Fractality and entropic scaling in the chromosomal distribution of conserved noncoding elements in the human genome

• The chromosomal distribution of conserved noncoding elements (CNEs) is analyzed.
• CNEs are scattered across chromosomes with intriguing fractal-like patterns.
• Box-counting and scaling of block-entropy quantify the degree of fractality.
• Pronounced fractality is evident in extremely conserved or ancient CNEs.
• An evolutionary model is proposed which accounts for the observed fractality traits.

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.