Inter-nucleosomal potentials from nucleosomal positioning data

• Published in: The European physical journal. E, Soft matter and biological physics Vol. 45; no. 4; p. 33
• Main Authors: Li, Kunhe, Oiwa, Nestor Norio, Mishra, Sujeet Kumar, Heermann, Dieter W.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.04.2022; Springer Nature B.V
• Subjects: Biological and Medical Physics; Biophysics; Chromosomes; Cluster analysis; Clustering; Complex Fluids and Microfluidics; Complex Systems; Compressibility; Condensed matter physics; Euchromatin; Genomes; Lennard-Jones potential; Mechanical properties; Nanotechnology; Nucleosomes - genetics; Optimization; Parameterization; Physics; Physics and Astronomy; Polymer Sciences; Regular - Living Systems; Regular Article - Living Systems; Soft and Granular Matter; Surfaces and Interfaces; Thermodynamics; Thin Films; Vector quantization
• ISSN: 1292-8941; 1292-895X
• DOI: 10.1140/epje/s10189-022-00185-3

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.