Compositional segmentation and long-range fractal correlations in DNA sequences

Bernaola‐Galván, Pedro; Román-Roldán, Ramón; Oliver, José Luis Tejera

doi:10.1103/physreve.53.5181

Cited by 187 publications

(225 citation statements)

References 25 publications

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“…During the past ten years, there has been intense discussion about the existence, the nature and the origin of LRC in DNA sequences. Besides Fourier and autocorrelation analysis, different techniques including mutual information functions [61,71,77,78], DNA walk representation [64,75,79,80,81,82,83,84], Zipf analysis [85,86,87] and entropies [88,89,90,91] were used for statistical analysis of DNA sequences. A lot of effort has been spent to adress rather struggling questions.…”

Section: Introductionmentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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Section: Introductionmentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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“…Among these, nonextensive properties (nonlinearities) at nanoscale as a likely possibility would be mentioned. In fact, some evidence in this direction could be inferred from [4].…”

Section: Introductionmentioning

confidence: 99%

“…In this regard, it is noted that there are several studies in the literature showing nonlinear aspects of DNA molecule [18]. For instance, studies of long-range correlations in DNA indicate that the length (L) of homogeneous sequences in noncoding regions obeys a power-law-type distribution (a fingerprint for nonextensiveness), while in widely encoded regions these distributions are exponential [4].…”

Section: Introductionmentioning

confidence: 99%

Fragmentation of Plasmid DNA Produced by Gamma Radiation: A Theoretical Approach

2012

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Breaks in DNA, resulting in fragmented parts, can be produced by ionizing radiation which, in turn, is the starting point in the search for novel physical aspects of DNA strands. Double-strand breaks in particular cause disruption of the DNA strand, splitting it into several fragments. In order to study effects produced by radiation in plasmid DNA, a new simple mechanical model for this molecule is proposed. In this model, a Morse-like potential and a high-LET component are used to describe the DNA-radiation interaction. Two power laws, used to fit results of the model, suggest that, firstly, distribution of fragment size is nonextensive and, secondly, that a transition phase is present in the DNA fragment distribution pattern.

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“…This is al- ready true in systems as small as the DNA molecule [7], to those as large as galaxy conglomerates [8]. Taylor's Power Law, with its fractionary exponent β (see Equation (1)), is inserted in this nonextensive/nonlinear scenario.…”

Section: Complex Nonextensive Systemsmentioning

confidence: 99%

Taylor’s Power Law for Ecological Communities—An Explanation on Nonextensive/Nonlinear Statistical Grounds

Arruda‐Neto¹,

Righi²,

Cascino³

et al. 2014

JAMP

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A new idea on how to conceptually interpret the so-called Taylor's power law for ecological communities is presented. The core of our approach is based on nonextensive/nonlinear statistical concepts, which are shown to be at the genesis of all power laws, particularly when a system is constituted by long-range interacting elements. In this context, the ubiquity of the Taylor's power law is discussed and addressed by showing that long-range interactions are at the heart of the internal dynamics of populations.

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Compositional segmentation and long-range fractal correlations in DNA sequences

Cited by 187 publications

References 25 publications

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Fragmentation of Plasmid DNA Produced by Gamma Radiation: A Theoretical Approach

Taylor’s Power Law for Ecological Communities—An Explanation on Nonextensive/Nonlinear Statistical Grounds

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