Inter-nucleosomal potentials from nucleosomal positioning data

Abstract

No systematic method exists to derive inter-nucleosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical properties of chromosomes. Thus, indirectly, they shed light on a possible mechanical genomic code along a chromosome. To develop a method yielding effective inter-nucleosomal potentials between nucleosomes, a generalized Lennard-Jones potential for the parameterization is developed based on nucleosomal positioning data. This approach eliminates some of the problems that the underlying nucleosomal positioning data have, rendering the extraction difficult on the individual nucleosomal level. Furthermore, patterns on which to base a classification along a chromosome appear on larger domains, such as hetero- and euchromatin. An intuitive selection strategy for the noisy optimization problem is employed to derive effective exponents for the generalized potential. The method is tested on the Candida albicans genome. Applying k-means clustering based on potential parameters and thermodynamic compressibilities, a genome-wide clustering of nucleosome sequences is obtained for C. albicans. This clustering shows that a chromosome beyond the classical dichotomic categories of hetero- and euchromatin is more feature-rich.

Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes

“…As passive elements incorporated into DNA sequences, dinucleotides may have become relevant players for 3D chromatin folding and spatial organization. Assuming that further studies support our hypothesis, dinucleotide contents might have strong impact on nucleosome positioning and accordingly on inter-nucleosomal potentials [ 33 ], thus indirectly influencing 3D chromatin organization, together with epigenetic interactions, to form a powerful control system for genome functioning [ 34 ].…”