Analysis of the changes in the structure and hydration of the nucleosome core particle at moderate ionic strengths

Abstract

In order to better understand the conformational changes induced in the nucleosome core particle by changes in the ionic strength of the media in the range from 0.1 to 0.6 M NaCl, we have conducted a very detailed structural analysis, combining circular dichroism, DNase I digestion, and sedimentation equilibrium. The results of such analysis indicate that the secondary structure of both DNA and histones exhibits small (approximately 5%) but noticeable changes as the salt increases within this range. In the case of DNA, the data are consistent with a trend toward a more relaxed secondary structure. The DNase I pattern of digestion is also altered by the salt and suggests a DNA relaxation around the flanking ends. From the hydrodynamic measurements, we also observe a significant change in the virial coefficients of the particle as the salt increases, which in turn are in very good agreement with the theoretically expected values. Furthermore, the preferential hydration parameter is also found to increase with the salt. We believe that the self-dependent conformational change of the nucleosome core particle is the result of the conjunction of all these subtle changes. Yet, from the present data, their exact relationship to the tertiary structure of the whole particle at the different ionic strengths cannot be exactly defined.

Structural States of the Nucleosome

“…A further conformational change to a less oblate form observed in this study by microscopy of particles prepared in the presence of 400 mM NaCl is supported by findings of a transition between 150 and 400 mM NaCl by fluorescence studies (9,11). This change is consistent with the overall structural change of the nucleosome characterized by Dong et al (50) in the range of 100 -600 mM NaCl. Using detailed physicochemical analyses in that study, it was concluded that both DNA and histones exhibit changes as salt is increased in this range, consistent with a trend to a more relaxed secondary structure (50).…”

Characterization of the Stability and Folding of H2A.Z Chromatin Particles

“…We (25,32,33,47,48) and others (35, 49 -51) have shown that nucleosomes in solution are not static entities but rather they are highly transient structures. A dynamic equilibrium exists between the constitutive histone octamer and the nucleosomal DNA (32), which besides the ionic strength is also dependent on many other physical parameters such as temperature and sample concentration.…”

Alteration of Nucleosome Structure as a Mechanism of Transcriptional Regulation

“…Initial studies revealed surprisingly few changes in the properties of mononucleosomes following trypsinization (92,93). The extended structure that mononucleosomes form as salt increases was not significantly altered by removal of the tails; nor were there significant changes in circular dichroism (CD) spectra.…”