title: Fractality and entropic scaling in the chromosomal distribution of conserved noncoding elements in the human genome.
abstract: Conserved non-coding elements (CNEs) are defined using various degrees of sequence identity and thresholds of minimal length. Their conservation frequently exceeds the one observed for protein-coding sequences. We explored the chromosomal distribution of different classes of CNEs in the human genome. We employed two methodologies: the scaling of block entropy and box-counting, with the aim to assess fractal characteristics of different CNE datasets. Both approaches converged to the conclusion that well-developed fractality is characteristic of elements that are either extremely conserved between species or are of ancient origin, i.e. conserved between distant organisms across evolution. Given that CNEs are often clustered around genes, we verified by appropriate gene masking that fractal-like patterns emerge even when elements found in proximity or inside genes are excluded. An evolutionary scenario is proposed, involving genomic events that might account for fractal distribution of CNEs in the human genome as indicated through numerical simulations.
authors.affiliation: Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310 Athens, Greece.
authors.forename: Dimitris
authors.initials: D
authors.lastname: Polychronopoulos
authors.affiliation: Department of Τheoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia.
authors.forename: Labrini
authors.initials: L
authors.lastname: Athanasopoulou
authors.affiliation: Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310 Athens, Greece. Electronic address: yalmir@bio.demokritos.gr.
authors.forename: Yannis
authors.initials: Y
authors.lastname: Almirantis
mesh_terms: D002877:Chromosomes, Human; D019277:Entropy; D017709:Fractals; D015894:Genome, Human; D006801:Humans
keywords: Block-entropy; Box-counting; CNE; Conserved noncoding elements; Entropic scaling; Fractality; Shannon entropy; Ultraconserved elements