The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin

TL;DR

This paper introduces an improved chromatin model accounting for cylindrical nucleosomes and H1 defects, revealing significant effects on phase behavior and proposing mechanisms for chromatin compaction consistent with experimental data.

Contribution

The model incorporates nucleosome shape and H1 defects, providing new insights into chromatin phase diagrams and compaction mechanisms.

Findings

Shape of the excluded-volume boundary changes with nucleosome geometry

Vertical DNA strand distance significantly affects forbidden chromatin states

H1 defects can lead to highly compact chromatin fibers

Abstract

We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$ between the in and outgoing DNA strands. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the vertical distance $d$ has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded volume borderline or missing H1 histones which can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values.