The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 9 106 to 3.0 9 107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens. The local correlation coefficients show a species-specific multi-scaling behaviour: close to random correlations on the scale of a few base pairs, a first maximum from 40 to 3,400 bp (for Arabidopsis thaliana and Drosophila melanogaster divided in two submaxima), and often a region of one or more second maxima from 105 to 3 9 105 bp. Within this multi-scaling behaviour, an additional fine-structure is present and attributable to codon usage in all except the human sequences, where it is related to nucleosomal binding. Computer-generated random sequences assuming a block organization of genomes, the codon usage, and nucleosomal binding explain these results. Mutation by sequence reshuffling destroyed all correlations. Thus, the stability of correlations seems to be evolutionarily tightly controlled and connected to the spatial genome organization, especially on large scales. In summary, genomes show a complex sequential organization related closely to their three-dimensional organization.

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Keywords *Genome, Algorithms, Animals, Arabidopsis/genetics, Chromosomes, Fungal/chemistry/genetics/ultrastructure, Chromosomes, Human/chemistry/genetics/ultrastructure, Chromosomes, Plant/chemistry/genetics/ultrastructure, Chromosomes/*chemistry/genetics/*ultrastructure, Codon/chemistry, Computer Simulation, DNA sequence classification, DNA/*chemistry, Drosophila melanogaster/genetics, Humans, Models, Genetic, Mutation, Nucleosomes/chemistry, Saccharomyces cerevisiae/genetics, Schizosaccharomyces/genetics, Sequence Analysis, DNA, genome organization, long-range correlations, nuclear architecture, scaling analysis
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Journal European Biophysics Journal
Knoch, T.A, Göcker, M, Lohner, R, Abuseiris, A, & Grosveld, F.G. (2009). Fine-structured multi-scaling long-range correlations in completely sequenced genomes - features, origin and classification.. European Biophysics Journal, 38(6), 757–779. doi:10.1007/s00249-009-0489-y