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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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2D DNA graphs of all genes from a chromosome for different organisms.(a) - bacteria (Bacillus anthracis Ames), (b) - archaea (Sulfalobus solfataricus), (c)–fungi (Saccharomyces cerevisiae, chromosome 12), (d) - Homo sapiens (chromosome 8). Trajectories of the genes in the original order are shown on the left, GSS transformed trajectories on the right.
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pone-0006396-g001: 2D DNA graphs of all genes from a chromosome for different organisms.(a) - bacteria (Bacillus anthracis Ames), (b) - archaea (Sulfalobus solfataricus), (c)–fungi (Saccharomyces cerevisiae, chromosome 12), (d) - Homo sapiens (chromosome 8). Trajectories of the genes in the original order are shown on the left, GSS transformed trajectories on the right.

Mentions: 2D DNA walks of most bacterial chromosomes have a symmetrical linear form with one transition point [9] (Figure 1a). Accumulation of one nucleotide compared to its complementary is usually observed on one half of the bacterial chromosome, which corresponds to the 2D DNA trajectory before the transition point. After the transition point the same nucleotide is reduced by the value of its initial accumulation, and the trajectory nearly returns to its starting point. This phenomenon was given the name of compositional asymmetry of bacterial chromosomes, and the property was used in the Oriloc tool [10] for prediction of origins of replication in bacteria. Bacterial compositional asymmetry was explained by compositional asymmetry of leading and lagging strands [11], [12]. In those bacteria, which have a single replication origin, leading and lagging strands are defined at Ori-site in the inverse way, so that one half of a single-stranded DNA is a leading and another is a lagging strand. The leading strand tends to accumulate G over C, while the preference for accumulation of T or A may vary between species.


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)

2D DNA graphs of all genes from a chromosome for different organisms.(a) - bacteria (Bacillus anthracis Ames), (b) - archaea (Sulfalobus solfataricus), (c)–fungi (Saccharomyces cerevisiae, chromosome 12), (d) - Homo sapiens (chromosome 8). Trajectories of the genes in the original order are shown on the left, GSS transformed trajectories on the right.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0006396-g001: 2D DNA graphs of all genes from a chromosome for different organisms.(a) - bacteria (Bacillus anthracis Ames), (b) - archaea (Sulfalobus solfataricus), (c)–fungi (Saccharomyces cerevisiae, chromosome 12), (d) - Homo sapiens (chromosome 8). Trajectories of the genes in the original order are shown on the left, GSS transformed trajectories on the right.
Mentions: 2D DNA walks of most bacterial chromosomes have a symmetrical linear form with one transition point [9] (Figure 1a). Accumulation of one nucleotide compared to its complementary is usually observed on one half of the bacterial chromosome, which corresponds to the 2D DNA trajectory before the transition point. After the transition point the same nucleotide is reduced by the value of its initial accumulation, and the trajectory nearly returns to its starting point. This phenomenon was given the name of compositional asymmetry of bacterial chromosomes, and the property was used in the Oriloc tool [10] for prediction of origins of replication in bacteria. Bacterial compositional asymmetry was explained by compositional asymmetry of leading and lagging strands [11], [12]. In those bacteria, which have a single replication origin, leading and lagging strands are defined at Ori-site in the inverse way, so that one half of a single-stranded DNA is a leading and another is a lagging strand. The leading strand tends to accumulate G over C, while the preference for accumulation of T or A may vary between species.

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