title: Scaling properties and fractality in the distribution of coding segments in eukaryotic genomes revealed through a block entropy approach.
abstract: Statistical methods, including block entropy based approaches, have already been used in the study of long-range features of genomic sequences seen as symbol series, either considering the full alphabet of the four nucleotides or the binary purine or pyrimidine character set. Here we explore the alternation of short protein-coding segments with long noncoding spacers in entire chromosomes, focusing on the scaling properties of block entropy. In previous studies, it has been shown that the sizes of noncoding spacers follow power-law-like distributions in most chromosomes of eukaryotic organisms from distant taxa. We have developed a simple evolutionary model based on well-known molecular events (segmental duplications followed by elimination of most of the duplicated genes) which reproduces the observed linearity in log-log plots. The scaling properties of block entropy H(n) have been studied in several works. Their findings suggest that linearity in semilogarithmic scale characterizes symbol sequences which exhibit fractal properties and long-range order, while this linearity has been shown in the case of the logistic map at the Feigenbaum accumulation point. The present work starts with the observation that the block entropy of the Cantor-like binary symbol series scales in a similar way. Then, we perform the same analysis for the full set of human chromosomes and for several chromosomes of other eukaryotes. A similar but less extended linearity in semilogarithmic scale, indicating fractality, is observed, while randomly formed surrogate sequences clearly lack this type of scaling. Genomic sequences always present entropy values much lower than their random surrogates. Symbol sequences produced by the aforementioned evolutionary model follow the scaling found in genomic sequences, thus corroborating the conjecture that "segmental duplication-gene elimination" dynamics may have contributed to the observed long rangeness in the coding or noncoding alternation in genomes.
authors.affiliation: Institute of Biology, NRCPS Demokritos, 15310 Athens, Greece.
authors.forename: Labrini
authors.initials: L
authors.lastname: Athanasopoulou
authors.forename: Stavros
authors.initials: S
authors.lastname: Athanasopoulos
authors.forename: Kostas
authors.initials: K
authors.lastname: Karamanos
authors.forename: Yannis
authors.initials: Y
authors.lastname: Almirantis
mesh_terms: D000818:Animals; D002417:Cattle; D002875:Chromosomes / Q000235:genetics; D019277:Entropy; D056890:Eukaryota / Q000235:genetics*; D017709:Fractals; D020440:Gene Duplication; D023281:Genomics; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D016366:Open Reading Frames / Q000235:genetics*; D011336:Probability; D051381:Rats; D013269:Stochastic Processes