Lack of correlation between histone H4 acetylation and transcription during the Physarum cell cycle

Histone H4 acetylation during interleukin-2 stimulation of mouse T cells

Proliferation and cell cycle progression of eukaryotic cells are closely linked to changes in chromatin structure and gene expression. By reversible histone acetylation the cell is able to modulate chromatin condensation and accessibility of specific regions within the chromatin. Here, we examined histone H4 acetylation patterns during growth induction of the murine interleukin-2 dependent T cell line B6.1. In order to detect acetylation on each of the four potential target residues we produced a set of antibodies recognizing specifically acetylated lysine 5, 8, 12 and 16 in the N-terminal tail of histone H4. Acetylation was generally low in resting T cells, but increased after stimulation with a specific kinetics for each lysine. Lysine 16 was acetylated during the G1 phase and deacetylated during S phase. H4 acetylation on lysine 5, 8 and 12, in contrast, was induced before cells started to replicate, and persisted until cells entered mitosis. Treatment of resting B6.1 cells with the specific deacetylase inhibitor trichostatin A (TSA) led to H4 hyperacetylation at all four lysine residues indicating that the histone modification can occur in the absence of replication. After release from TSA treatment normal H4 acetylation levels were reestablished by extremely rapid deacetylation of lysines 5, 8, 12 and 16. The deacetylation step was 60-100 times faster than TSA induced acetylation and equally efficient in resting and exponentially growing T cells. Our results indicate the presence of cell cycle regulated lysine specific acetylating and deacetylating activities in mouse T cells.

Interaction between N-terminal domain of H4 and DNA is regulated by the acetylation degree

To study whether the acetylation of one or more of the four acetylatable lysines of histone H4 affects its binding to DNA, we have designed a protection experiment with a model system consisting in phage lambda DNA as substrate, StuI as restriction endonuclease and histone H4 with different degrees of acetylation as the protective agent. It can be deduced from the experimental data that the protection afforded by the histone is not dependent on the number of positive charges lost by acetylation. Thus, non-acetylated H4 and mono-acetylated H4 cause similar protection, while di-acetylation of the histone seems to be the crucial step in significantly weakening the interaction between H4 and DNA. This is confirmed by the results obtained in protection experiments carried out using H4 peptide (1-24) with different degrees of acetylation as the protecting agent. As restriction enzyme can imitate any trans-acting factor with sequence recognition, the di-acetylated isoform of histone H4 can be the starting point, through acetylation, to unmask DNA sequences, allowing the accessibility of regulatory factors to DNA in the chromatin.

Nuclear matrix and the cell cycle

The facts that the nuclear matrix represents a structural framework of the cell nucleus and that nuclear events, such as DNA replication, transcription, and DNA repair, are associated with this skeletal structure suggest that its components are subject to cell cycle-regulatory mechanisms. Cell cycle regulation has been shown for nuclear lamina assembly and disassembly during mitosis and chromatin reorganization. Little attention has so far been paid to internal nuclear matrix proteins and matrix-associated proteins with respect to the cell cycle. This survey attempts to summarize available data and presents experimental evidence that important metabolic functions of the nucleus are regulated by the transient, cell cycle-dependent attachment of enzymes and regulatory proteins to the nuclear matrix. Results on thymidine kinase and RNA polymerase during the synchronous cell cycle of Physarum polycephalum demonstrate that reversible binding to the nuclear matrix represents an additional level of regulation for nuclear processes.

Histone acetylation: facts and questions

The DNA of eukaryotic cells is organized in a complex with proteins, either as interphase chromatin or mitotic chromosomes. Nucleosomes, the structural subunits of chromatin, have long been considered as static structures, incompatible with processes occurring in chromatin. During the past few years it has become evident that the histone part of the nucleosome has important regulatory functions. Some of these functions are mediated by the N-terminal core histone domains which contain sites for posttranslational modifications, among them lysine residues for reversible acetylation. Recent results indicate that acetylation and deacetylation of N-terminal lysines of nucleosomal core histones represent a means of molecular communication between chromatin and the cellular signal transduction network, resulting in heritable epigenetic information. Data on enzymes involved in acetylation and the pattern of acetylated lysine sites on chromosomes, as well as genetic data on yeast transcriptional repression, suggest that acetylation may lead to structural transitions as well as specific signalling within distinct chromatin domains.

Transcription of mononucleosomal particles acetylated in the presence of n-butyrate

Although a correlation between chemical acetylation of the amino-terminal tails of core histones and stimulation of RNA synthesis has been reported for nucleosomal core particles (Piñeiro et al. (1991) Biochem. Biophys. Res. Commun. 177:370), no differences in transcription are detected between acetylated and nonacetylated mononucleosomal particles obtained from HeLa cells in the presence and absence of n-butyrate. Apparently, the lysine residues modified in the presence of n-butyrate are not the same responsible for the observed acetylation-induced transcription. The acetylation obtained with n-butyrate might be significantly different from that present in transcriptionally active chromatin.

Enzymes involved in the dynamic equilibrium of core histone acetylation of Physarum polycephalum

DEAE-Sepharose chromatography of extracts from plasmodia of the myxomycete Physarum polycephalum revealed the presence of multiple histone acetyltransferases and histone deacetylases. A cytoplasmic histone acetyltransferase B, specific for histone H4, and two nuclear acetyltransferases A1 and A2 were identified; A1 acetylates all core histones with a preference for H3 and H2A, whereas A2 is specific for H3 and also slightly for H2B. Two histone deacetylases, HD1 and HD2, could be discriminated. They differ with respect to substrate specificity and pH dependence. For the first time the substrate specificity of histone deacetylases was determined using HPLC-purified individual core histone species. The order of acetylated substrate preference is H2A much greater than H3 greater than or equal to H4 greater than H2B for HD1 and H3 greater than H2A greater than H4 for HD2, respectively; HD2 is inactive with H2B as substrate. Moreover histone deacetylases are very sensitive to butyrate, since 2 mM butyrate leads to more than 50% inhibition of enzyme activity.

Isolation, characterisation and growth-related changes of an HMG-like protein from microplasmodia of Physarum polycephalum

An alanine, lysine and glutamic acid-rich nuclear protein (P2) of Mr approximately 19,500 co-extracts with the histones from nuclei of Physarum polycephalum when using the CaCl2 method for histone extraction [1] and was found to have the composition previously ascribed to a putative histone H1(0) isolated from microplasmodia using 5% PCA (Yasuda, H., Mueller, R.D., Logan, K.A. and Bradbury, E.M. (1986) J. Biol. Chem. 261, 2349-2354). P2 has very similar electrophoretic properties to chicken erythrocyte histone H5, calf thymus histone H1(0) and the Physarum HMG-like protein AS-2, but does not appear to be immunologically or structurally similar to H5 or H1(0). An increase in the abundance of P2 was observed during exponential growth in microplasmodia, reaching an approximately 1:1 ratio with histone H1 by 48 h of culture. Standard amino acid analysis and NMR show that P2 is more HMG-like than H1-like and CD measurements demonstrated that P2 contains only 5% secondary structure in its maximally structured state and is, therefore, essentially unstructured under in vivo conditions. Also possible clustering of acidic residues is detected using CD and may be of functional significance. Analysis of post-translational modification of P2 shows that it is phosphorylated at up to three sites as isolated from immature spherules. The relationship of P2 to the HMG family of proteins and AS-2 is discussed.

ADP-ribosylation of core histones and their acetylated subspecies

ADP-ribosylation of core histones was investigated in isolated nuclei of Physarum polycephalum. Core histone species differed in the mode of modification. Whereas ADP-ribosylation of H2A and H2B is sensitive to inhibition by 3-methoxybenzamide, as with most other nuclear acceptor proteins, the modification of H3 and H4 is not inhibited. Cleavage experiments with hydroxylamine indicate a carboxylate ester type ADP-ribose-protein bond for H2A and H2B and arginine-linked ADP-ribose residues for H3 and H4. ADP-ribosylation preferentially occurs on acetylated histone subspecies, as shown for H4. These data are substantiated by the use of n-butyrate, which induces hyperacetylation of core histones; the butyrate-induced shift towards more acetylated H4 subspecies is accompanied by an increase of ADP-ribose incorporation into highly acetylated H4 subspecies.

Patterns of histone acetylation

The N-terminal domains of all four core histones are subject to reversible acetylation at certain lysine residues. This modification has been functionally linked to transcription, histone deposition at replication and to histone removal during spermatogenesis. To increase understanding of the significance of this modification we have studied the specificity of site utilisation in the monoacetyl, diacetyl and triacetyl forms of histones H3, H4 and H2B (histone H2A has only a single modification site), using pig thymus and HeLa cells as the source of histones. The HeLa histones were extracted from cells grown both with and without butyrate treatment. It is found that for histone H3 there is a fairly strict order of site occupancy: Lys14, followed by Lys23, followed by Lys18 in both pig and HeLa histones. Since the order and specificity is the same when butyrate is added to the HeLa cell cultures, we conclude that addition of the fatty acid does not scramble the specificity of site utilisation, but merely allows more of the natural forms of modified histone to accumulate. For histone H4, the monoacetyl form is exclusively modified at Lys16, but further addition of acetyl groups is less specific and progresses through sites 12, 8 and 5 in an N-terminal direction. Similar results were obtained for H4 from both pig thymus and butyrate-treated HeLa cells. Histone H2B could be studied in detail only from butyrate-treated HeLa cells and a much lower level of site specificity was found: sites 12 and 15 were preferred to the more N- and C-terminal sites at Lys5 and Lys20. The data reinforces the view that lysine acetylation in core histones is a very specific phenomenon that plays several functionally distinct roles. The high degree of site specificity makes it unlikely that the structural effects of acetylation are mediated merely by a generalised reduction of charge in the histone N-terminal domains.

Acetylation and deacetylation of histone H4 continue through metaphase with depletion of more-acetylated isoforms and altered site usage

Antibodies specific for acetylated isoforms of histone H4 have been used to compare acetylation of this histone in interphase and metaphase cells. Two rabbit antisera (R5 and R6) were used, each specific for H4 molecules acetylated at one of the four possible acetylation sites, namely Lys-5 (R6) and Lys-12 (R5). Both antisera bound preferentially to the more-acetylated H4 isoforms (H4Ac2-4). To test for continued H4 acetylation in metaphase chromosomes. Chinese hamster ovary cells were blocked in metaphase and treated for one hour with the deacetylase inhibitor sodium butyrate. Isolated chromosomes were assayed for H4 acetylation by antibody labeling and flow cytometry. H4 acetylation was increased several fold by this brief butyrate treatment. The increase was in direct proportion to DNA content, with no evidence for exceptionally high- or low-labeling chromosomes. The results demonstrate that a cycle of H4 acetylation and deacetylation continues within metaphase chromosomes. Immunofluorescence microscopy showed labeling to be distributed throughout the chromosome, but with variable intensity. Western blotting and immunostaining with R5 and R6 showed a net reduction in labeling of H4 from metaphase cells, with major reductions in the more-acetylated isoforms H4Ac3-4. In contrast, labeling of H4Ac1 was reduced to a lesser extent (R6) or increased (R5). This increase indicates more frequent use of the acetylation site at lysine 12 in H4Ac1 from metaphase cells.

Estrogen effects on modifications of chromatin proteins in the rat uterus

ADP-ribosylation and phosphorylation of chromatin proteins was studied in rat uterine nuclei isolated after estrogen treatment and then incubated with [adenylate-32P]NAD or [gamma-32P]ATP. Histone acetylation was studied in uteri from immature rats treated with estradiol by incubating the whole uterus in a medium containing [14C]acetic acid. Chromatin proteins were isolated from uterine nuclei and separated by electrophoresis on SDS polyacrylamide gels followed by autoradiography or fluorography. Chromatin proteins H1, H2B, H3, HMG 14 and HMG 17 were almost exclusively ADP-ribosylated. Uterine histones H1, H3, H4, HMG 14 and HMG 17 were phosphorylated. There was a general increase in [32P]ADP-ribose uptake in chromatin proteins after estrogen stimulation, whereas [32P]phosphate incorporation into chromatin proteins showed a biphasic pattern. The [14C]acetate activity associated with all histone proteins increased gradually after estrogen treatment.

Towards an understanding of the biological function of histone acetylation

A model is presented which explains the biological function of posttranslational acetylation of core histones in chromatin. Along the lines of this model histone acetylation serves as a general mechanism to destabilize nucleosome core particles during various processes occurring in chromatin. Acetylation acts as a signal that modulates histone-protein and histone-DNA interactions and finally leads to the displacement of particular histones from nucleosome cores. The high specificity of the acetylation signal for different processes (DNA replication, transcription, differentiation-specific histone replacement) is achieved by site specificity and asymmetry of acetylation in nucleosomes. The essential features of this model are in accord with the more recent results on histone acetylation.

Postsynthetic acetylation of histones during the cell cycle: a general function for the displacement of histones during chromatin rearrangements

Postsynthetic acetylation of core histones exhibits a peak during S-phase of the Physarum cell cycle. The maximum 3H-acetate incorporation precedes the maximum of histone synthesis. Acetate is incorporated into all core histones during S-phase, but only into H2A and H2B during G2-period. Resolution of acetylated H4-subspecies reveals acetate incorporation into preexisting H4, but not into newly synthesized molecules during mitosis and early S-phase. In a protamine competition assay histones from S-phase chromatin are released at lower protamine concentrations as compared to the lower acetylated G2-chromatin. We demonstrate a preferential release of highly acetylated H4-subspecies at low protamine concentrations. Our results fit into a general model of the relationship between histone acetylation and chromatin assembly. According to this model acetylation of core histones would serve as a signal for displacement of histones from nucleosomes by modulating histone-protein or histone-DNA interactions. We propose that this mechanism operates during DNA-replication and transcription, as well as during other chromatin rearrangements.

Histone acetyltransferase activity during the cell cycle

Histone acetyltransferase activity was measured in isolated nuclei during the synchronous cell cycle of the myxomycete Physarum polycephalum. Nuclei were incubated with [14C]acetyl-coenzyme A and an excess of exogenous calf thymus histones. The activity is periodic during the cell cycle; it rises during the S-phase to reach a maximum in the early G2-period with a decline in mid and late G2. Comparison of the pattern of enzyme activity with the in vivo acetylation of histones during the cell cycle reveals that the enzyme activity does not wholly determine the acetylation state, indicating that other factors, including possibly the structural state of chromatin, are responsible for the observed cell cycle pattern of in vivo histone acetylation.

Biosynthesis and posttranslational acetylation of histones during spherulation of Physarum polycephalum

Plasmodia of Physarum polycephalum can be induced to differentiate into dormant spherules: DNA-, RNA- and protein-synthesis cease during this process. Analysis of the histone H4 acetylation during spherulation revealed no significant changes of the relative acetate content and percentage of acetylated H4 subspecies. This result does not support a close correlation of histone acetylation and transcriptional activity. Posttranslational incorporation of 3H-acetate into core histones decreased rapidly after start of spherulation. However, acetate incorporation increased significantly at a late stage of spherulation (30 h). To elucidate the role of this elevated acetate incorporation we followed histone synthesis during spherulation. Histone synthesis decreased upon induction of differentiation and stopped after 12 h. After 38 h of spherulation histone synthesis again occurred in the absence of DNA synthesis. The peak of acetate incorporation into core histones clearly preceded this late histone synthesis, indicating acetylation of preexisting histones. We suggest, that this acetate incorporation is part of the mechanism, by which preexisting histones are replaced by newly synthesized histones. Pulse treatment with actinomycin D or cycloheximide during spherulation suggested, that the observed histone synthesis is essential for the germination of spherules. Obviously, new histones have to be synthesized for the coordinate course of the differentiation program.

Histone hyperacetylation: its effects on nucleosome conformation and stability

We have prepared nucleosome particles from HeLa cells that have been subjected to butyrate treatment. Fractions containing different levels of acetylation have been obtained within the range 7-17 acetyl groups per nucleosome. We have put special emphasis in the characterization of the particles with the highest level of histone acetylation. At low to physiological ionic strengths, these nucleosomes exhibit only small differences in hydrodynamic behavior and circular dichroism from control particles with minimal acetylation. There are, however, significant differences in thermal denaturation and nuclease sensitivity. In terms of stability toward high salt, the hyperacetylated and control particles behave identically. A model that reconciles these results is proposed. The major conclusion from our results, however, is that, at physiological ionic strength and in the absence of factors other than acetylation, the highly hyperacetylated nucleosomes remain essentially folded.

Partial purification and properties of two histone acetyltransferases from the yeast, Saccharomyces cerevisiae

Two histone acetyltransferases, A and B, have been extracted and partially purified from yeast cells. The purification scheme included ammonium sulfate precipitation, and chromatography on DEAE-Sepharose and Sephadex G-200. The basic properties of both enzymes closely correspond to those of acetyltransferase A and B found in higher eucaryotes. Yeast enzyme A elutes from DEAE-Sepharose prior to acetyltransferase B, and it is activated by low concentrations of DNA and strongly inhibited by p-chloromercuribenzoate (PCMB). Enzyme B is inhibited by DNA over the entire range of concentrations tested and it is less sensitive to PCMB than enzyme A. When assayed with yeast whole histones, enzyme B shows a marked specificity toward histone H4, although H3 and H2B are also accepted as substrates. Enzyme A preferentially catalyzes the acetylation of yeast H2B and H3, with the other two core histones being acetylated to a much lesser extent.

Transcriptionally active chromatin

Eukaryotic chromatin has a dynamic, complex hierarchical structure. Active gene transcription takes place on only a small proportion of it at a time. While many workers have tried to characterize active chromatin, we are still far from understanding all the biochemical, morphological and compositional features that distinguish it from inactive nuclear material. Active genes are apparently packaged in an altered nucleosome structure and are associated with domains of chromatin that are less condensed or more open than inactive domains. Active genes are more sensitive to nuclease digestions and probably contain specific nonhistone proteins which may establish and/or maintain the active state. Variant or modified histones as well as altered configurations or modifications of the DNA itself may likewise be involved. Practically nothing is known about the mechanisms that control these nuclear characteristics. However, controlled accessibility to regions of chromatin and specific sequences of DNA may be one of the primary regulatory mechanisms by which higher cells establish potentially active chromatin domains. Another control mechanism may be compartmentalization of active chromatin to certain regions within the nucleus, perhaps to the nuclear matrix. Topological constraints and DNA supercoiling may influence the active regions of chromatin and be involved in eukaryotic genomic functions. Further, the chromatin structure of various DNA regulatory sequences, such as promoters, terminators and enhancers, appears to partially regulate transcriptional activity.

Patterns of histone acetylation in Physarum polycephalum. H2A and H2B acetylation is functionally distinct from H3 and H4 acetylation

Histone acetylation has previously been correlated with both chromosome replication and transcription. We present evidence that (a) confirms both correlations in the true slime mold, Physarum polycephalum and (b) shows that quite a different pattern of acetate turnover is associated with replication compared with transcription. The pattern associated with replication involves turnover of acetate on all four core histones on species containing one or two acetates per molecule. This pattern was resolved from the transcription-associated pattern by three different procedures: (a) detailed analysis of gels of histones pulse-labelled with acetate; (b) the pattern of acetylation of histones pulse-labelled with [3H]lysine; and (c) the pattern of acetylation of soluble histones. The pattern associated with transcription is restricted to histones H3 and H4 and occurs mostly on highly acetylated species. This pattern was resolved by (a) analysis of gels of histones pulse-labelled with acetate; (b) the pattern of histone acetylation in G2 phase of the cell cycle; and (c) the pattern of histone acetylation in the presence of cycloheximide.

RNA polymerase activity and template activity of chromatin after butyrate induced hyperacetylation of histones in Physarum

We have studied the effect of sodium-n-butyrate on endogenous RNA polymerase in Physarum polycephalum. 1 mM butyrate strongly reduces RNA polymerase activity measured in isolated nuclei or chromatin; both RNA polymerase A as well as the alpha-amanitin sensitive RNA polymerase B are equally affected. Despite a concomitant hyperacetylation of histone H4 the template activity of chromatin, as analyzed by in vitro transcription of the chromatin with exogenous RNA polymerase from E. coli or RNA polymerase II from wheat germ, remains unaltered as compared to untreated control chromatin, indicating that there is no positive correlation between histone acetylation and template activity of chromatin for transcription in this organism. The results further indicate, that butyrate acts primarily as a quick but reversible inhibitor of protein synthesis in Physarum; the fast decrease of endogenous RNA polymerase activity after butyrate treatment is due to inhibition of enzyme synthesis rather than inactivation of other factors necessary for transcription.