Irregular chromatin: packing density, fiber width and occurrence of heterogeneous clusters

Abstract

How chromatin is folded in the lengthscale of a gene is an open question. Recent experiments have suggested that, in vivo, chromatin is folded in an irregular manner and not as an ordered fiber with a width of 30 nm expected from theories of higher order packaging. Using computational methods, we examine how the interplay between DNA-bending non histone proteins, histone tails, intra-chromatin electrostatic and other interactions decide the nature of packaging of chromatin. We show that while the DNA-bending non histone proteins make the chromatin irregular, they may not alter the packing density and size of the fiber. We find that the length of the interacting region and intra-chromatin electrostatic interactions influence the packing density, clustering of nucleosomes, and the width of the chromatin fiber. Our results suggest that the actively maintained heterogeneity in the interaction pattern will play an an important role in deciding the nature of packaging of chromatin.