Reconstitution of chromatin. The sequential binding of histones to DNA in the presence of salt and urea

CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly

Centromere-specific nucleosomes are a central feature of the kinetochore complex during mitosis, in which microtubules exert pulling and pushing forces upon the centromere. CENP-A nucleosomes have been assumed to be structurally unique, thereby providing resilience under tension relative to their H3 canonical counterparts. Here, we directly test this hypothesis by subjecting CENP-A and H3 octameric nucleosomes, assembled on random or on centromeric DNA sequences, to varying amounts of applied force by using single-molecule magnetic tweezers. We monitor individual disassembly events of CENP-A and H3 nucleosomes. Regardless of the DNA sequence, the force-mediated disassembly experiments for CENP-A and H3 nucleosomes demonstrate similar rupture forces, life time residency and disassembly steps. From these experiments, we conclude that CENP-A does not, by itself, contribute unique structural features to the nucleosome that lead to a significant resistance against force-mediated disruption. The data present insights into the mechanistic basis for how CENP-A nucleosomes might contribute to the structural foundation of the centromere in vivo.

NaCl-aided Hoechst 33258 staining method for DNA quantification and its application

We investigated the effect of salt on the fluorescence staining procedure for quantification of the amount of DNA in cell nuclei in situ. For this, NaCl was added at various concentrations to the Hoechst 33258 fluorochrome (Hoe) medium for staining DNA. The fluorescence intensity of free DNA-Hoe solution was not changed by the addition of NaCl, but that of the nuclei-Hoe complex in situ increased 4-fold on increasing the NaCl concentration up to 1 M. SDS polyacrylamide gel electrophoresis showed that histones H1, H2A, and H2B dissociated from cell nuclei in the presence of 1 M NaCl, resulting in increasing accessibility of DNA to the fluorochrome. The applicability of the NaCl-aided fluorescence staining method was evaluated by measuring the ploidy classes of various cells. The amount of DNA in spermatozoa is half that in 2 n hepatocytes, but by the conventional Hoe staining procedure the fluorescence intensity of spermatozoa is higher than that of 2 n hepatocytes, due to differences in accessibility of the dye to DNA. In contrast, by the NaCl-aided procedure, the fluorescence intensity of 2 n hepatocytes was twice that of spermatozoa. The effectiveness of the NaCl-aided Hoe staining method was checked using cultivated human gingival cells and hepatocytes of LEC rats with hereditary hepatitis. In all cases, reasonable proportionality between the fluorescence intensity and the amount of DNA was observed.

Accurate determination of DNA content in single cell nuclei stained with Hoechst 33258 fluorochrome at high salt concentration

In an attempt to achieve accurate quantification of DNA levels in cell nuclei, we studied the influence of salt concentration on the fluorescence of cell nuclei complexed with Hoechst-33258 (Hoe) fluorochrome. The fluorescence of cell nuclei was compared with that of extracted DNA as well as that of nucleosome core. Conformational changes in these complexes were examined by measuring both fluorescence anisotropy and fluorescence lifetime in the nanosecond region. The results showed that the fluorescence of DNA-Hoe was quenched by the nucleosomal structure, there being an associated increase in anisotropy and a decrease in the fluorescence lifetime; however, the fluorescence was restored to the original level by the addition of a high concentration of NaCl, CsCl, or LiCl. The reduction in fluorescence may have been due to loss of fluorescence energy caused by collision of the fluorophore with histones in the nucleosome. The addition of 1 M NaCl to the medium used for staining with Hoe greatly stabilized the fluorescence of DNA in cell nuclei. The DNA content of individual cell nuclei was determined by comparing the fluorescence of these nuclei with that of a standard DNA solution. For lymphocytes and liver ploidy cells, reasonably accurate values were obtained by applying the present method.

Exposed hydrophobic regions in histone oligomers studied by fluorescence

The interaction of the fluorescent hydrophobic probe 1-anilinonaphthalene-8-sulfonate (ANS) with histone oligomers and with histone H1 has been studied. The enhancement of ANS fluorescence produced by histones Hv (a roughly equimolar mixture of histones H2A, H2B, H3 and H4) in 2.0 M NaCl, pH 7.5, is higher than that produced by histone H1 under identical conditions. In addition, the fact that the wavelength of maximum emission of the H1-ANS complex is larger than that of the Hv-ANS complex indicates that histone H1 has a weaker hydrophobic character than histones Hv. The increase in ANS concentration produces a red shift of the emission maximum of the Hv-ANS complex, indicating some heterogeneity in the ANS binding sites. Both the H2A-H2B and the H3-H4 complexes cause a similar enhancement of the ANS fluorescence. Trypsin digestion of N-terminal sequences of histones Hv produces only small changes in the intensity of ANS fluorescence. This result indicates that the hydrophobic regions of histones Hv to which ANS binds are not located in the N-terminal portions of histone sequences. It is suggested that these exposed hydrophobic regions may be important in the maintenance of chromatin structure.

On mechanisms determining the interrelationships between DNA and histone components of chromatin

The relative affinity of histones for DNA was studied by the analysis of competitive histone binding to DNA in whole histone/DNA mixtures at physiological and low ionic strengths as well as in water. Use of polyphosphate in similar experiments, as a model of DNA deprived of hydrophobic functional groups allowed us to reject the hypothesis that hydrophobic DNA-histone interaction plays a decisive role in the determination of the relative affinity of histones for DNA, because the orders of histone preference for DNA and for polyphosphate were the same. The relative histone affinity for DNA does not depend on the secondary structure of DNA or on the ionic strength of salt solutions, though the differences in the histone affinities for DNA decrease on lowering the salt concentration. The binding orders of the first and the last molecules of histone type to DNA, studied at various DNA/histone ratios in the medium of physiological ionic strength, are the following: H3+H4, H2A+H2B, H1 and H3+H4, H2A, H2B, H1. In water the binding orders of the first and the last histone molecules to DNA are identical: H3+H4, H2A, H2B+H1. It is concluded that the relative histone affinity for DNA in water/salt solutions is determined by non-ionic interactions between histones bound to DNA. The folding of DNA induced by histone-histone interaction seems to lead to the increase in the correlation between amino acid residues in the histone regions bound to DNA and the ionic DNA-histone interaction becoming stronger.

Fractionation of native and reconstituted chromatin by digesting with deoxyribonuclease ii

Native and reconstituted chromatin from Ehrlich ascites tumor cells were fractionated into template-active and inactive fractions by the DNAase II/Mg2+-solubility method of Gottesfeld et al. (Gottesfeld, J.M., Garrard, W.T., Bagi, G., Wilson, R.F. and Bonner, J. (1974) Proc. Natl. Acad. Sci. U.S.A. 71, 2193-2197). The Mg2+-soluble (template-active) fractions were compared in respect to sedimentation behavior in sucrose gradients and the relative content of specific transcribed (ribosomal) and non-transcribed (satellite) DNA sequences. It was found that the Mg2+-soluble fraction of the native chromatin was enriched in ribosomal DNA while almost completely devoid of satellite DNA; the nucleoprotein monomer of this fraction sedimented in sucrose gradient at 14 S. Similar-results were obtained if chromatin was fractionated in the presence of 3 M urea. With reconstituted chromatin, however, neither the sedimentation profile, nor the relative content of ribosomal and satellite DNA sequences were recovered, thus indicating that reconstitution did not yield nucleoprotein structurally similar to native chromatin.

Salt-induced structural changes in nucleosomes

Ehrlich ascites tumor (EAT) nucleosomes treated with increasing NaCl concentrations were analyzed by sucrose density gradient centrifugation. Two events were found to take place in the course of the salt treatment: a) increasing amounts of nucleosomes dissociated into free DNA and protein in the interval 0.6M-1.5M NaCl, and b) the sedimentation coefficient of the nucleosomes decreased from 11S to 8S in the interval 0.6M - 1M NaCl. This decrease was not caused by loss of protein and was fully reversible upon slow and gradual lowering of the ionic strength. This shows that before dissociation of the protein core from DNA, nucleosomes undergo a structural transition. The electron microscopic observations revealed that it consisted in detachment of the ends of nucleosomal DNA from the protein core. It is suggested that an arginine-rich domain in the protein core exists, which holds more tightly the central part of the nucleosomal DNA, while its ends are relatively loosely bound to lysine-rish domains.

The histone core complex: an octamer assembled by two sets of protein-protein interactions

A protein complex, extracted from calf thymus chromatin with 2 M NaCl, pH 7.5, containing approximately equal molar ratios of histones H2A, H2B, H3, and H4, has been characterized in this study. Gel filtration, sedimentation velocity, and sedimentation equilibrium experiments demonstrate that this complex, known as the core complex, has a molecular weight near that expected for a histone octamer (108 000 for a unit containing two each of the four inner histones) and far exceeding that of a histone tetramer (54 400). This finding suggests that the histone octamer, postulated to be the fundamental histone unit in chromatin, is stable in 2 M NaCl, pH 7.5, in the absence of DNA or chemical cross-linking reagents. In the second part of this study, we demonstrate that the bonds maintaining the octameric complex in 2 M NaCl are weak and distinctly different from the forces stabilizing the H2A-H2B dimer or H3-H4 tetramer. The octamer is dissociated into two H2A-H2B dimers and one H3-H4 tetramer by (i) increasing temperature; (ii) decreasing NaCl concentration; (iii) adding low concentrations of urea or guanidine hydrochloride; and (iv) lowering the pH below 7 or raising it above 10. These findings indicate that the octamer is assembled by two sets-of protein-protein interactions. The first set involves mostly hydrophobic interactions and yields the H2A-H2B dimer and the H3-H4 tetramer subunits. The second set involves the weak association of one H3-H4 tetramer with two H2A-H2B dimers to form an octamer. We suggest that these weak interactions might be derived predominantly from histidine-lysine or histidine-tyrosine hydrogen bonds between the dimer and tetramer subunits.

Complexes of DNA with arginine-rich and slightly lysine-rich histones. Transcription and electron microscopy

Calf thymus DNA was reconstituted with arginine-rich histones H3 and H4 and slightly lysine-rich histones H2A and H2B respectively. Complexes containing histones H3 and H4 exhibit nucleosome-like structures when examined in the electron microscope and show a restriction of in vitro transcription similar to that obtained for reconstitutes made up from the four histones H2A, H2B, H3 and H4. One the contrary, complexes of DNA and histones H2A and H2B create different morphological structures of short stretches of bound histones and do not cause a template restriction in vitro.

Reconstitution of chromatin subunits

The recovery of the subunit structure of chromatin after dissociation and reconstitution is markedly affected by the procedure used. Some procedures give complete regeneration of subunits, but the procedure most commonly used for reconstitution gives poor yields of subunit-containing chromatin.

Effects of estrogen on gene expression in the chick oviduct. Isolation and fractionation of chromatin non-histone proteins

Non-histones isolated from hen oviduct chromatin have been fractionated by a variety of methods. Chromatin was dissociated in 2 M NaC1, 5 M Urea, 0.1% beta-mercaptoethanol and 0.01 M Tris - HC1, pH 8.3, and the DNA removed by ultracentrifugation. After desalting by gel filtration the chromatin proteins were separated into three distinct fractions by stepwise elution with 0.10 M NaC1, 0.25 M Na C1 and 15% guanidine - HC1 from Bio-Rex 70 columns. Fractions I and II contain only non-histones and Fraction III contains histones plus a small amount of non-histones. Further fractionation of the non-histones was achieved by ammonium sulfate precipitation and DEAE-cellulose chromatography for Fraction I and phosphocellulose chromatography and gel filtration on Bio-Gel A-15 m for Fraction II. The histone and non-histones present in Fraction III were separated by gel filtration on Bio-Gel A-0.5 m. All fractionation methods have been used preparatively with reasonable recoveries of protein (greater than or equal to 60%). The fractions have been characterized by acrylamide gel electrophoresis. The integrity of the histones was maintained during the fractionation procedure indicating that proteolytic degradation was unlikely to have occurred. There was no selective loss of chromatin proteins during the ultracentrifugation and desalting steps and the non-histones were separated into distinct fractions with enrichment of some species not apparent prior to fractionation of the chromatin proteins.

Mode of reconstitution of chicken erythrocyte and reticulocyte chromatin

The mode of reconstitution of chicken erythrocyte and reticulocyte chromatin has been investigated. Chromatin was dissociated in 2 M NaCl, 5 M urea, and 0.01 M potassium phosphate (pH 7.2) and was dialyzed against various NaCl concentrations in 5 M urea and 0.01 M potassium phosphate (pH 7.2). Histone reassociation to DNA occurs with the binding of histone H5 at 0.5 M NaCl in 5 M urea, followed by histone H1 at 0.4 M NaCl in 5 M urea. All the classes of histones are reassociated with DNA at 0.2 M NaCl in 5 M urea and binding of all classes of histones is complete in 0.1 M NaCl and 5 M urea. Nonhistone proteins reassociate with DNA before and at the same time that histones reassociate with DNA. Binding of nonhistone proteins to DNA appears to be complete in 5 M urea and 0.01 M potassium phosphate (pH 7.2). There is also found in both erythrocyte and reticulocyte chromatin a nonhistone protein present in relatively high concentrations, which remains associated with DNA in 2 M NaCl and 5 M urea. This tightly bound protein appears as one major band when chromatographed on sodium dodecyl sulfate-polyacrylamide gels, with a molecular weight of 95 000. This protein is soluble in phenol and sodium dodecyl sulfate but is insoluble in 5 M urea or 4 M guanidine hydrochloride. A fraction of reticulocyte nonhistone proteins was found to bind to DNA-cellulose in 5 M urea. The majority of these proteins elute at 0.15 M NaCl in 5 M urea but a significant fraction elutes at NaCl concentrations at which the bulk of the histones do not bind to DNA. The proteins that bind to free DNA have low molecular weights and do not show species speciificity. Approximatley 50% of the reticulocyte nonhistone protein does not bind to a DNA-cellulose column in 5 M urea and may require histones for complete reassociation.

Complete displacement of somatic histones during transformation of spermatid chromatin: a model experiment

Displacement of histones from calf thymus chromatin has been studied in an attempt to postulate the mechanisms involved in the total removal of somatic-type histones during transformation of spermatid chromatin. When chromatin is saturated with protamine (protamine/DNA, 0.5), histone I becomes displaceable at 0.15-0.3 M NaCl, suggesting that direct replacement by highly basic sperm histone could be a mechanism for its removal. While histone I is the only histone which is extensively degraded upon incubation of chromatin and, therefore, proteolysis might provide an additional mechanism for the removal of this histone, acetylation of chromatin by acetic anhydride greatly increases suscpetibility of histones IIb1, IIb2, and III to the chromosomally associated protease. These histones are extensively degraded and displaced from the DNA upon incubation of the acetylated chromatin. Although histone IV is not appreciably degraded, the proteolytic removal of acetylated histone III from chromatin weakens the interaction of acetylated histone IV to the DNA, and this histone becomes dissociable at 0.3 M NaCl. A comparison of the extent of chemical acetylation of individual histones observed in this investigation with that of enzymatic acetylation which can be achieved in vivo suggests that acetylation and proteolysis could be a mechanism for the removal of histone IIb2 and III. The displacement of histones IIb1 and IV could be explained on the basis of decreased binding to DNA as a result of their acetylation together with the proteolytic removal of their respective partner histones, IIb2 and III.

Physical studies of chromatin. The recombination of histones with DNA

Experiments have been carried out to define clearly which histone combinations can induce a higher order structure when combined with DNA. The criterion for a higher order structure being the series of low-angle X-ray diffraction maxima nominally at 5.5 nm, 3.7 nm, 2.7 nm and 2.2 nm. Such a pattern, with resolution similar to that of H1-depleted chromatin, is readily attainable by recombining histones H2A + H2B + H3 + H4 with DNA using a salt-gradient dialysis method. However, the use of urea in the recombination procedure is shown to be detrimental to the production of a higher order structure. Low-angle ring patterns are not obtained by recomgining DNA with single pure histones or any combination of histone pairs exept H3 + H4. The diffraction maxima from the latter are, however, weaker than those from chromatin and there are pronounced semi-equatorial arcs. The presence of a third histone, either H2A or H2B in the H3 + H4 recombination mixture tends to distort the recognised low-angle pattern. It is concluded that the histone pair H3 + H4 is essential for the formation of a regular higher order structure in chromatin, although for a complete structural development the presence of H2A + H2B is also required.

A study of the interaction of histones with DNA using isopycnic centrifugation in metrizamide gradients

Isopycnic sedimentation in metrizamide gradients has shown that mouse-liver histones bind co-operatively to both homologous and bacterial DNA's. However, at low input ratios of histone to DNA, two types of stable complex are formed, depending on the histone concentration. One complex contains half as much histone as DNA while the other contains approximately equal amounts of histone and DNA. At high input ratios of histone to DNA extra histone is bound giving complexes containing up to twice as much histone as DNA. Poly-L-lysine and protamine were also found to bind co-operatively to DNA.

The F3-F2a1 complex as a unit in the self-assembly of nucleoproteins

A specific and stable interaction between histones f3 and f2a1 was demonstrated to take place in the absence of DNA. When a mixture of these histones was subjected to velocity sedimentation under conditions in which the separate histones are aggregated and precipitate, the mixture of f3 and f2a1 remained soluble and these histones appeared to cotransport through the gradient, indicating the establishment of an isolatable, stable f3-f2a1 complex. This isolated complex subsequently binds to DNA quantitatively to form nucleohistone. Stoichiometry data strongly suggest that histones f3 and f2a1 bind to DNA as a unit; this is the only type of f2a1 binding to DNA that can take place under mild conditions. Histone f1 can act as a modifier of the f3-f2a1-DNA interactions by augmenting the formation of the f3-f2a1 complex and consequently enhancing the overall binding of these histones to DNA. No significant interactions of histones f2b and f2a2 with other histones could be demonstrated. Because of the findings reported here and the known affinity characteristics of the arginine-rich histones to DNA in native chromatin (in particular their stimultaneous extraction from chromatin by salt), we suggest that the (f3 + f2a1)-DNA complex is a structural component of native chromatin. We would also like to propose that, in vivo, histones may possess a considerable amount of quaternary structure, which would greatly increase the specificity of their role as potential regulators of the structure and function of the eucaryotic chromosomes.

Reconstitution of chromatin: mode of reassociation of chromosomal proteins

The mode of reassociation of Ehrlich ascites histones and non-histone proteins during chromatin reconstitution was studied by sodium dodecyl sulfate polyacryl-amide gel electrophoresis. In the procedure of Bekhor et al. (I. Bekhor, G. M. Kung, and J. Bonner, (1969), J. Mol. Biol. 39, 351) most of histones and non-histone proteins reassociate with DNA in the last dialysis step of the dissociated chromatin, that is the dialysis of the chromatin in 0.4 M NaCl-5 M urea against a dilute buffer. The reassociation of histones and non-histone proteins with DNA is more gradual in the procedure of L. Kleiman and R.-C. C. Huang [(1972), J. Mol. Biol. 64, 1]. However, in both procedures the bulk of the Ehrlich ascites non-histone proteins reassociate with DNA after the binding of histones to DNA. There are small amounts of non-histone proteins which reassociate with DNA before and at the same time as histones reassociate with DNA.

Histone-histone associations within chromatin. Cross-linking studies using tetranitromethane

Treatment of chromatin with the protein cross-linker tetranitromethane (TNM) results in a product identified as an F2a1-F2b dimer. The same product appears after treatment with TNM of HeLa cells growing in culture. Furthermore acid-extracted histones which have been fractionated into the five separate species can be recombined and mixed with DNA to produce a nucleohistone preparation which is also cross-linked by TNM to give the F2a1-F2b dimer. F1 and F3 can be excluded from the reconstitution mixture without effect on the dimer production. In contrast, the presence of F2a2 is essential to the proper reconstitution of F2a1 and F2b with DNA. The specificity of TNM and the characteristics of the reaction suggest that F2a1 and F2b are cross-linked at their specific binding sites. These results provide evidence that F2a1, F2a2, and F2b interact specifically in chromatin.

Interaction of quinacrine mustard with mononucleotides and polynucleotides

1. The interaction between quinacrine mustard and mononucleotides and polynucleotides was investigated by fluorimetry and absorbance spectrophotometry. 2. The fluorescence spectrum of quinacrine mustard is independent of the ionic strength and pH. The dependence of the quinacrine mustard fluorescence intensity on ionic strength, pH and anions is described. 3. The fluorescence intensity of quinacrine mustard was enhanced with the mononucleotide adenylic acid and polynucleotides such as poly(rA), poly(rU) and poly(rA,rU). 4. Quenching of the fluorescence intensity of quinacrine mustard occurred with the mononucleotide guanylic acid and with poly(rG) and poly(rC,rG). 5. The mononucleotide cytidylic acid or poly(rC) showed no effect on the fluorescence intensity of quinacrine mustard. 6. The interaction between the dye and native DNA species was also dependent on the presence of base-specific binding sites in the DNA. The higher the (G+C) content was in the native DNA tested the higher was the quenching effect on the fluorescence intensity of quinacrine mustard. 7. No interaction was found between the dye and methylated DNA. The binding between quinacrine mustard and apurinic DNA was confirmed to be in the phosphate groups of the purines.