Structural States of the Nucleosome

Abstract

The nucleosome is the fundamental component of the eukaryotic chromosome, participating in the packaging of DNA and in the regulation of gene expression. Its numerous interactions imply a structural dynamism. Previous biophysical studies under limited sets of conditions have not been able to reconcile structural differences and transitions observed. We have determined a series of nucleosome conformations over a >10,000-fold range in salt concentration using a combination of biochemical methods, spectroscopic electron microscopy, and three-dimensional reconstruction techniques for randomly oriented single particles. This study indicates several ionic strength-dependent nucleosome conformations and also reconciles the differences between currently existing divergent models for the nucleosome. At low ionic environments, the particle appears highly elongated, becoming more compact and prolate ellipsoidal as ionic strength is increased to 10 mm NaCl. At 30 mM NaCl, the particle exhibits a spheroidal conformation. As ionic strength is increased to 150 mM NaCl, the nucleosome conformation changes and becomes oblate. Above 450 mM NaCl, the structure becomes highly elongated again. The result of this study is a unifying concept in which the three-dimensional structure of the nucleosome is inferred to be dynamic in response to ionic interactions and in accord with biochemical and genetic studies.

Nucleosome Structural Transition during Chromatin Unfolding Is Caused by Conformational Changes in Nucleosomal DNA

“…1, A and B) resemble those at 2 and 0.1 mM divalent cations, respectively (Fig. 2, B and C) confirming previous observations that monovalent cations affect the nucleosome structure at approximately 2 orders of magnitude higher concentrations than divalent cations (36,38,39). We also tested various monovalent and divalent cations, such as K ϩ , Li ϩ , Cs ϩ , Mg 2ϩ , Zn 2ϩ for their ability to change histone H4/ H2B contacts, and as expected, different cations that have the same charge had an identical effect on the analyzed contacts at the same concentrations.…”

“…This indicates that an increase in the nucleosomal DNA stiffness, induced by low ionic strength, affects the analyzed histone-DNA contacts in isolated core particles much the same as the stretching of linker DNA during chromatin unfolding and suggests similar changes in the conformation of the nucleosomal DNA, which may result in the structural transition of the nucleosome (27). This suggestion is supported by the recent observation of an alteration in the shape of core particles from the oblate to the prolate form at the same low salt concentrations (36).…”

“…In the case of an axial transition, DNA straightens along the superhelical axis and thereby stretching the nucleosome core into the prolate form. Recent observations of the altered core particle shape to a prolate form (36) that have a decreased (36,60) or unchanged (61) radius of gyration at concentrations of monovalent cations below 30 mM provide strong support for the second model. This model is also in agreement with the expected repulsion of adjacent superhelical turns of the nucleosomal DNA induced by low salt concentrations, which also tends to stretch the core particle in the direction of the superhelical axis.…”

Ultrasound imaging of apoptosis: high-resolution non-invasive monitoring of programmed cell death in vitro, in situ and in vivo

“…The in vitro experiments implicate the cell's nuclear chromosomal material as the major source of ultrasound scattering. This is not necessarily surprising since in the chromosome, the fundamental repeating subunit of chromatin, the nucleosome (Czarnota and Ottensmeyer, 1996;Czarnota et al, 1997b), is comprised of a protein density of 1.3 g cm -3 , and a DNA density of 1.7 g cm -3 in approximately equal proportions. Some 25 million of the protein units in combination with 2 m of DNA are packed into chromosomes which are approximately 6-8 µm in length when condensed (van Holde, 1988).…”

Three-dimensional Structure of Myelin Basic Protein

“…5) (94,95). This approach has recently been applied to the signal sequencebinding protein (103), nucleosomes (104,105), ribosomal subunits (100), and other protein complexes. These successful previous endeavors provide confidence in our further application of this algorithm to the randomly oriented projections of the present data.…”