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 translationa l position in terms of the bending free energy that depends on the nea rest-neighbor interactions between base-pairs. The available data on t he nucleosome positioning on defined DNA sequences in the reconstitute d 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 ver y important for nucleosome translational positioning. The anisotropic flexibility modulates the sequence-dependent preference and defines th e precise rotational placement. The analysis points to a possible invo lvement of DNA bendability in nucleosome structural transitions. To mo del the nucleosome positioning within the chromatin fiber, the derived algorithm has been applied to random DNA sequences, The nucleosome di stribution obtained is close to random, but nucleosomes, according to calculations, are placed on sites with a low value of bending free ene rgy and decreased G + C-content. Relations with other work and some im plications are discussed.