Universal internucleotide statistics in full genomes: a footprint of the DNA structure and packaging?

Uncovering the fundamental laws that govern the complex DNA structural organization remains challenging and is largely based upon reconstructions from the primary nucleotide sequences. Here we investigate the distributions of the internucleotide intervals and their persistence properties in complete...

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Published inPloS one Vol. 9; no. 12; p. e112534
Main Authors Bogachev, Mikhail I, Kayumov, Airat R, Bunde, Armin
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 01.12.2014
Public Library of Science (PLoS)
Subjects
Archaea
Bacteria
Base Sequence
Biology and Life Sciences
Computer and Information Sciences
Databases, Genetic
Deoxyribonucleic acid
DNA
DNA Packaging
DNA structure
DNA, Archaeal - genetics
DNA, Bacterial - genetics
Eukaryotes
Evolution
Exponential functions
Gene expression
Genome, Archaeal - genetics
Genome, Bacterial - genetics
Genomes
Genomics
Humans
Molecular Sequence Data
Nucleotides - genetics
Physical Sciences
Prokaryotes
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Summary:Uncovering the fundamental laws that govern the complex DNA structural organization remains challenging and is largely based upon reconstructions from the primary nucleotide sequences. Here we investigate the distributions of the internucleotide intervals and their persistence properties in complete genomes of various organisms from Archaea and Bacteria to H. Sapiens aiming to reveal the manifestation of the universal DNA architecture. We find that in all considered organisms the internucleotide interval distributions exhibit the same [Formula: see text]-exponential form. While in prokaryotes a single [Formula: see text]-exponential function makes the best fit, in eukaryotes the PDF contains additionally a second [Formula: see text]-exponential, which in the human genome makes a perfect approximation over nearly 10 decades. We suggest that this functional form is a footprint of the heterogeneous DNA structure, where the first [Formula: see text]-exponential reflects the universal helical pitch that appears both in pro- and eukaryotic DNA, while the second [Formula: see text]-exponential is a specific marker of the large-scale eukaryotic DNA organization.
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Competing Interests: The authors have declared that no competing interests exist.
Conceived and designed the experiments: MB AK AB. Performed the experiments: MB AK AB. Analyzed the data: MB AK AB. Contributed reagents/materials/analysis tools: MB AK AB. Wrote the paper: MB AK AB.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0112534