Methods for analysis of histones

Structure and chromosomal DNA binding of the SWIRM domain

The evolutionarily conserved Swi3p, Rsc8p and Moira (SWIRM) domain is found in many chromosomal proteins involved in chromatin modifications or remodeling. Here we report the three-dimensional solution structure of the SWIRM domain from the human transcriptional adaptor ADA2alpha. The structure reveals a five-helix bundle consisting of two helix-turn-helix motifs connected by a central long helix, reminiscent of the histone fold. Using structural and biochemical analyses, we showed that the SWIRM domains of human ADA2alpha and SMARC2 bind to double-stranded and nucleosomal DNA, and we identified amino acid residues required for this function. We demonstrated that the ADA2alpha SWIRM domain is colocalized with lysine-acetylated histone H3 in the cell nucleus and that it potentiates the ACF remodeling activity by enhancing accessibility of nucleosomal linker DNA bound to histone H1. These data suggest a functional role of the SWIRM domain in chromatin remodeling.

Histone synthesis in Trypanosoma cruzi

Trypanosoma cruzi is an ancient, parasitic eukaryote which does not undergo chromatin condensation during cell division. This behavior may be explained if one considers the strong amino acid sequence divergence of Trypanosoma histones compared to higher eukaryotes. In the latter organisms histone synthesis is coupled to DNA replication. Considering the nonconserved amino acid sequence of T. cruzi histones, as well as the absence of chromatin condensation in this organism, we have studied histone synthesis in relation to DNA replication in this parasite. We have found that core histones and a fraction of histone H1 are synthesized concomitantly to DNA replication. However, another fraction of histone H1 is constitutively synthesized.

In vivo binding of diethylstilbestrol to nuclear proteins of kidneys of Syrian hamsters

We demonstrate here that stilbene estrogen (diethylstilbestrol) is converted to nuclear protein binding metabolite(s) both in vitro and in vivo. In vitro reaction of DES with nuclei from hamster liver or kidney in the presence of cumene hydroperoxide or NADPH revealed binding of [3H]DES in nuclear proteins (histones; nonhistones precipitable by 2% TCA, NH2; nonhistones soluble in 2% TCA, NH30). The binding was significantly inhibited by cytochromes P450 inhibitors. In an in vitro system [3H]DES quinone, one of the metabolites of DES, was able to bind to pure nonhistone proteins RNA polymerase and DNA polymerase. The binding of [3H]DES quinone to nonhistones RNA polymerase and DNA polymerase was inhibited by low molecular weight thiols, i.e. glutathione and cysteine, or thiol modifiers, such as n-ethylmaleimide, dithionitrobenzoic acid and hydroxymercuric benzoate. DES and DES metabolites inhibited transcriptional activity. In vivo [3H]DES was able to bind to nuclear proteins of hamster liver, kidneys and testes. The level of in vivo [3H]DES binding to all three types of nuclear proteins (histones, NH2, NH30) in the kidney (target organ) was two or more fold higher than that observed in the liver or testis (nontarget organs). Four nuclear NH30 proteins (mol wts.: 56, 37, 33 and 28 kDa) were irreversibly bound to [3H]DES in vivo. The in vivo binding of [3H]DES to transcriptionally active chromatin NH30 proteins also was observed. The data reported here establish that DES was able to bind to liver or kidney nuclear proteins in vitro, which was catalyzed by nuclear enzymes when fortified with an appropriate cofactor. DES quinone may be one of the protein binding metabolites. DES and DES metabolites inhibited transcriptional activity. The level of in vivo binding of [3H] DES to nuclear proteins of kidney (target organ) was double in comparison with that observed in liver or testis (nontarget organs). In vivo modifications in the chromatin proteins may be a factor in the development of DES-induced renal carcinogenesis is not clear.

Histone nuclear proteins are irreversibly modified by reactive metabolites of diethylstilbestrol

We demonstrate for the first time that diethylstilbestrol (DES), a synthetic estrogen, is converted by nuclei to histone-binding metabolite(s). Reaction of [3H]DES with nuclei in the presence of cumene hydroperoxide or NADPH revealed binding of [3H]DES to histone nuclear proteins. Gel electrophoresis experiments revealed that all five histones, 1, 2A, 2B, 3, and 4, were irreversibly bound to [3H]DES. Histones 1 and 3 were more susceptible to the attack by [3H]DES quinone, a metabolite of DES, than histones 2A, 2B, or 4. The kinetic constants, Km and Vmax, of this binding reaction in the presence of cumene hydroperoxide were 10 microM and 750 pmol/mg protein/30 min, respectively. This binding was significantly inhibited by cytochromes P-450 inhibitors. Low-molecular-weight thiols, such as glutathione and cysteine, or thiol modifiers, such as n-ethylmaleimide, dithionitrobenzoic acid, and hydroxymercuric benzoate, drastically inhibited binding of [3H]DES quinone to histone 3. The binding of [3H]DES metabolites to both transcriptionally active and inactive chromatin histone proteins was observed. We conclude that DES is metabolized to histone-binding metabolites, presumably by nuclear cytochrome P-450. DES quinone may be one of the histone-binding DES metabolites. These data suggest that an analogous in vivo modification in the transcriptionally active chromatin histones by DES metabolites may influence gene function.

Selective adsorption of phosphoproteins on gel-immobilized ferric chelate

Ferric ions are very strongly adsorbed to iminodiacetic acid substituted agarose. This firmly immobilized complex acts as a selective immobilized metal affinity adsorbent for phosphoproteins. Chromatography based on this principle is illustrated by the adsorption-desorption behavior of egg yolk phosvitin before and after dephosphorylation as well as by the change in the chromatographic pattern before and after enzymic phosphorylation of selected histones. The strength of binding is dependent on the phosphate content. The difference in binding before and after phosphorylation of a single amino acid residue is demonstrated. Affinity elution can be accomplished by inclusion in the buffer of phosphoserine or a displacing metal ion such as Mg2+.

Inhibition of rat heart ornithine decarboxylase by basic polypeptides

Purified and partially purified ornithine decarboxylase (ODC) from rat heart was inhibited by basic polypeptides in vitro. Poly-L-arginine, the most effective, was inhibitory at a concentration as low as 0.1 microgram/ml; protamine and histone clearly inhibited ODC at concentrations higher than 2 micrograms/ml, but poly-L-lysine was less effective. The ability to inhibit ODC appeared to correlate with the arginine-residue content of basic polypeptides. The inhibition effect could be decreased by increasing substrate concentration and ionic strength.

Electron-microscopical evidence that ribosomal chromatin of human circulating lymphocytes is devoid of histones

We have studied the distribution of histones in the nucleolus of human circulating lymphocytes in situ, using thin sections, either treated with antibodies against the core histones revealed by colloidal gold, or stained with the acrolein-silver methenamine technique for basic proteins. Gold particles were not found in the fibrillar centre, nor were silver-stained structures visible in this nucleolar component. Since the fibrillar centre contains the bulk of the ribosomal chromatin which is in a completely extended, non-nucleosomal configuration, our results indicate that this chromatin is devoid of histones.

A placental polypeptide activator of a membranous protein kinase and its relation to histone 1

Crude transforming growth factor preparations of placenta contain a polypeptide that is required for the activity of a protein kinase that has been purified from plasma membrane preparations of Ehrlich ascites tumor cells. The kinase activator has been separated from transforming growth factor beta by reversed-phase HPLC and affinity chromatography. Like the transforming growth factor, it is heat stable and trypsin labile, but it is not inactivated by dithiothreitol. In sodium dodecyl sulfate/polyacrylamide gel electrophoresis the purified preparation shows a major double band at about 31,000 daltons. Comparisons of electrophoretic mobility, protein kinase stimulatory activity, and cross-reactivity with an antibody against histone 1 suggest that the placental activator is identical with histone 1.

Characterization of a new antigen-antibody system (Su) in patients with systemic lupus erythematosus

A new antigen (Su) from calf thymus nuclear extract that reacts with sera from patients with systemic lupus erythematosus (SLE) is described. Antibodies to Su, demonstrated by immunodiffusion, were most frequently found in patients with a diagnosis of probable or definite SLE. Thirty-seven percent of patients with Su antibodies and a diagnosis of SLE were positive for antinuclear antibodies by indirect immunofluorescence, but lacked specific antibodies previously associated with SLE. Patients with Su antibodies exhibited a higher frequency of Raynaud's phenomenon, but exhibited a lower frequency of malar rash, alopecia, and arthritis when compared with SLE patients in previously published reports. The Su antigen is weakly acidic, heat-stable at 37 degrees C, heat-sensitive at 56 degrees C, resistant to DNase and RNase, but sensitive to trypsin. Its molecular weight approximated 154,000 daltons by Sepharose chromatography. The Su antibody may be associated with a subset of SLE patients with distinct clinical features, and may serve as a serologic marker for patients who are positive for fluorescent antinuclear antibodies but have no other detectable SLE-associated antibodies.

An octamer of histones H3 and H4 forms a compact complex with DNA of nucleosome size

Equimolar mixtures of histones H3 and H4 have been reconstituted onto DNA of nucleosome core size. Two distinct complexes are formed in a relative abundance that depends on the starting ratio of H3 + H4 to DNA. One of these complexes contains two H3-H4 dimers for each DNA molecule, and has a sedimentation coefficient of 7.5S. The other complex contains an octamer consisting of four H3-H4 dimers, and has a sedimentation coefficient of 10.4S. On the basis of these measurements, we conclude that the octamer complex (but not the tetramer complex) is a fully folded, compact structure resembling the nucleosome.

Properties of the complex between histone H1 and poly(ADP-ribose synthesised in HeLa cell nuclei

Preparations of H1 histone from HeLa cell nuclei incubated with [3H]NAD to permit poly(ADP-ribose) synthesis were electrophoresed on polyacrylamide gels. The incorporated radioactivity migrated as a sharply defined peak in association with a protein band which moved more slowly than H1, the major protein component. The following observations indicate that this complex is composed of two molecules of H1 and a single chain of poly(ADP-ribose) with one detectable covalent linkage of polymer to protein. 1. The [14C]arginine/[3H]lysine ratio is identical in H1 histone and in the protein moiety of the complex. 2. Protein is displaced from H1 histone to the complex during poly(ADP-ribose) synthesis. At least 90% of the protein in the complex (stainable protein and labelled protein) is derived from H1. 3. Sedimentation rate studies indicate a molecular weight of the complex about twice that of H1 histone. 4. The average chain length of the polymer is 15 ADP-ribose units and there are 7--8 ADP-ribose units for each molecule of H1 histone in the 'complex'. 5. Poly(ADP-ribose) glycohydrolase, which hydrolyses the polymer exoglycosidically from the AMP terminus, degrades the complex producing ADP-ribose and mono-ADP-ribosylated H1 histone which co-electrophoreses with unmodified H1. Although only one covalent linkage between protein and polymer has been detected, the 'complex' does not dissociate when electrophoresed on dodecylsulfate gels. Nor can the noncovalently linked H1 histone of the complex readily exchange with free H1. Complex formation does not occur when purified poly(ADP-ribose) and H1 are mixed.

Dibutyryl cyclic AMP mimics ovariectomy: nuclear protein phosphorylation in mammary tumor regression

Growth of mammary carcinoma induced by 7,12-dimethyl-benz(a) anthracene is arrested by either ovariectomy or treatment with N6,O2-dibutyryl cyclic adenosine 3',5'-monophosphate (dibutyryl cyclic AMP). When this occurs, a new nonhistone protein species becomes the predominant endogenous substrate of cyclic AMP-dependent protein kinase in the tumor nuclei. Phosphorylation of this regression-associated protein ceases when resumption of tumor growth is induced by either the injection of 17 beta-estradiol or cessation of dibutyryl cyclic AMP treatment. Thus phosphorylation of regression-associated protein may play a role in the regression of hormone-dependent mammary tumors.

The organization of histones and DNA in chromatin: evidence for an arginine-rich histone kernel

We have examined the role played by various histones in the organization of the DNA of the nucleosome, using staphylococcal nuclease as a probe of DNA conformation. When this enzyme attacks chromatin, a series of fragments evenly spaced at 10 base pair intervals is generated, reflecting the histone-DNA interactions within the nucleosome structure. To determine what contribution the various histones make to DNA organization, we have studied the staphylococcal nuclease digestion patterns of complexes of DNA with purified histones. Virtually all possible combinations of homogeneous histones were reconstituted onto DNA. Exhaustive digestion of a complex containing the four histones H2A, H2B,H3, and H4 yields a DNA fragment pattern very similar to that of whole chromatin. The only other combinations of histones capable of inducing chromatin-like DNA organization are H2A/H2B/H4 and those mixtures containing both H3 and H4. From an examination of the kinetics of digestion of H3/H4 reconstitutes, we conclude that although the other histones have a role in DNA organization within the nucleosome, the arginine-rich histone pair, H3/H4, can organize DNA segments the length of the nucleosome core in the absence of all other histones.