Anisotropic Internucleosome Interactions and Geometrical Constraints in the Organization of Chromatin

Abstract

Chromatin structure at the high-density characteristic of the silent phase is strongly influenced by the packing of nucleosome core particles (NCPs), the anisotropic attractive interactions between two of them and constraints, such as the DNA length and bending, imposed to the wrapped and linker DNA segments. In this work, coarse-grained models of chromatin are studied. For a pair of NCPs, a simple single-site anisotropic potential energy function is designed on the basis of the experimental data reported for the ordered phases of NCPs. This potential energy function is employed in random-walks of chromatin models where the NCP DNA wrapping is modulated in length, while the linker segments are modulated in both length and curvature. For chromatin in the absence of linker histones, these models support a two-start helical organization characterized by poorly bent linkers and by a moderate reduction of wrapped DNA in the NCP.