A Survey on Structural Analysis of Nucleosome Core Particles

Xi      Yang; Weiqiang      Zhou; Debby      D. Wang; Qinqin      Wu; Hong      Yan

doi:10.2174/1574893611308010016

Abstract

The histone octamer induced bending of DNA into the superhelix structure in nucleosome core particle is important for DNA packing into chromatin, which is directly associated with gene expression and transcription regulation. In this paper, we review current computational methodologies of nucleosome positioning signal recognition based on the sequence and structural features. Sequence-based methods can be effectively applied to genomic nucleosome mapping and genomic texture analysis around the nucleosome regions. The nucleosomal region has been proved to be more flexible than its surrounding regions. Structure-based methods incorporate physical and stereochemical properties of DNA molecules and employ signal processing and pattern recognition techniques to identify the structural significance hidden in the regularity of sequence composition. The special structural information of the specific dinucleotides in the nucleosome structure indicates their important roles in the formation of nucleosome complex. CA/TG shows the greatest flexibility in the structural variation along the DNA path, thus playing the role of “hinge” in the bending of DNA into superhelix. AA/TT and GC, on the other hand, have the highest probability of closely contacting with histone and play the role of facilitating nucleosome positioning.

Keywords: Alpha-shape model, dimensionality reduction, DNA stereochemical properties, nucleosome positioning, sequence features, statistical analysis, hinge, Matched Mirror Position Filtering, Sequence-Dependent DNA Flexibility Models, Nucleosome Core Particle Crystals