Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness

A model has been derived that accounts for the nucleosome translational position in terms of the bending free energy that depends on the nearest-neighbor interactions between base-pairs. The available data on the nucleosome positioning on defined DNA sequences in the reconstituted systems have been analyzed. It has been shown that the model allows one to predict the preferred nucleosome translational positioning with an accuracy of about one turn of the double helix. The conclusion is made that the isotropic elastic properties of the DNA molecule are very important for nucleosome translational positioning. The anisotropic flexibility modulates the sequence-dependent preference and defines the precise rotational placement. The analysis points to a possible involvement of DNA bendability in nucleosome structural transitions. To model the nucleosome positioning within the chromatin fiber, the derived algorithm has been applied to random DNA sequences. The nucleosome distribution obtained is close to random, but nucleosomes, according to calculations, are placed on sites with a low value of bending free energy and decreased G+C-content. Relations with other work and some implications are discussed.