Influence of histone hyperacetylation on nucleosomal particles as visualized by electron microscopy

High resolution microanalysis and three-dimensional nucleosome structure associated with transcribing chromatin

The nucleosome is the ubiquitous and fundamental DNA-protein complex of the eukaryotic chromosome, participating in the packaging of DNA and in the regulation of gene expression. Biophysical studies have implicated changes in nucleosome structure from chromatin that is quiescent to active in transcription. Since DNA within the nucleosome contains a high concentration of phosphorus whereas histone proteins do not, the nucleosome structure is amenable to microanalytical electron energy loss mapping of phosphorus to delineate the DNA within the protein-nucleic acid particle. Nucleosomes associated with transcriptionally active genes were separated from nucleosomes associated with quiescent genes using mercury-affinity chromatography. The three-dimensional image reconstruction methods for the total nucleosome structure and for the 3D DNA-phosphorus distribution combined quaternion-assisted angular reconstitution of sets of single particles at random orientations and electron spectroscopic imaging. The structure of the active nucleosome has the conformation of an open clam-shell, C- or U-shaped in one view, elongated in another, and exhibits a protein asymmetry. A three-dimensional phosphorus map reveals a conformational change in nucleosomal DNA compared to DNA in the canonical nucleosome structure. It indicates an altered superhelicity and is consistent with unfolding of the particle. The results address conformational changes of the nucleosome and provide a direct structural linkage to biochemical and physiological changes which parallel gene expression.

Structural states of the nucleosome

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.

Modulation of chromatin folding by histone acetylation

A homogeneous oligonucleosome complex was prepared by reconstitution of highly hyperacetylated histone octamers onto a linear DNA template consisting of 12 tandemly arranged 208-base pair fragments of the 5 S rRNA gene from the sea urchin Lytechinus variegatus. The ionic strength-dependent folding of this oligonucleosome assembly was monitored by sedimentation velocity and electron microscopy. Both types of analysis indicate that under ionic conditions resembling those found in the physiological range and in the absence of histone H1, the acetylated oligonucleosome complexes remain in an extended conformation in contrast to their nonacetylated counterparts. The implications of this finding in the context of a multistate model of chromatin folding (Hansen, J. C., and Ausio, J. (1992) TIBS 197, 187-191) as well as its biological relevance are discussed.

Histone hyperacetylation can induce unfolding of the nucleosome core particle

A direct correlation exists between the level of histone H4 hyperacetylation induced by sodium butyrate and the extent to which nucleosomes lose their compact shape and become elongated (62.0% of the particles have a length/width ratio over 1.6; overall mean in the length/width ratio = 1.83 +/- 0.48) when bound to electron microscope specimen grids at low ionic strength (1mM EDTA, 10mM Tris, pH 8.0). A marked proportion of elongated core particles is also observed in the naturally occurring hyperacetylated chicken testis chromatin undergoing spermatogenesis when analyzed at low ionic strength (36.8% of the particles have a length/width ratio over 1.6). Core particles of elongated shape (length/width ratio over 1.6) generated under low ionic strength conditions are absent in the hypoacetylated chicken erythrocyte chromatin and represent only 2.3% of the untreated Hela S3 cell core particles containing a low proportion of hyperacetylated histones. The marked differences between control and hyperacetylated core particles are absent if the particles are bound to the carbon support film in the presence of 0.2 M NaCl, 6mM MgCl2 and 10mM Tris pH 8.0, conditions known to stabilize nucleosomes. A survey of the published work on histone hyperacetylation together with the present results indicate that histone hyperacetylation does not produce any marked disruption of the core particle 'per se', but that it decreases intranucleosomal stabilizing forces as judged by the lowered stability of the hyperacetylated core particle under conditions of shearing stress such as cationic competition by the carbon support film of the EM grid for DNA binding.

Histone hyperacetylation. Its effects on nucleosome core particle transitions

Effects of histone hyperacetylation on transitions of HeLa cell nucleosome core particles were studied. The transitions examined were induced by low salt concentrations, pH, temperature, and nondissociating high salt. Effects of salt dissociation were also examined. The low-salt transition was found to shift to higher ionic strength by approximately three fold for hyperacetylated particles, a change which may be due simply to the increased overall negative charge on the particles caused by acetylation of lysine residues. Some differences were also seen in the way in which core particles refold after exposure to very low salt (which induces a nonreversible change in the particles). Otherwise no significant effects of hyperacetylation were observed.

Treatment with sodium butyrate inhibits the complete condensation of interphase chromatin

The effects of histone hyperacetylation on chromatin fiber structure were studied using direct observations with the electron microscope. Histone hyperacetylation was induced in HeLa cells by treatment with sodium butyrate, and the ultrastructure of control and of acetylated chromatin fibers examined after fixation at different stages of compaction. No differences between control and acetylated chromatin were seen when the fibers were partially unfolded (10 mM NaCl, 20 mM NaCl, 50 mM NaCl), but in 100 mM NaCl, control chromatin showed further compaction to the "30 nm" fiber, while hyperacetylated chromatin failed to undergo this final compaction step. These results strongly suggest that histone acetylation causes a moderate "relaxation" rather than complete decondensation of interphase chromatin fibers. The relationship of these findings to the increased DNase I sensitivity of acetylated chromatin, and to transcription and replication, is discussed.

Histone acetylation in replication and transcription: turnover at specific acetylation sites in histone H4 from Physarum polycephalum

Histone H4 from growing cells is partially acetylated at lysines 5, 8, 12, and 16. The turnover rate at each of these sites was investigated by pulse-labeling plasmodia of Physarum polycephalum with [3H]acetate for 55 min in either S phase or G2 phase of the cell cycle. Labeled histone H4 was purified and digested with a protease which cleaves on the carboxyl side of arginine residues. The peptide containing the acetylation sites was purified by high-performance liquid chromatography. Subfractions of the peptide were obtained due to differences in acetyllysine content. Each subfraction was subjected to automated Edman degradation and the radioactivity released after each cycle was determined. Histone H4 was acetylated uniformly in vitro and acetylated peptide 1-23 was used as a control. The results show a very striking preference for turnover on lysine-5 in the "low acetyl" subfraction from cells in S phase; the "high acetyl" subfraction showed turnover at all four sites. The peptides labeled in G2 phase showed turnover mainly at positions -8, -12, and -16. The data imply that the patterns of histone acetyl turnover associated with replication and transcription are nonrandom and distinct. The results have implications for nucleosome structure particularly the possible role of lysine-5 in chromosome maturation and for the design of experiments to test chromatin function in vitro.

Histones and their modifications

Histones constitute the protein core around which DNA is coiled to form the basic structural unit of the chromosome known as the nucleosome. Because of the large amount of new histone needed during chromosome replication, the synthesis of histone and DNA is regulated in a complex manner. During RNA transcription and DNA replication, the basic nucleosomal structure as well as interactions between nucleosomes must be greatly altered to allow access to the appropriate enzymes and factors. The presence of extensive and varied post-translational modifications to the otherwise highly conserved histone primary sequences provides obvious opportunities for such structural alterations, but despite concentrated and sustained effort, causal connections between histone modifications and nucleosomal functions are not yet elucidated.

Changes in the structural organization of chromatin during spermatogenesis in the rat

In this study, histone H4 was shown to be extensively hyperacetylated in mid-spermatids of the rat during the time period when the entire complement of histones is replaced by basic spermatidal transition proteins. The degree of hyperacetylation of histone H4 was minimal in pachytene spermatocytes. Therefore, the hyperacetylation appears to be directly involved in the histone replacement process late in spermatogenesis in mid-spermatids. In order to investigate further the possible effects of histone H4 hyperacetylation and the other dramatic changes in the nuclear proteins on the structure of chromatin in germinal cells, we examined the thermal denaturation profiles of chromatin from various purified germinal cell types. Our analyses revealed that chromatins from pachytene spermatocytes and early spermatids have similar thermal denaturation profiles, with their major thermal transitions slightly lower than those for rat liver. However, the major thermal transitions for chromatin from mid-spermatids are much lower than those from pachytene spermatocytes and early-spermatids. We propose that the greatly lowered thermal stability of mid-spermatid chromatin represents a dramatic relaxation or decondensation of the chromatin in this cell type in preparation for the replacement of histone by the basic spermatidal transition proteins and that the decondensation is due in large part to the extensive histones hyperacetylation which occurs in these cells.