Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome

Abstract

Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent.

Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes

“…Other studies found that these DNA properties were relevant for key functions of DNA, especially the binding of proteins [ 7 ], including binding affinities for transcription factors [ 8 , 9 , 10 ] and histones [ 11 ], as well as DNA phase separation [ 12 ]. Furthermore, nucleosome occupancy is a determinant of bending properties of chromatin [ 3 , 13 ] and the binding of transcription factors. In addition, transcription factors, such as the transcriptional repressor CTCF, not only regulate the transcription of nearby genes but are also key players in models for chromatin 3D organization (e.g., loop extrusion models [ 14 ]).…”