Widespread occurrence of power-law distributions in inter-repeat distances shaped by genome dynamics

Klimopoulos, Alexandros; Sellis, Diamantis; Almirantis, Yannis

doi:10.1016/j.gene.2012.02.005

Cited by 16 publications

(29 citation statements)

References 67 publications

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“…This treatment is suggested by the finding that, always, the most extended power-laws in inter-repeat distances' size distributions are found excluding the most deteriorated and/or truncated copies. As we discuss later on, this property is in accordance with the model we propose for the generation of fractality and long-rangeness in genomes (see following sections and references [10,11]). …”

Section: Resultssupporting

confidence: 85%

“…Additionally, some cases of full repeat populations are also presented, in order to show the effect of heavily deteriorated TE copies on the observed fractal pattern. The reasons for a maximum divergence (or minimum length) dependent treatment is presented in detail in [10,11] and discussed herein, later on, in relation to the proposed model. The 33 cases of eukaryotic chromosomes we chose to study, exhibit power-law-like distributions of the inter-repeat distances (data from references [10,11]).…”

Section: Genomic Sequences Retrieval and Repeat-coordinates Extractionmentioning

confidence: 99%

“…The reasons for a maximum divergence (or minimum length) dependent treatment is presented in detail in [10,11] and discussed herein, later on, in relation to the proposed model. The 33 cases of eukaryotic chromosomes we chose to study, exhibit power-law-like distributions of the inter-repeat distances (data from references [10,11]). When chromosomes lacking this feature are examined, box-counting and entropic scaling invariably fail to identify any indication of fractality (figures not shown).…”

Section: Genomic Sequences Retrieval and Repeat-coordinates Extractionmentioning

confidence: 99%

“…In previous works we formulated an evolutionary model describing genomic dynamics relevant to TE evolution [10,11]. We here briefly describe the structure of the model and refer the reader to these previous works for a detailed description of the biological background.…”

Section: The "Insertion-elimination Model"mentioning

confidence: 99%

“…The other major class of TEs, DNA transposons, do not go through RNA intermediates during their self-replication. In previous works [10,11] we have shown, by studying the size distribution of inter-repeat distances, that the spatial arrangement of all principal classes of TEs in 14 representative genomes from phylogenetically distant organisms exhibit long-range correlations. Often, these distributions are power-law-like, with their linear region in double logarithmic scale extending up to three orders of magnitude.…”

Section: Introductionmentioning

confidence: 95%

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A Study of Fractality and Long-Range Order in the Distribution of Transposable Elements in Eukaryotic Genomes Using the Scaling Properties of Block Entropy and Box-Counting

Athanasopoulou

Sellis

Almirantis

2014

Entropy

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Repeats or Transposable Elements (TEs) are highly repeated sequence stretches, present in virtually all eukaryotic genomes. We explore the distribution of representative TEs from all major classes in entire chromosomes across various organisms. We employ two complementary approaches, the scaling of block entropy and box-counting. Both converge to the conclusion that well-developed fractality is typical of small genomes while in large genomes it appears sporadically and in some cases is rudimentary. The human genome is particularly prone to develop this pattern, as TE chromosomal distributions therein are often highly clustered and inhomogeneous. Comparing with previous works, where occurrence of power-law-like size distributions in inter-repeat distances is studied, we conclude that fractality in entire chromosomes is a more stringent (thus less often encountered) condition. We have formulated a simple evolutionary scenario for the genomic dynamics of TEs, which may account for their fractal distribution in real genomes. The observed fractality and long-range properties of TE genomic distributions have probably contributed to the formation of the "fractal globule", a model for the confined chromatin organization of the eukaryotic nucleus proposed on the basis of experimental evidence.

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Section: Resultssupporting

confidence: 85%