Position-specific deformation pattern of the nucleosome DNA revealed by principal component analysis and sequence alignment-based statistics

The anisotropic deformation of nucleosome DNA during its bending into a superhelix implies that its constituent parts have different geometrical settings. In order to establish the relationship between the position and deformation characteristics, a nucleosome structural database is constructed and studied using principal component analysis to obtain the principal conformational subspace (PCS). For each nucleosome DNA sequence, the regions with high scores in PCS are regarded as special structural contributors and the corresponding positions are recorded and classified. By using sequence alignment-based statistics, the positions which have a high probability of acting as structural contributors are finally determined. The result shows that there is a high consistency as to the position-specific structural contribution to the overall superhelix among the crystal structures of nucleosome DNA.