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Hidden chromosome symmetry: in silico transformation reveals symmetry in 2D DNA walk trajectories of 671 chromosomes.

Poptsova MS, Larionov SA, Ryadchenko EV, Rybalko SD, Zakharov IA, Loskutov A - PLoS ONE (2009)

Bottom Line: This is also true for human coding sequences (CDS), which comprise only several percent of the entire chromosome length.We found that frequency distributions of the length of gene clusters, continuously located on the same strand, have close values for both strands.Contribution of different subsystems to the noted symmetries and distributions, and evolutionary aspects of symmetry are discussed.

View Article: PubMed Central - PubMed

Affiliation: University of Connecticut, Storrs, Connecticut, United States of America. maria.poptsova@gmail.com

ABSTRACT
Maps of 2D DNA walk of 671 examined chromosomes show composition complexity change from symmetrical half-turn in bacteria to pseudo-random trajectories in archaea, fungi and humans. In silico transformation of gene order and strand position returns most of the analyzed chromosomes to a symmetrical bacterial-like state with one transition point. The transformed chromosomal sequences also reveal remarkable segmental compositional symmetry between regions from different strands located equidistantly from the transition point. Despite extensive chromosome rearrangement the relation of gene numbers on opposite strands for chromosomes of different taxa varies in narrow limits around unity with Pearson coefficient r = 0.98. Similar relation is observed for total genes' length (r = 0.86) and cumulative GC (r = 0.95) and AT (r = 0.97) skews. This is also true for human coding sequences (CDS), which comprise only several percent of the entire chromosome length. We found that frequency distributions of the length of gene clusters, continuously located on the same strand, have close values for both strands. Eukaryotic gene distribution is believed to be non-random. Contribution of different subsystems to the noted symmetries and distributions, and evolutionary aspects of symmetry are discussed.

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Cluster model of chromosome organization.(a)–chromosome clusters after GSS transformation, (b)–chromosome clusters in the original order.
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pone-0006396-g004: Cluster model of chromosome organization.(a)–chromosome clusters after GSS transformation, (b)–chromosome clusters in the original order.

Mentions: An illustration of GSS transformation algorithm that leads to a symmetrical effect on 2D DNA walk map is given in Figure 4. Symmetrically correlated regions are drawn in the same color. If we observe correlated symmetry of regions (composed of genes or gene clusters) located equidistantly from the transition point (Figure 4A), then the position of genes (gene clusters) in the original order in chromosome should comply with Figure 4B. Figure 5 shows examples of emerging correlated symmetry for two chromosomes of Saccharomyces cerevisiae and one of Encephalitozoon cuniculi. Ellipses highlight symmetrically correlated areas located on the opposite strands. After GSS transformation some of these regions form the so-called strand “metasequences” that show correlated symmetrical properties of a 2D DNA walk trajectory (Figure 5). Some of these regions contain BLAST hits (Table S2) of the whole genes or domains, but some (regions 3 and 4 for Saccharomyces cerevisiae, chrom. 1 (Figure 5b) and region 2 of Encephalitozoon cuniculi, chrom. X (Figure 5f)) do not have any hits. Cases of intra-chromosomal duplications in subtelomeric regions in fungi were reported in [32], and region 1 in Saccharomyces cerevisiae, chrom. 1 (Figure 5b) contain such an example of duplication of flo-family genes. Regions that do not have significant BLAST hits may still represent the remnants of duplicated areas. As it was pointed out in [32], a significant part of the duplications in fungi could be concealed as a result of an intensive mutation process. Correlated areas of 2D DNA walk maps may potentially reveal cases of unrecoginzed paralogy, and detected hits, however scarce, could serve as seeds for distant similarity searches. We can see that correlated sequences in a GSS-transformed trajectory are more often located equidistantly from the transition point. However some of the symmetrical pairs have one site close to the transition point and another at the beginning or in the end of the chromosome sequence. One of the possible explanations for such symmetry is that it could emerge as a result of duplication, which takes place during the recombination process in subtelomeric sites of repeats. This type of duplication can organize paralogs distantly and also locally, in a palindromic way on different strands. However, correlated areas located in the central regions of the GSS transformed trajectories could be a result of a similar compositional structure of a locus, from where the genes from the different strands were separated. A region in Saccharomyces cerevisiae, highlighted with a green ellipse, indicates an area where the trajectory sharply changes direction (Fig. 5B). This particular region corresponds to a retrotransposon and is indicative of insertion. In general, the regions where DNA trajectory deviates from the common direction may potentially contain recently horizontally transferred genes [33], [34].


Hidden chromosome symmetry: in silico transformation reveals symmetry in 2D DNA walk trajectories of 671 chromosomes.

Poptsova MS, Larionov SA, Ryadchenko EV, Rybalko SD, Zakharov IA, Loskutov A - PLoS ONE (2009)

Cluster model of chromosome organization.(a)–chromosome clusters after GSS transformation, (b)–chromosome clusters in the original order.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2712679&req=5

pone-0006396-g004: Cluster model of chromosome organization.(a)–chromosome clusters after GSS transformation, (b)–chromosome clusters in the original order.
Mentions: An illustration of GSS transformation algorithm that leads to a symmetrical effect on 2D DNA walk map is given in Figure 4. Symmetrically correlated regions are drawn in the same color. If we observe correlated symmetry of regions (composed of genes or gene clusters) located equidistantly from the transition point (Figure 4A), then the position of genes (gene clusters) in the original order in chromosome should comply with Figure 4B. Figure 5 shows examples of emerging correlated symmetry for two chromosomes of Saccharomyces cerevisiae and one of Encephalitozoon cuniculi. Ellipses highlight symmetrically correlated areas located on the opposite strands. After GSS transformation some of these regions form the so-called strand “metasequences” that show correlated symmetrical properties of a 2D DNA walk trajectory (Figure 5). Some of these regions contain BLAST hits (Table S2) of the whole genes or domains, but some (regions 3 and 4 for Saccharomyces cerevisiae, chrom. 1 (Figure 5b) and region 2 of Encephalitozoon cuniculi, chrom. X (Figure 5f)) do not have any hits. Cases of intra-chromosomal duplications in subtelomeric regions in fungi were reported in [32], and region 1 in Saccharomyces cerevisiae, chrom. 1 (Figure 5b) contain such an example of duplication of flo-family genes. Regions that do not have significant BLAST hits may still represent the remnants of duplicated areas. As it was pointed out in [32], a significant part of the duplications in fungi could be concealed as a result of an intensive mutation process. Correlated areas of 2D DNA walk maps may potentially reveal cases of unrecoginzed paralogy, and detected hits, however scarce, could serve as seeds for distant similarity searches. We can see that correlated sequences in a GSS-transformed trajectory are more often located equidistantly from the transition point. However some of the symmetrical pairs have one site close to the transition point and another at the beginning or in the end of the chromosome sequence. One of the possible explanations for such symmetry is that it could emerge as a result of duplication, which takes place during the recombination process in subtelomeric sites of repeats. This type of duplication can organize paralogs distantly and also locally, in a palindromic way on different strands. However, correlated areas located in the central regions of the GSS transformed trajectories could be a result of a similar compositional structure of a locus, from where the genes from the different strands were separated. A region in Saccharomyces cerevisiae, highlighted with a green ellipse, indicates an area where the trajectory sharply changes direction (Fig. 5B). This particular region corresponds to a retrotransposon and is indicative of insertion. In general, the regions where DNA trajectory deviates from the common direction may potentially contain recently horizontally transferred genes [33], [34].

Bottom Line: This is also true for human coding sequences (CDS), which comprise only several percent of the entire chromosome length.We found that frequency distributions of the length of gene clusters, continuously located on the same strand, have close values for both strands.Contribution of different subsystems to the noted symmetries and distributions, and evolutionary aspects of symmetry are discussed.

View Article: PubMed Central - PubMed

Affiliation: University of Connecticut, Storrs, Connecticut, United States of America. maria.poptsova@gmail.com

ABSTRACT
Maps of 2D DNA walk of 671 examined chromosomes show composition complexity change from symmetrical half-turn in bacteria to pseudo-random trajectories in archaea, fungi and humans. In silico transformation of gene order and strand position returns most of the analyzed chromosomes to a symmetrical bacterial-like state with one transition point. The transformed chromosomal sequences also reveal remarkable segmental compositional symmetry between regions from different strands located equidistantly from the transition point. Despite extensive chromosome rearrangement the relation of gene numbers on opposite strands for chromosomes of different taxa varies in narrow limits around unity with Pearson coefficient r = 0.98. Similar relation is observed for total genes' length (r = 0.86) and cumulative GC (r = 0.95) and AT (r = 0.97) skews. This is also true for human coding sequences (CDS), which comprise only several percent of the entire chromosome length. We found that frequency distributions of the length of gene clusters, continuously located on the same strand, have close values for both strands. Eukaryotic gene distribution is believed to be non-random. Contribution of different subsystems to the noted symmetries and distributions, and evolutionary aspects of symmetry are discussed.

Show MeSH
Related in: MedlinePlus