Intra-Chromosomal Potentials from Nucleosomal Positioning Data

• Published in: arXiv.org
• Main Authors: Li, Kunhe, Nestor Norio Oiwa, Mishra, Sujeet Kumar, Heermann, Dieter W
• Format: Paper Journal Article
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 22.12.2021
• Subjects: Chromosomes; Cluster analysis; Clustering; Compressibility; Genomes; Lennard-Jones potential; Mechanical properties; Optimization; Parameterization; Physics - Biological Physics; Quantitative Biology - Biomolecules; Quantitative Biology - Quantitative Methods; Vector quantization
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.2112.11785

No systematic method exists to derive intra-chromosomal 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 intra-chromosomal 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 has, 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 Candida albicans. This clustering shows that a chromosome beyond the classical dichotomic categories of hetero- and euchromatin, is more feature-rich.