Histone H3 thiol reactivity as a probe of nucleosome structure

Identification of autoreactive B cells with labeled nucleosomes

The pathogenesis of autoimmune diseases has not been completely elucidated yet, and only a few specific treatments have been developed so far. In autoimmune diseases mediated by pathogenic autoantibodies, such as systemic lupus erythematosus, the specific detection and analysis of autoreactive B cells is crucial for a better understanding of the physiopathology. Biological characterization of these cells may help to define new therapeutic targets. Very few techniques allowing the precise detection of autoreactive B cells have been described so far. Herein we propose a new flow cytometry technique for specific detection of anti-nucleosome B cells, which secrete autoantibodies in systemic lupus erythematosus, using labeled nucleosomes. We produced different fluorochrome-labeled nucleosomes, characterized them, and finally tested them in flow cytometry. Nucleosomes labeled via the cysteines present in H3 histone specifically bind to autoreactive B cells in the anti-DNA transgenic B6.56R mice model. The present work validates the use of fluorochrome-labeled nucleosomes via cysteines to identify anti-nucleosome B cells and offers new opportunities for the description of autoreactive B cell phenotype.

Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants

Bioorthogonal chemical reporters are useful tools for visualizing and identifying post-translational modifications on proteins. Here we report the proteomic analysis of mammalian proteins targeted by a series of fatty acid chemical reporters ranging from myristic to stearic acid. The large-scale analysis of total cell lysates from fully solubilized Jurkat T cells identified known fatty-acylated proteins and many new candidates, including nuclear proteins and in particular histone H3 variants. We demonstrate that histones H3.1, H3.2, and H3.3 are modified with fatty acid chemical reporters and identify the conserved cysteine 110 as a new site of S-acylation on histone H3.2. This newly discovered modification of histone H3 could have implications for nuclear organization and chromatin regulation. The unbiased proteomic analysis of fatty-acylated proteins using chemical reporters has revealed a greater diversity of lipid-modified proteins in mammalian cells and identified a novel post-translational modification of histones.

Retinoblastoma protein transcriptional repression through histone deacetylation of a single nucleosome

The retinoblastoma protein, pRb, controls transcription through recruitment of histone deacetylase to particular E2F-responsive genes. We determined the acetylation level of individual nucleosomes present in the cyclin E promoter of RB(+/+) and RB(-/-) mouse embryo fibroblasts. We also determined the effects of pRb on nucleosomal conformation by examining the thiol reactivity of histone H3 of individual nucleosomes. We found that pRb represses the cyclin E promoter through histone deacetylation of a single nucleosome, to which it and histone deacetylase 1 bind. In addition, the conformation of this nucleosome is modulated by pRb-directed histone deacetylase activity. Thus, the repressive role of pRb in cyclin E transcription and therefore cell cycle progression can be mapped to its control of the acetylation status and conformation of a single nucleosome.

Characterization of specific nucleosomal states by use of selective substitution reagents in model octamer and tetramer structures

Packaging of the DNA in nucleosomes restricts its access to regulatory factors and enzymatic complexes, making a local remodeling of the nucleosome structure a prerequisite to the establishment of protein-DNA interactions. The use of an experimental system in which one nucleosome is reconstituted on a topologically constrained DNA minicircle allows the visualization of different conformations of the nucleoprotein particle. The single cysteine located at position 110 of histone H3 can be titrated with thiol reagents, such as iodoacetamide (IAM), N-ethylmaleimide (NEM), and dithiobisnitrobenzoic acid (DTNB), in both histone octamers and histone (H3-H4)(2) tetramers. Treatment of histone H3 with IAM, NEM, and DTNB allows the trapping of different conformations of the (H3-H4)(2) tetramer within the nucleoprotein particle. When H3 cysteines are titrated within the histone octamer, IAM, NEM, and DTNB block the tetramer in the left-handed conformation, the conformation it adopts within the nucleosome. The left-handed conformation is initially dictated by H2A-H2B dimers and then frozen by the thiol reagents. When cysteines are titrated within the histone tetramer, the flexibility of the particle becomes apparent. NEM and IAM behave differently from DTNB. The first two reagents block the particle in its left-handed conformation while DTNB treatment favors the right-handed conformation. These thiol reagents that block the nucleoprotein particles in a given conformation should allow their structural analysis. They may also help the investigation of the role of the (H3-H4)(2) nucleoprotein particle structural transition in biological processes involving nucleosome dynamics, such as DNA transcription, replication, and repair.

Sequential arrangement, not transcriptional activity, determines conformational stability of nucleosomes

Gel electrophoresis in urea gradient was applied to study the unfolding effect of increasing concentrations of urea on the nucleosome structure. We showed that conformational stability of nucleosomes is determined by nucleotide sequence but not by transcriptional activity of DNA in chromatin.

H3 Cys-110 is in close proximity to the C-terminal regions of H2B and H4 in a nucleosome core with an altered internal arrangement of histones

A particle obtained by nuclease digestion of nucleohistone complexes prepared by direct mixing of histones with DNA in 0.15 M NaCl was indistinguishable by composition and physical properties from nucleosome cores prepared under the same conditions from nucleohistone preannealed in 0.6 M NaCl. We show here that different photo-cross-links form when these particles are prepared from H3 labeled with photoaffinity reagents on the unique histone H3 cysteine. H3-H3 histone dimers were dominant when the particles were prepared by dilution of the nucleohistone from 0.6 M NaCl while H3-H2B and H3-H4 histone dimers were prominent if the nucleohistone complex was prepared directly in 0.15 M NaCl. Peptide mapping of the novel H3-H4 and H3-H2B dimers showed that Cys-110 of histone H3 is cross-linked to the 18 amino acid C-terminal end of H4 or to the 66 amino acid C-terminal half of H2B.

Reversible and irreversible changes in nucleosome structure along the c-fos and c-myc oncogenes following inhibition of transcription

A new affinity chromatographic procedure for the separation of transcriptionally active nucleosomes has been used to study the changes that take place in chromatin structure along the c-fos and c-myc genes when RNA synthesis is inhibited. Mercury-affinity chromatography separates the sulfhydryl-reactive nucleosomes of transcriptionally active genes from the compactly beaded, non-reactive nucleosomes of transcriptionally inert DNA sequences. The new procedure also discriminates between nucleosomes that have "unfolded" to reveal the previously shielded SH groups of histone H3 and nucleosomes that bind to the mercury column because of their association with thiol-containing non-histone proteins located in the transcription unit. Both classes of Hg-bound nucleosomes contain the c-fos and c-myc sequences, but only when they are being transcribed. We compared the effects of alpha-amanitin and actinomycin D on the transcription of c-fos and c-myc with the effects of each inhibitor on the distribution of the corresponding oncogenic DNA sequences in the chromatographically separated nucleosome fractions. It was found that the inhibition of RNA polymerase II by alpha-amanitin (added at the peaks of c-fos or c-myc expression in serum-stimulated BALB/c 3T3 cells) resulted in a rapid loss of affinity of the oncogene-containing nucleosomes for the mercury column. There was no corresponding effect on the mercury-binding properties of nucleosomes containing 28 S ribosomal gene sequences, which continue to be transcribed by amanitin-resistant RNA polymerase I. Therefore, the binding of the c-fos and c-myc nucleosomes to the mercury column seems to depend upon reversible structural changes associated with their transcription. Surprisingly, there was no corresponding loss of affinity of the c-fos and c-myc nucleosomes for the mercury column when actinomycin D was employed to inhibit RNA synthesis, despite the fact that transcription of both genes had been arrested abruptly. Measurements of [3H]actinomycin D binding show its preferential intercalation into the transcriptionally active nucleosomes. We suggest that the intercalation of actinomycin D into the DNA of active nucleosomes can lock the transcription complex into an "unfolded" but potentially active configuration. This was confirmed by run-off transcription assays showing a restoration of c-fos and c-myc RNA synthesis when actinomycin D was displaced by proflavine.

Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences

The unfolding of nucleosome cores in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3, making them accessible to SH-reagents. This has suggested that nucleosomes from active genes could be retained selectively on organomercurial/agarose columns. When nucleosomes released from rat liver nuclei by limited digestion with micrococcal nuclease were passed through an Hg affinity column, a run-off fraction of compact, beaded nucleosomes was separated from a retained nucleosome fraction. Although both contained monomer-length DNA and a full complement of core histones, histones in the retained fraction were hyperacetylated. Dot blot hybridizations showed the Hg-bound nucleosome fraction to be enriched in DNA sequences transcribed by hepatocytes (serum albumin and transferrin genes), while a brain-specific gene (preproenkephalin) was not retained, but appeared in the nucleosomes of the run-off fraction. The results are discussed in light of other evidence linking hyperacetylation of histones H3 and H4 to conformational changes at the middle of the nucleosome core.

Nucleosomal structure as probed by H3 histone thiol reactivity. Conformation of H3 histone variants is differently affected by thiol group reagents

Two H3 histone variants are found in equal amount in HeLa cells, and they have been characterized by two-dimensional gel electrophoresis followed by reaction with specific antibodies. These molecules are the only cysteine-containing histones, and they have been used as the target for thiol-specific reagents, in intact nuclei, isolated nucleosomes, histone complexes, and purified histones. Cysteine residues are available to N-ethylmaleimide only when histones are disassembled from the core particles. Upon reaction with these reagents, one of the H3 variants undergoes profound conformational changes, as revealed by an altered electrophoretic mobility.

Thiol reactivity of histone H3 in soluble and DNA-associated histone complexes: evidence for allosteric and torsional regulation

The reactivity of chick erythrocyte and calf thymus histone H3 thiol groups toward 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) has been investigated both in the soluble, DNA-free state and in various nucleohistone complexes. We have found that the thiol reactivity of both tetramers and octamers decreases continuously as the ionic strength of the assay is increased, up to and beyond 2.0 M NaCl. Upon association of dimers with tetramers, there is loss of labeling by DTNB at one site, suggesting the existence of allosteric regulation [see also Godfrey, J. E., Eickbush, T. H., & Moudrianakis, E. N. (1980) Biochemistry 19, 1339-1346] of dimer-tetramer interfaces emanating from within the tetramer complex. Comparison of the thiol reactivities of chick and calf tetramers indicates that the thiol groups at amino acid positions 96 and 110 are not chemically equivalent. When the histones are associated with DNA, in either reconstituted complexes, core particles, or long soluble chromatin, the thiol reactivity is greatly diminished, and this "DNA effect" overwhelms any influence of dimers. However, if single-strand nicks are introduced into the DNA backbone of core particles and other chromatin-like complexes by the action of DNase I, the influence of the DNA double helix upon thiol reactivity is reduced, and the effect of dimers can be detected once again. We can therefore conclude that the DNA effect derives from intranucleosomal torsional strain of the continuum of the double helix in equilibrium with coupled protein conformational changes. These observations support the concept that the octamer complex is a dynamic tripartite structure whose properties can be modulated through its interactions with DNA and by changes occurring in the dimer-tetramer interfaces.

Reversible changes in nucleosome structure and histone H3 accessibility in transcriptionally active and inactive states of rDNA chromatin

The sulfhydryl reagent iodoacetamidofluorescein (IAF) was used to probe the structure of chromatin subunits in transcribed and nontranscribed regions of Physarum rDNA. IAF labels histone H3 -SH groups in the elongated monomeric subunits (A particles) from the transcribed region, but it does not label H3 in the 11S monomers from the nontranscribed central spacer. All H3 reactivity is lost from rDNA chromatin in the inactive spherule stage of Physarum. Restriction cleavage of rDNA chromatin generates fragments from the transcription unit with reactive H3 -SH groups, whereas fragments containing nontranscribed spacer sequences are unreactive. The extended rDNA chromatin contains all four core histones and other prominent proteins. Electron microscopy shows that most of the extended subunits consist of two roughly spherical bodies connected by a 50 bp nucleoprotein bridge.

Crystallization of the tetramer of histones H3 and H4

Crystals of the histone tetramer (H3-H4)2 from calf thymus have been grown. The crystals yield x-ray diffraction patterns with Bragg spacings as small as 3.5 angstroms. Crystals grown from two types of preparations have the symmetry of the space group P61 (or P65). The best crystals were grown from histones that had the amino terminal arms removed by mild trypsinization.

Parameters affecting the superreactivity of the cysteine side chain in histone H3. Characterization of a 32-amino-acid peptide including Cys-110

Tryptic digestion of the whole histone mixture from chicken erythrocytes is used to isolate the hydrophobic portion (residues 84-115) of histone H3. The phenomenon of a superreactive thiol at Cys-110 was reinvestigated by the reaction of a neutral, fluorogenic reagent, N-[p-(2-benzimidazolyl)phenyl]maleimide, with this peptide and with the intact histone. Removing the highly basic portions of H3 leads to a strong reduction of Cys-110 reactivities, even if a stoichiometric complex with histone H4 is reconstituted. An apparent superreactivity is found only for a non-degraded histone H3 under conditions of low ionic strength but not for the histone complex in its native conformation. It is concluded that thiol activation is due to an artifactual cluster of positive charges around Cys-110 rather than to a stable microenvironment.

Possible structures for the nucleosome core of chromatin at the molecular level

This paper integrates data from four sources into a single hypothesis of the overall structure of the histones making up the core of the nucleosome. The data collated are (i) the overall size and shape of the particle and number and symmetry of histones involved; (ii) the known loci of attachment of the individual histones to specified loci on the DNA super coil; (iii) the known loci of individual amino acid residues known to bind to DNA; and (iv) the Chou and Fasman predictions of secondary structures from sequences of the individual histones. The overall structure suggested in two inner struts made up by the two H4 molecules. These struts are strengthened by H3 alpha and beta-structure and H2 beta alpha-helices.

Reactivity of individual functional groups of histones in calf thymus chromatin

Using the technique of competitive labelling (Kaplan, H., Stevenson, K.J. and Hartley, B.S. (1971) Biochem. J. 124, 289-299) with 1-fluoro-2,4-dinitro-[3,5-3H]benzene ([3H]Dnp-F), the chemical reactivity of the alanyl amino-terminus of H3, the prolyl amino-terminus of H2B and the sulphydryl groups of H3 within calf thymus chromatin were determined. Over pH values from 6 to 10, none of the groups had pH-reactivity profiles which fit titration curves, indicating that they are involved in specific interactions with other structural elements of chromatin. The alanyl amino-terminus is completely nonreactive over the entire pH range studied. The prolyl amino-terminus is reactive but its reactivity is considerably lower than expected for a secondary amino group. An unusual feature of this group is that its pH-reactivity profile has sharp discontinuities at pH values of 7.8 and 9. The average reactivity of the two sulphydryl groups of H3, unlike the two amino-termini, appears to approximate that expected of a free sulphydryl group.

The in situ labeling of histone H3 in chromatin by a fluorescent probe

A sulfhydryl-specific fluorescent probe, N-3-pyrene maleimide, has been shown to label with high efficiency the sulfhydryl groups of histone H3 in nonsheared chromatin. The probe labels chromatin preparations obtained by mild homogenization or nuclease treatment of rat liver and mouse thymocyte, but not chick erythrocyte nuclei. Mononucleosomes from all nuclear preparations are labeled by the probe. The reaction is inhibited by prior reaction of the chromatin with N-ethyl maleimide. The reaction kinetics show fast and slow components representing reactions with cysteinyl sulfhydryl groups and lysyl epsilon-amino groups, respectively. Dissociation of the chromatin by urea (6 M) or sodium dodecyl sulfate (SDS) increases the fluorescence intensity (2-3 fold) and is maximal at approx. 0.01-0.02% (w/v) SDS. Histones extracted from the labelled chromatin show that approx. 80-90% of the label is associated with the histone fraction and column chromatography of this fraction shows that the label is primarily associated with histone H3. Labelling of the isolated histone fractions shows significant labelling only of histone H3. The intrinsic fluorescence of tryptophan is quenched by the labelled histone H3, but not by iodide, suggesting that non-histone (tryptophan-containing) proteins lie in close proximity to the labelled histone H3 but are not immediately accessible to external solvent. The labelled chromatin exhibits fluorescence anistropy, the anistropy parameter being 0.19 +/- 0.003 for chromatin, 0.05 +/- 0.01 for mononucleosomes and 0.0 for isolated histone H3. This demonstrates the restriction placed on the label's mobility by the chromatin fiber. The formation of a superhelix at 60-100 mM NaCl has been monitored with the probe. An increase in fluorescence intensity at 80 mM NaCl is observed with intact chromatin (but not H-1 depleted chromatin) followed by dissociation of the octamer in 1.50-2.0 M salt accompanied by a large increase in labelling.

Effect of histone H3 sulfhydryl modifications on histone-histone interactions and nucleosome formation and structure

The effect of histone H3 sulfhydryl mnodification and disulfide bridge formation on histone-histone interactions, nucleosome reconstitution and structure has been examined for calf and chicken mononucleosomes. For intramolecular disulfide bridge formation histone H3-H4 complexation is disrupted and no nucleosome-like particle containing all four of the histones could be prepared. Intermolecular disulfide bridge formation between H3 residues 110 and 110 as well as chemical modification of this site with small and with bulky groups allowed histone H3-H4 complexation and the reconstituatioin of a nucleosome-like particle. However, the yield of such particles is decreased and their thermal denaturation properties indicate a reduced stability. These results suggest that the histone core is destabilized or even structurally altered by even a minor modification at H3 position 110, such as carboxymethylation, and therefore this site must be used with caution for the attachment of reporter groups.

Transcription by eukaryotic RNA polymerases A and B of chromatin assembled in vitro

Chromatin was assembled in vitro from simian virus 40 DNA form I and the calf-thymus four histones H2A, H2B, H3 and H4. Transcription with calf thymus RNA polymerases A and B (I and II) was greatly inhibited. Nucleosomes were found to inhibit both RNA chain initiation and elongation. The inhibition of elongation could be relieved by increasing ionic strength, suggesting that electrostatic interactions between histone octamer and DNA have to be broken for RNA polymerase to transcribe DNA organised into nucleosomes.