Fig 1.
The relationship between (A) a DNA or RNA sequence, (B) a G-tetrad, and (C) the tertiary structure of a G4.
Fig 2.
Three types of information available in sequences identified by Quadparser.
This information is represented in a sequence code taking the form x:y:z. For each type, example sequences are displayed on the right along with their associated sequence code on the left. Red boxes indicate the position holding that particular information in the sequence code.
Table 1.
The number of putative G4 sequences and the percentage identified with different numbers of guanine tracts.
Table 2.
The number of putative G4 sequences and the percentage of total sequences identified that would support the formation of one G4 or the simultaneous formation of multiple G4.
Fig 3.
Pattern of G4 sequence density across DNA strands in relation to gene transcripts on each strand.
The number of G4 sequences per megabase for the forward strand (green, top) and the reverse strand (blue, bottom) is displayed as a histogram above and below each chromosome. Gene transcripts are displayed inside of each chromosome in corresponding strand colors. Gaps in the reference assembly are represented in black. Centromeres appear in orange.
Table 3.
Mean guanine and cytosine bases (GC) and G4 sequences per 100,000 bases for each cytoband category.
The categories gneg (lightest), gpos25, gpos50, gpos75, and gpos100 (darkest) refer to the level of staining achieved. The gvar category refers to areas that tend to be heterochromatic. The acen category refers to centromeric regions. The stalk category refers to the short arm of acrocentric chromosomes.
Fig 4.
Boxplots representing the range of correlation between the number of G4 sequences on the forward and reverse strands for all chromosomes at different bin sizes.
The boxes represent the 25th to 75th percentile, and the end of each line is either the end of the data range or 1.5 of the interquartile range. Dots extending beyond the lines are correlations considered outliers.
Fig 5.
Boxplots representing the range of distances on a log10 scale between G4 sequences across all chromosomes and for each strand (represented as a + for the forward strand and a − for the reverse strand).
Gaps in the reference assembly are subtracted from all distance measures where they occur. The boxes represent the 25th to 75th percentile, and the end of each line is either the end of the data range or 1.5 of the interquartile range. Dots extending beyond the lines are distances considered outliers for that chromosome.
Fig 6.
Boxplots representing the range of distances for the highest density megabase interval, measured as the shortest distance to one end of a chromosome, for G4, gene transcripts, transcription factor binding sites (TFBS), and histone binding sites (HBS).
The boxes represent the 25th to 75th percentile, and the end of each line is either the end of the data range or 1.5 of the interquartile range. Dots extending beyond the lines are distances considered outliers for that range of distances.
Fig 7.
The fifty DNA binding proteins on each chromosome with the greatest number of DNA protein binding sites overlapping G4 sequences.
Numbers indicate the rank for a particular DNA binding protein with 1 indicating the highest number of binding sites on a chromosome (darker red) and 50 indicating the lowest number on a chromosome (white).
Fig 8.
Comparison of Sen and Gilbert (A) to chromosome 1 observations (B).
In part A, sister chromatids are attached to the nuclear envelope during meiosis. G-rich bands (A,A’,B,B’,C,C’) serve to align the chromosomes. In part B, highly correlated G4 sequence banding patterns are found along both DNA strands on chromosome 1. Part A reprinted by permission from Macmillan Publishers Ltd: NATURE (Sen and Gilbert 1988), copyright (1988).