Next Article in Journal
District Heating Mode Analysis Based on an Air-cooled Combined Heat and Power Station
Previous Article in Journal
An Entropy-Based Contagion Index and Its Sampling Properties for Landscape Analysis
Article Menu

Export Article

Open AccessArticle
Entropy 2014, 16(4), 1860-1882; doi:10.3390/e16041860

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

1
Department of Τheoretical Physics, Jožef Stefan Institute, SI-1000, Ljubljana, Slovenia
2
Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
3
Institute of Biosciences and Applications, NCSR "Demokritos" 15310 Athens, Greece
*
Author to whom correspondence should be addressed.
Received: 11 December 2013 / Revised: 5 February 2014 / Accepted: 13 March 2014 / Published: 26 March 2014
View Full-Text   |   Download PDF [2071 KB, uploaded 24 February 2015]   |  

Abstract

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. View Full-Text
Keywords: fractality; block-entropy; Shannon entropy; entropic scaling; box-counting; power-law distribution; genome evolution; transposable elements; eukaryotic genome fractality; block-entropy; Shannon entropy; entropic scaling; box-counting; power-law distribution; genome evolution; transposable elements; eukaryotic genome
Figures

This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Athanasopoulou, L.; Sellis, D.; Almirantis, Y. 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. Entropy 2014, 16, 1860-1882.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Entropy EISSN 1099-4300 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top