. Motifs conserved across the sensu stricto species are highlighted in red.
Table 3.
Comparison of the length and physical properties of all nuclear, non-telomeric G4 DNA motifs in S. cerevisiae with those conserved across the sensu stricto species.
Table 4.
Significant associations between genome features and G4 DNA motifs.
Figure 5.
The distribution of G4 DNA motifs across the S. cerevisiae mitochondrial DNA.
The horizontal black line represents the 75kb mtDNA genome. The rectangles above mark the location of tRNA genes (green), rRNA genes (red), and ORFs (blue). ORFs that encode multiple genes (like COX1, subunit I of cytochrome c oxidase) are drawn as a single rectangle. The vertical black lines below indicate the location of the 32 G4 DNA motifs across the mtDNA. The width of these lines reflects the actual length of the G4 DNA motif. (Note that several motifs are so close that they overlap in the figure.) All motifs are drawn below the mtDNA sequence regardless of the strand on which they occur. The distribution of mitochondiral G4 DNA motifs is biased against overlapping these genomic features; only two of the 32 motifs overlap a tRNA, rRNA, or ORF (q<0.001).
Figure 6.
G4 DNA motifs form G4 DNA structures in vitro.
(A) Characterization of the five experimentally tested G4 DNA motifs. The motifs were selected to represent a range of genome locations and conditions. (B) Circular dichroism analysis of the three of the five G4 DNA motifs tested demonstrates that they form parallel G4 DNA structures. The G4 motif tested is indicated by the chromosome number above the graph. (C) Native acrylamide gel comparing the migration of oligonucleotides before and after the formation of the G4 DNA structure. The G4 DNA structure (indicated by the cartoon on the right) migrates more slowly than linear DNA. The G4 motif tested is indicated by the chromosome number beneath the gel.