Hidden Chromosome Symmetry: In Silico Transformation Reveals Symmetry in 2D DNA Walk Trajectories of 671 Chromosomes

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.

Intermittency as a universal characteristic of the complete chromosome DNA sequences of eukaryotes: From protozoa to human genomes

“…As a result, the second Chargaff's parity rule, is just as valid for coding sequences and is totally defined by the gene strand positions. With a gene-vector model, as it has been obtained in [8], the majority of the genes incline to accumulate guanine (G) over cytosine (C) and adenine (A) over thymine (T ).These results supplement the question about stochastic or deterministic nature of evolutionary processes that shape up the observable properties of chromosome sequences, especially, the gene number balance on DNA strands for complete chromosomes. How can this balance exist without any restrictions in the presence of recombinations and random segmental duplications?…”

“…Such regions may arise as a consequence of various mechanisms, including inverse intrachromosomal duplication [21,22], subtelomeres and telomeres repeats, transposon insertions, recombinationcaused strand switches of genes with close compositional structure, strand-specific mutational pressure, etc. The second process reflects the fact that in full-length chromosomes there is a balance in the number of genes on the strands [8], and thus this process represents a statistically confirmed hidden symmetry. As discussed above, the first of the processes can be effectively modeled by the map with type-I intermittency, which is characterized by the presence of a narrow 'tunnel' that produces the global compositional symmetry (Fig.3).…”

“…Copy number variants, segmental duplications and gigantic palindromes compose a class of large-scale DNA duplications in eukaryotic chromosomes. How these polymorphisms coexist with the processes that maintain the regularity of the most important genomic functions and with the global compositional symmetry of chromosomal DNA sequence, and how they are reflected in the complexity of sequence structure poses a question about random and deterministic properties of the complete chro- * Electronic address: rybalko@polly.phys.msu.ru; corresponding author mosome sequences.In our recent paper [8] we examined, by the 2D DNA walk method, large-scale properties of genome sequences of 671 chromosomes of bacteria, archaea, fungi and human. We found that via in silico gene sorting by strand position one can obtain a completely symmetrical form of 2D DNA walk of the coding sequences.…”

“…By adjusting the width and profile of the tunnel in the map (3) it is possible to attain a sufficiently wide variety of generated walks with the inverse-complementary type of sequences (see Fig.4b). As it was shown [8], the 2D DNA walk of real chromosomes can be transformed into a symmetrical trajectory by sorting the genes on strands, and thus, full chromosome sequences contain a hidden symmetry. Based on the discovered symmetrical properties of chromosome sequences, we suggest that in the proposed model the 2D DNA walk of chromosomes can be generally divided into two types of dynamic processes.…”

The Bacterial Chromosomal Sequence and Related Issues

“…It has been reasoned that the difference in frequencies of oligomers in the leading and lagging strands are probably due to different causes such as the distribution of nucleotides in the chromosome, the biased distribution of genes and corresponding regulation signals in the two replicating strands (Rocha, 2004). Another study transformed the gene order and strand position in a chromosome in silico turned the chromosome out to be symmetric (Poptsova et al, 2009). …”