The salt dependence of chicken and yeast chromatin structure. Effects on internucleosomal organization and relation to active chromatin

Abstract

The ionic strength dependences of yeast and chicken erythrocyte chromatin structure have been examined by analysis of nuclear DNase I and Staphylococcal nuclease digestions done under various salt and divalent cation concentrations. The basic features of yeast DNase I profiles (intracore/intercore patterns and their 5-base pair offset) remain present under all conditions tested. However, there are changes in specific parts of the patterns. In very low salt, the intercore DNase I pattern is enhanced; even very small intercore bands can be detected. Staphylococcal nuclease intracore cleavage becomes prominent. Increasing salt enhances the large DNase I intracore bands and the frequency of spacer cleavage for both nucleases. Thus, yeast has a salt-dependent higher order structure: a chromatin fiber with a prominent spacer/core distinction in (physiological) salt; a fiber with a decreased distinction between spacer and core, i.e. a more uniform fiber, in very low salt. The salt-dependent bulk changes resemble single gene chromatin changes during gene expression and may provide a model for that process. Above bands 16.5-17.5, chicken and yeast intercore patterns are coincident. Thus, at least a fraction of chicken chromatin has discrete length spacers like yeast does. This fraction may be significant, for the prominence of the intercore pattern, and hence the apparent abundance of discrete spacers, can be significantly enhanced by digestion in very low salt. The major differences between the two chromatins are in the intracore/intercore transition region: the region is larger and more complex in chicken; ionic strength changes affect the chicken transition region more strongly. Since this region of the profile corresponds to digestion near the ends of the core, that part of the nucleosome must differ in structure and in conformational flexibility in the two chromatins.