Statistical investigation of position-specific deformation pattern of nucleosome DNA based on multiple conformational properties

The histone octamer induced bending of DNA into the super-helix structure in nucleosome core particle, is very unique and vital for DNA packing into chromatin. We collected 48 nucleosome crystal structures from PDB and applied a multivariate analysis on the nucleosome structural data. Based on the anisotropic nature of DNA structure, a principal conformational subspace (PCS) is derived from multiple properties to represent the most significant variances of nucleosome DNA structures. The coupling of base pair-oriented parameters with sugar phosphate backbone parameters presented in principal dimensionalities reveals two main deformation modes that have supplemented the existing physical model. By using sequence alignment-based statistics, a position-dependent conformational map for the super-helical DNA path is established. The result shows that the crystal structures of nucleosome DNA have much consistency in position-specific structural varitions and certain periodicity is found to exist in these variations. Thus, the positions with obvious deformation patterns along the DNA path in nucleosome core particle are relatively conservative from the perspective of statistics.