The use of DNA-cellulose for analyzing histone-DNA interactions. Discovery of nucleosome-like histone binding to single-stranded DNA.

In this report, we introduce the use of DNA-cellulose chromatography for evaluating the strength of binding of histones to DNA under a variety of conditions. We have found that histones added directly to DNA-cellulose at physiological salt concentrations bind relatively weakly, with all histones eluting together at about 0.5 M NaCl when a salt gradient is applied. However, much tighter binding of the four nucleosomal histones to DNA-cellulose is obtained if gradual histone-DNA reconstitution conditions are used. In this case, the binding of histones H2A, H2B, H3, and H4 to DNA-cellulose closely resembles their binding to native chromatin. The nativeness of the binding is indicated both by the distinctive sodium chloride elution profile of these histones from DNA-cellulose and by their relative resistance to trypsin digestion when DNA-bound. The binding to DNA-cellulose of histones H2A, H2B, H3, and H4, which have had the first 20 to 30 amino acid residues removed from their NH2 termini, is indistinguishable from the binding to DNA-cellulose of the same intact histones, as judged by their salt elution profile. Thus, even though the NH2 termini contain 40 to 50% of the positively charged amino acid residues (thought to interact with the DNA backbone), a major contribution to the DNA binding comes from the remainder of the histone molecule. Finally, we have discovered that histones can form a "nucleosome-like" complex on single-stranded DNA. The same complex does not appear to form on RNA. Histones H3 and H4 play a predominant role in organizing this histone complex on single-stranded DNA, as they do on double-stranded DNA in normal nucleosomes. We suggest that, in the cell nucleus, nucleosomal structures may form transiently on single strands of DNA, as DNA and RNA polymerases traverse DNA packaged by histones.     

Stimulating effect of histones on DNA synthesis in the regenerating rat liver]

Effect of exogenous histones, nuclear globulins and acid proteins on DNA synthesis is studied in regenerating liver of rats in which the synthesis of their own proteins and thus DNA replication are inhibited by cycloheximide. In these conditions histones from regenerating rat liver are found to stimulate 3H-thymidine incorporation into DNA of hepatectomyzed rat liver. Nuclear globulins and acid proteins from regenerating liver, and histones from intact liver produced no stimulating effect on DNA sythesis.     

Cyclic nucleotides and calcium in human lymphocytes induced to divide

Intracellular concentrations of cyclic adenosine 3'-5' monophosphate (cAMP) and cyclic guanosine 3'-5' monophosphate (cGMP) were measured in human lymphocytes induced to divide by the addition of lectins, 12-O-tetra-decanoylphorbol-13-acetate (TPA) and the calcium ionophore A 23187. cGMP levels rose within minutes without concomitant alterations in cAMP concentration. The cAMP and cGMP levels rose during the prereplicative and replicative phases respectively. Under calcium depleting conditions, both the fluctuations in cyclic nucleotide levels and the increase in [3H[ thymidine incorporation into DNA were abolished, suggesting a role for calcium ions in the regulation of lymphocyte proliferation.     

Isolation of liposomes containing serotonin and their effect on cAMP accumulation in the rat liver

To prolong the biological effect of serotonin the latter was enclosed into liposomes. The use of liposomes of phosphatidyl choline, cholesterol and dicetylphosphate in the 2:1:1 ratio permits increasing the level of serotonin incorporation inside the vesicles and reaching the slow release of serotonin out of them. It is shown by electron microscopy that sizes of liposomes enlarge due to the serotonin incorporation. When the liposomal form of serotonin is introduced to animals the amine effect on the cAMP accumulation in the liver is prolonged and intensified; an increase of the cAMP accumulation is observed in the prereplicative and replicative phases of hepatocytes synchronized by cycloheximide. The above mentioned permits a conclusion to be made that liposomes modify considerably the effect of serotonin on the cAMP system of the rat liver cells.     

Synthesis and phosphorylation of histones and nonhistone proteins as affected by irradiation and serotonin in cycloheximide-synchronized hepatocytes

Phosphorylation and synthesis of histones and nonhistone proteins were studied after the inhibition of translation by sublethal cycloheximide doses. Activation of the chromatin protein phosphorylation was noted: (1) at the stage of recovery and stimulation of the protein synthesis (18-24 h), and (2) at the stage of activation of the replicative DNA synthesis (30-60 h). Phosphorylation and synthesis of the chromatin proteins depended upon the individual or combined effect of X-radiation and serotonin. The authors discuss the possible role of the chromatin protein phosphorylation in the response of the nuclear apparatus to the effect of radiation and serotonin the latter being used as a radioprotective agent.     

Chromosome remodeling related to hepatitis B virus replication in HepG2 cells

Hepatitis B Virus (HBV) covalently closed circular DNA (cccDNA) is the main replicative intermediate of HBV and is organized into minichromosomes by the interaction with histone and nonhistone proteins. The remodeling of HBV minichromosomes such as post-translational modifications of histone proteins plays an important role in regulating HBV replication. To determine whether other remodeling occurs in addition to acetylation of cccDNA-bound H3 histones in the presence of HBV replication, a cell culture replication model of HBV was used to assess the dynamic status of acetylation, phosphorylation, and methylation of cccDNA-bound H3 histones at various times after transient transfection of linear HBV DNA into human hepatoma, HepG2 cells. H3 histones bound to cccDNA were found to be phosphorylated, mono-methylated, and acetylated in HepG2 cells containing replicating HBV. The acetylation and methylation status of H3 histones bound to cccDNA paralleled HBV replication. Our results demonstrate that phosphorylation and methylation occur in the remodeling of HBV minichromosomes during HBV replication. The modifications of cccDNA-bound H3 histones were associated with the level of HBV replication. These findings suggest that alterations in the extent of minichromosome remodeling might be a potential target to inhibit HBV replication in the development of effective novel antiviral agents.     

Regulation of dog thyroid epithelial cell cycle by forskolin, an adenylate cyclase activator

Dog thyroid epithelial follicular cells in primary culture are quiescent in an insulin-supplemented serum-free medium. They are induced, after a 16- to 20-h prereplicative phase, to synthesize DNA upon stimulation by forskolin, a general adenylate cyclase activator that mimics all the effects of thyrotropin in these cells. The characteristics of adenylate cyclase activation by forskolin make this drug a convenient tool to enhance cellular cyclic AMP levels for well-defined periods of the cell cycle, allowing determination of which parts of the prereplicative phase are controlled by cyclic AMP. We observe that induction of DNA synthesis by forskolin requires its continuous presence for most of the prereplicative phase until a point that little precedes the initiation of DNA replication. Before this point, interruptions in forskolin presence as short as 2 h delay the onset of DNA synthesis, indicating a rapid regression of the cells to an earlier part of G1 from which they can be rescued by forskolin readdition. Similar delays in the onset of S phase are also induced by reversible protein synthesis inhibitions using pulses of cycloheximide. These data suggest that in dog thyrocytes elevated cyclic AMP levels stimulate the progression into G1 phase until a late commitment point before DNA synthesis. This progression depends on peculiarly labile cyclic AMP-stimulated events which might well be the induction by cyclic AMP of the synthesis of labile proteins.     

Growth control of differentiated fetal rat hepatocytes in primary monolayer culture. IX. Specific inhibition of DNA synthesis initiation by very low density lipoprotein and possible significance to the problem of liver regeneration

Rat serum very low density lipoprotein (VLDL) inhibits initiation of DNA synthesis in fetal rat hepatocyte cultures; cells engaged in synthesizing DNA resist inhibition. VLDL action is specific and apparently blocks prereplicative protein synthesis. These and other results, from studies of altered blood VLDL levels and [3H] thymidine incorporation into isolated liver nuclei in 70% hepatectomized normal and mutant hyperlipoproteinemic rats, as well as from infusion studies with a "mitogenic" hormone solution, suggest that hepatic VLDL metabolism is linked to the suppression of hepatocyte proliferation.     

Effect of ribonuclease on the physico-chemical properties of estrogen receptor

Estrogen receptors (ER) from rat and rabbit uterine cytosol were examined for their sensitivity to ribonuclease (RNase). After RNase treatment, a major part of rabbit uterine ER was converted from the 7S to 3-4S form, and its binding to DNA-cellulose was increased by 40%. Similar treatment on rat uterine ER showed a shift from 7S to 4.5S, and the DNA-cellulose binding was stimulated by 20%. Measurement of endogenous RNase levels showed that lower RNase concentration in rabbit uterine cytosol coincided with larger stimulation of DNA-cellulose binding by exogenous RNase. These results indicate that a major part of 7S ER is susceptible to RNase, and cleavage of bound RNA seems to uncover additional binding sites for DNA. In contrast to the general thinking that 4S to 5S transformation is essential for nuclear binding, we have observed that RNase-treated rat uterine ER did not undergo such a transformation by warming at 25 degrees C, while DNA-cellulose binding of the receptors increased. Thus, temperature activation could occur independent of 4S to 5S transformation.     

Onset of DNA replication in nuclei of proliferating and resting NIH 3T3 fibroblasts following fusion

NIH 3T3 mouse fibroblasts arrested in medium containing 0.5% serum were fused with stimulated cells taken at 2-h intervals after replacing the medium with one containing 10% serum, and DNA synthesis was studied in mono-, homo- and heterokaryons using radioautography with double-labelling technique. The presence of a resting nucleus in a common cytoplasm with a stimulated nucleus from the prereplicative period has an inhibitory effect on the entry of the stimulated nucleus into the S period in medium containing either 0.5 or 10% serum, but ongoing DNA synthesis continues. After a 24-h stay in a common cytoplasm with resting nuclei the stimulated nuclei return into the state of rest. When resting cells are stimulated by 10% serum, their inhibitory effect on stimulated nuclei in heterokaryons still persists, at least for 2 h following stimulation. Preincubation of resting cells with cycloheximide for 4 h abolishes their ability to suppress DNA synthesis in stimulated nuclei.The data suggest that resting cells produce an endogenous inhibitor of cell proliferation, whose formation depends upon the synthesis of protein. When stimulated, the cells can proliferate only after decreasing the level of this inhibitor. The results obtained are consistent with the idea of a negative control of cell proliferation.     

Identification and isolation of soluble histones from bovine milk and serum.

An immunoassay for soluble histones as trace components of biological fluids was developed on the basis of the dual capacity of histones to bind solid-phase DNA and monoclonal anti-histone antibody. Application of this histone-capture assay to bovine milk resulted in a positive signal, and DNA-cellulose chromatography was used to isolate histone-like material in microgram quantities. Western-blot analysis using a panel of anti-histone antibodies demonstrated the presence of histones H2A, H2B and H4 in apparently intact form. DNAase digestion experiments indicated that at least a portion of milk histone was complexed to DNA. Bovine serum was analysed in the same manner on serial DNA-cellulose columns, and H4 and partially degraded H2A were detected by Western-blot analysis. The finding of soluble histones in bovine milk and serum may account for unexpected results when these biological fluids are used as blocking reagents in Western blots and other immunoassays and may have ramifications in the origin and significance of anti-histone antibodies in human disease.     

Effect of biotin on phosphorylation,acetylation, methylation of rat liver histones

Biotin deficient rat liver histones showed decreased phosphorylation and methylation, and increased acetylation rates as compared to normal rat liver histones: these alterations may be related to the observed lower stability of the interactions between histones and DNA. The modifications of the metabolic process might be the consequence of an alteration of the synthesis of the enzymes involved in histone phosphorylation, acetylation and methylation mechanisms and are presumably related to a biotin effect upon the synthesis of RNA and proteins.     

Thyroxine stimulation of tadpole liver histone phosphorylation in vivo

The in vivo phosphorylation of histones in the livers of Rana catesbeiana tadpoles was followed during the course of thyroxine-induced metamorphosis. Phosphorylation of histones H1 and H2a, and possibly of histone H4 at a low level, was observed in all animals. After correction for specific radioactivity of liver inorganic phosphate pools, an apparent wave of phosphorylation of histones was found to occur between 2 and 8 days of thyroxine treatment, with a peak increase of approximately 2- to 5-fold for histones H2a and H1. The increases in liver histone phosphorylation are approximately coincident with well-documented increases in the levels of various liver enzymes and occur in the absence of any change in the low basal rate of histone or DNA synthesis in this organ. This is apparently the first instance of increased phosphorylation of both H1 and H2a which is not coincident with or precedent to increases in cellular proliferation rates.     

Effect of biotin on DNA and histone phosphorylation in the rat liver

The results offer further evidence for biotin activity in the phosphorylation mechanism. The decreased 32p incorporation into DNA and histones found in the biotin deficient rat liver is indicative of the importance of the vitamin in the DNA and histones synthesis and in the interactions between histone proteins and DNA, and consequently on the RNA and proteins synthesis.     

The topoisomerase II inhibitor VM-26 induces marked changes in histone H1 kinase activity, histones H1 and H3 phosphorylation, and chromosome condensation in G2 phase and mitotic BHK cells

We have examined the effects of topoisomerase inhibitors on the phosphorylation of histones in chromatin during the G2 and the M phases of the cell cycle. Throughout the G2 phase of BHK cells, addition of the topoisomerase II inhibitor VM-26 prevented histone H1 phosphorylation, accompanied by the inhibition of intracellular histone H1 kinase activity. However, VM-26 had no inhibitory effect on the activity of the kinase in vitro, suggesting an indirect influence on histone H1 kinase activity. Entry into mitosis was also prevented, as monitored by the absence of nuclear lamina depolymerization, chromosome condensation, and histone H3 phosphorylation. In contrast, the topoisomerase I inhibitor, camptothecin, inhibited histone H1 phosphorylation and entry into mitosis only when applied at early G2. In cells that were arrested in mitosis, VM-26 induced dephosphorylation of histones H1 and H3, DNA breaks, and partial chromosome decondensation. These changes in chromatin parameters probably reverse the process of chromosome condensation, unfolding condensed regions to permit the repair of strand breaks in the DNA that were induced by VM- 26. The involvement of growth-associated histone H1 kinase in these processes raises the possibility that the cell detects breaks in the DNA through their effects on the state of DNA supercoiling in constrained domains or loops. It would appear that histone H1 kinase and topoisomerase II work coordinately in both chromosome condensation and decondensation, and that this process participates in the VM-26- induced G2 arrest of the cell.     

Partial purification of the glucocorticoid receptor from rat liver: a rapid, two-step procedure using DNA-cellulose.

Glucocorticoid receptor from rat liver was purified 1800-fold by a rapid two-step procedure using DNA-cellulose. The procedure is based on increasing the affinity of the glucocorticoid-receptor complex for DNA by heating the complex. During a first chromatography step, unheated glucocorticoid-receptor complex is separated from cytosol proteins that bind to DNA-cellulose with high affinity. During a second chromatographic step, heat-treated glucocorticoid-receptor complex is separated from proteins with low affinity for DNA. The partially purified complex is functionally competent in that it is taken up by isolated rat liver nuclei.     

Activation of the glucocorticoid-receptor complex

A crucial step in the interaction of glucocorticoids with target cells is the activation step, which involves a conformational change in the cytoplasmic glucocorticoid-receptor protein complexes and facilitates their binding to the cell nucleus. Activation can be quantified by measuring the ability of glucocorticoid-receptor complexes to bind to polyanions, such as DNA-cellulose, and unactivated complexes can be separated from activated complexes by rapid ion exchange chromatography using diethylaminoethyl (DEAE)-Sephadex or DEAE-cellulose. Activation occurs in vivo under physiological conditions and the rate of activation of cytoplasmic glucocorticoid-receptor complexes can be enhanced in vitro by physical manipulations (elevated temperature, increased ionic strength, dilution). In vitro studies suggest that activation is a regulated process and a low molecular weight component termed modulator, which has been identified in rat hepatic cytosol, inhibits activation. Additional studies employing phosphatase inhibitors, such as molybdate, and purified calf intestinal alkaline phosphatase suggest that either the receptor protein or a regulatory component is dephosphorylated during activation. Results obtained with specific chemical probes suggest that activation results in the exposure of basic amino acid residues consisting minimally of lysine, arginine, and histidine. Pyridoxal 5'-phosphate, a specific probe for lysine residues, exerts dual effects on glucocorticoid-receptor complexes, since it stimulates the rate of activation and also inhibits the binding of previously activated complexes to nuclei or DNA-cellulose. The ability of 1,10-phenanthroline, a metal chelator, to inhibit the DNA-cellulose binding of activated complexes suggests that a metal ion(s) located at or near the DNA binding site may become exposed as a consequence of activation. Collectively, the results of these various experiments suggest that activation is a regulated biochemical phenomenon with physiological significance.     

Cooperative alignment of nu bodies during chromosome replication in the presence of cycloheximide

50% of control DNA is resistant to staphylococcal nuclease after digestion in isolated nuclei, while only 25% of the labeled DNA made in the presence of cycloheximide is resistant to nuclease. Nevertheless, cycloheximide DNA is folded into normal chromosomal subunits as evidenced by the observation that it generates nuclese limit-digest DNA fragments that are indistinguishable from controls. These results indicate that cycloheximide chromatin is associated with half the number of normal nu bodies. These nu bodies are probably recycled from the parental chromosome. Partial nuclease digestion of cycloheximide chromatin reveals that a normal pattern of monomer and multimer DNA fragments is generated up to octamers. The data are consistent with the idea that in the presence of cycloheximide, recycled parental histones become cooperatively aligned along the daughter double helices.