On the mechanism of nucleosome unfolding.

We have studied the relative stabilities to urea denaturation of histone-histone binding interactions as they occur both in chromatin and in histone complexes free in solution. We have used the two zero-length contact-site cross-linking agents, tetranitromethane and UV light, to measure the relative degree of H2B-H4 and H2A-H2B association under various conditions. The two interactions were disrupted coordinately when nuclei were treated with increasing concentrations of urea. In contrast, when histone complex in 2 M NaCl were treated with urea, the H2B-H4 interaction was found to be much less stable than the H2A-H2B interaction. We have shown previously that nucleosomes unfold at low ionic strengths such that the H2B-H4 but not the H2A-H2B interaction is broken in the process. We speculate that the preferential rupture of the H2B-H4 contact is of physiological significance.     

Analysis of the dynamic equilibrium of histone oligomers in a solution. The nature of forces stabilizing the (H2A-H2B-H3-H4)2 octamer structure

Dynamic equilibrium analysis of the (H2A-H2B-H3-H4)2 histone octamer with lower oligomers was performed in 2 M NaCl. Calculated data on the relative content of histone oligomers upon changing protein concentration in solution are given. The red shift of lambda max for histone tyrosine fluorescence spectra is shown to be due to hydrogen bond formation by tyrosyl OH-groups. Analysis of free energy changes of histone oligomers upon association (delta G = -17,37 +/- 0,14 kcal/mole) as well as the effect of urea on histone octamer dissociation made it possible to conclude that virtually all tyrosyls in octamer form hydrogen bonds. Intermolecular hydrogen bonds formed by tyrosyls contribute substantially to octamer stabilization. The (H2A-H2B) dimer positive cooperativity in association with the (H3-H4)2 tetramer was found. This cooperativity is caused by interaction between association sites with a two order increase in an apparent constant of dimers with tetramer association. The histone octamer was determined to be of asymmetric structure due to unequivolency of the two binding sites for the (H2A-H2B) dimers.     

Dynamic Solution Structures of Whole Human NAP1 Dimer Bound to One and Two Histone H2A-H2B Heterodimers Obtained by Integrative Methods

Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers, mediating their deposition on and eviction from the nucleosome. Human NAP1 (hNAP1) consists of a dimerization core domain and intrinsically disordered C-terminal acidic domain (CTAD), both of which are essential for H2A-H2B binding. Several structures of NAP1 proteins bound to H2A-H2B exhibit binding polymorphisms of the core domain, but the distinct structural roles of the core and CTAD domains remain elusive. Here, we have examined dynamic structures of the full-length hNAP1 dimer bound to one and two H2A-H2B heterodimers by integrative methods. Nuclear magnetic resonance (NMR) spectroscopy of full-length hNAP1 showed CTAD binding to H2A-H2B. Atomic force microscopy revealed that hNAP1 forms oligomers of tandem repeated dimers; therefore, we generated a stable dimeric hNAP1 mutant exhibiting the same H2A-H2B binding affinity as wild-type hNAP1. Size exclusion chromatography (SEC), multi-angle light scattering (MALS) and small angle X-ray scattering (SAXS), followed by modelling and molecular dynamics simulations, have been used to reveal the stepwise dynamic complex structures of hNAP1 binding to one and two H2A-H2B heterodimers. The first H2A-H2B dimer binds mainly to the core domain of hNAP1, while the second H2A-H2B binds dynamically to both CTADs. Based on our findings, we present a model of the eviction of H2A-H2B from nucleosomes by NAP1.     

Secondary structure of histones in solution

The secondary structure of histones H2B and H3 from calf thymus has been quantitatively studied in heavy water solutions in a wide range of histone concentrations, pD, and concentrations of sodium chloride by an infrared spectroscopy method. Also, the interactions between molecules of different histones in equimolar mixtures H2A-H2B, H2A-H3, H2A-H4, H2B-H3, H2B-H4, H3-H4, and H2A-H2B-H3-H4 have been investigated using the same method. For H2B and H3 conditions favourable for aggregation have been shown to induce the formation of pleated sheet structure. When the pD and concentration of NaCl are in a physiological range, the secondary structure of H2B and H3 contains about 15% of alpha-helix, 4% of parallel pleated sheet structure, 14% of antipatallel pleated sheet structure in H2B and 18% in H3. For mixtures in all cases, except H2A-H4, there is an interaction between molecules of different histones followed by a reduction of the antiparallel pleated sheet structure content. The data on the secondary structure of histones in different states (under self-association, in mixtures, in nucleosomes, and in chromatin) have been discussed and it is suggested that: 1) the secondary structure of histones in chromatin is essentially similar to that in the state of self-association; 2) in the core nucleosome particle the quantity of DNA (in nucleotide pairs), and the quantities of alpha-helix and antiparallel pleated sheet structure (in peptide groups) satisfy the relation 1 : 1 : 1.     

Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent

A new procedure is described which allows selective reversal of formaldehyde cross-linking in both histone-histone and histone-DNA of nuclei isolated from calf thymus. All ten possible dimers of the four non-H1 histones, H3, H2B, H2A and H4, are observed, the major dimers being H3-H3, H3-H2A, H2B-H2A, H2a-H2A and two separate dimers of H2B-H4. Although oligomers of the non-H1 histones are formed by prolonged treatment with this reagent, 50% of the histones continue to remain resistant to cross-linking with each other. For those histones which cross-linking with each other. For those histones which cross-link, the site of cross-linking within the molecules is located in the "core" (trysin-resistant) regionand therfore indicates proximities for these molecules within the nucleosome. The core region also cross-links to DNA, indicating intimate interactions between this region in all the non-H1 histones with DNA.     

Specific histone-histone contacts are ruptured when nucleosomes unfold at low ionic strength.

The ordered unfolding of the nucleosome core within chromatin at low ionic strengths has been studied. The results show that, when nuclei are lysed gently in solutions of very low ionic strength, their constituent nucleosomes rupture at a major H2B-H4 binding site but remain unperturbed at the site of the H2A-H2B interaction. These conclusions are based on data which show that at least four separate but closely spaced H2B-H4 contacts, identifiable by contact-site cross-linking in intact nuclei, are broken when nuclei are suspended in very dilute buffers. Appropriate controls on purified nucleosomes monomers demonstrate that the H2B-H4 contacts being broken are indeed intranucleosomal. Sedimentation of nucleosomes in the ultracentrifuge at various salt concentrations reveals that a significant conformational transition occurs in the range of ionic strength over which the H2B-H4 binding site ruptures.     

Nucleoplasmin Binds Histone H2A-H2B Dimers through Its Distal Face

Nucleoplasmin (NP) is a pentameric chaperone that regulates the condensation state of chromatin extracting specific basic proteins from sperm chromatin and depositing H2A-H2B histone dimers. It has been proposed that histones could bind to either the lateral or distal face of the pentameric structure. Here, we combine different biochemical and biophysical techniques to show that natural, hyperphosphorylated NP can bind five H2A-H2B dimers and that the amount of bound ligand depends on the overall charge (phosphorylation level) of the chaperone. Three-dimensional reconstruction of NP/H2A-H2B complex carried out by electron microscopy reveals that histones interact with the chaperone distal face. Limited proteolysis and mass spectrometry indicate that the interaction results in protection of the histone fold and most of the H2A and H2B C-terminal tails. This structural information can help to understand the function of NP as a histone chaperone.     

Equilibrium folding of the core histones: the H3-H4 tetramer is less stable than the H2A-H2B dimer

To compare the stability of structurally related dimers and to aid in understanding the thermodynamics of nucleosome assembly, the equilibrium stabilities of the recombinant wild-type H3-H4 tetramer and H2A-H2B dimer have been determined by guanidinium-induced denaturation, using fluorescence and circular dichroism spectroscopies. The unfolding of the tetramer and dimer are highly reversible. The unfolding of the H2A-H2B dimer is a two-state process, with no detected equilibrium intermediates. The H3-H4 tetramer is unstable at moderate ionic strengths (mu approximately 0.2 M). TMAO (trimethylamine-N-oxide) was used to stabilize the tetramer; the stability of the H2A-H2B dimer was determined under the same solvent conditions. The equilibrium unfolding of H3-H4 was best described by a three-state mechanism, with well-folded H3-H4 dimers as a populated intermediate. When compared to H2A-H2B, the H3-H3 tetramer interface and the H3-H4 histone fold are strikingly less stable. The free energy of unfolding, in the absence of denaturant, for the H3-H4 and H2A-H2B dimers are 12.4 and 21.0 kcal mol(-)(1), respectively, in 1 M TMAO. It is postulated that the difference in stability between the histone dimers, which contain the same fold, is the result of unfavorable tertiary interactions, most likely the partial to complete burial of three salt bridges and burial of a charged hydrogen bond. Given the conservation of these buried interactions in histones from yeast to mammals, it is speculated that the H3-H4 tetramer has evolved to be unstable, and this instability may relate to its role in nucleosome dynamics.     

Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos

Human Npm2 is an ortholog of Xenopus nucleoplasmin (Np), a chaperone that binds histones. We have determined the crystal structure of a truncated Npm2-core at 1.9 ? resolution and show that the N-terminal domains of Npm2 and Np form similar pentamers. This allowed us to model an Npm2 decamer which may be formed by hydrogen bonds between quasi-conserved residues in the interface between two pentamers. Interestingly, the Npm2 pentamer lacks a prototypical A1-acidic tract in each of its subunits. This feature may be responsible for the inability of Npm2-core to bind histones. However, Npm2 with a large acidic tract in its C-terminal tail (Npm2-A2) is able to bind histones and form large complexes. Fluorescence resonance energy transfer experiments and biochemical analysis of loop mutations support the premise that nucleoplasmins form decamers when they bind H2A-H2B dimers and H3-H4 tetramers simultaneously. In the absence of histone tetramers, these chaperones bind H2A-H2B dimers with a single pentamer forming the central hub. When taken together, our data provide insights into the mechanism of histone binding by nucleoplasmins.     

Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding

Eukaryotic chromatin is highly dynamic and turns over rapidly even in the absence of DNA replication. Here we show that the acidic histone chaperone nucleosome assembly protein 1 (NAP-1) from yeast reversibly removes and replaces histone protein dimer H2A-H2B or histone variant dimers from assembled nucleosomes, resulting in active histone exchange. Transient removal of H2A-H2B dimers facilitates nucleosome sliding along the DNA to a thermodynamically favorable position. Histone exchange as well as nucleosome sliding is independent of ATP and relies on the presence of the C-terminal acidic domain of yeast NAP-1, even though this region is not required for histone binding and chromatin assembly. Our results suggest a novel role for NAP-1 (and perhaps other acidic histone chaperones) in mediating chromatin fluidity by incorporating histone variants and assisting nucleosome sliding. NAP-1 may function either untargeted (if acting alone) or may be targeted to specific regions within the genome through interactions with additional factors.     

Amino acid contacts between histones are the same for plants and mammals. Binding-site studies using ultraviolet light and tetranitromethane.

Leek chromatin has been cross-linked by UV light and tetranitromethane. The same major H2A--H2B and H2B--H4 cross-linked dimers are formed as in mammalian chromatin. CNBr peptide mapping shows that the cross-links occur in the same regions of the histone sequence for both plants and mammals. Interspecies complexes formed between leek and calf H2A and H2B can be cross-linked by UV light with the same specificity as intraspecies H2A--H2B complexes. We conclude that certain geometric features of histone-histone binding sites are conserved precisely during evolution despite large changes in the overall histone sequence. Moreover, our data show that identification of cross-linked amino acids using binding-site probes such as UV light and tetranitromethane can yield significant information about thermodynamically important contacts within histone-histone binding sites.     

Fractionation of avian erythrocyte histones by hydrophobic interaction chromatography.

The interactions of H1 (H1A, H1B), H2A, H2B, H3, H4, and H5 with phenyl cross-linked agarose were studied. Procedures are described whereby all six histones can be bound, released, and fractionated by using appropriate salt concentrations or pH. The binding can be totally abolished by inclusion of hydrophobic disrupting agents. Control experiments with nonderivated cross-linked agarose ruled out a passive aggregation-disaggregation phenomenon governing the binding patterns. The absorption sequence based on the identification and quantitation of individual histones from either unfractionated (whole) histone or separate histone classes is as follows: H3 greater than or equal to H4 greater than H2B greater than or equal to H5 greater than or equal to H2A greater than H1A greater than or equal to H1B. The order differs only slightly from the reverse of the desorption sequence, H1B less than or equal to H1A less than or equal to H5 less than H2A less than or equal to H3. Preferential interaction of H2A-H2B, H3-H4, and H2A-H2B-H4 occur; these interactions can modify the original relative affinity of each individual component for the matrix. The variability in matrix affinity appears to involve simple stoichiometry of the histone components.     

A rapid method of preparing the (H3-H4-H2A-H2b)(2) histone octamer in large quantities]

A simple and fast method for isolation of large amounts of the histone octamer (H2A-H2B-H3-H4)2 is proposed. This method is based on chromatin adsorption by hydroxyapatite with subsequent extraction of the histone octamer with 50 mM sodium-phosphate buffer containing 4 M NaCl pH 8.0. It was shown that the properties of the histone octamer isolated by this extractive procedure are identical with those of the histone octamer obtained by elution on a Sephadex G-100 column. The histone tetramer (H3-H4)2 and dimer (H2A-H2B) were obtained after gel filtration on Sephadex G-100 in 50 mM sodium-acetate (pH 5.6).     

Sequence of histone 2B of Drosophila melanogaster.

The complete sequence of histone 2B of Drosophila has been determined by using an improved Beckman sequenator. Comparing these data with those previously published by other investigators on the histone 2B of calf [Iwai, K., Hayashi, H., & Ishikawa, K. (1972) J. Biochem. (Tokyo) 72, 357--367], trout [Koostra, A., & Bailey, G. S. (1978) Biochemistry 17, 2504--2510], and Patella (a limpet) [van Helden, P. D., Strickland, W. N., Brandt, W. F., & von Holt, C. (1979) Eur. J. Biochem. 93, 71--78], it is possible to assess the evolutionary stability of this protein. There is little conservation of sequence in the N-terminal portion of the molecule (residues 1--26 numbering according to calf H2B), while the remainder of the protein, which we designate the C-terminal portion, is highly conserved. In the region of 27--125 residues, there are 9 substitutions in the composite data among the 98 positions, 8 of them conservative. These data indicate that very different selective pressures operate on the two different portions of the H2B molecule, implying the existence of two well-defined regions. Studies on the structure of the nucleosome by others have suggested that the C-terminal portion of H2B is involved in histone-histone interactions while the N-terminal portion is a relatively free "tail" binding to DNA. The sequence data indicate that the function of the C-terminal region of H2B requires considerable sequence specificity while that of the N-terminal region does not.     

The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA

The nucleosome comprises two histone dimers of H2A-H2B and one histone tetramer of (H3-H4)₂, wrapped around by ~145 bp of DNA. Detailed core structures of nucleosomes have been established by X-ray and cryo-EM, however, histone tails have not been visualized. Here, we have examined the dynamic structures of the H2A and H2B tails in 145-bp and 193-bp nucleosomes using NMR, and have compared them with those of the H2A and H2B tail peptides unbound and bound to DNA. Whereas the H2A C-tail adopts a single but different conformation in both nucleosomes, the N-tails of H2A and H2B adopt two distinct conformations in each nucleosome. To clarify these conformations, we conducted molecular dynamics (MD) simulations, which suggest that the H2A N-tail can locate stably in either the major or minor grooves of nucleosomal DNA. While the H2B N-tail, which sticks out between two DNA gyres in the nucleosome, was considered to adopt two different orientations, one toward the entry/exit side and one on the opposite side. Then, the H2A N-tail minor groove conformation was obtained in the H2B opposite side and the H2B N-tail interacts with DNA similarly in both sides, though more varied conformations are obtained in the entry/exit side. Collectively, the NMR findings and MD simulations suggest that the minor groove conformer of the H2A N-tail is likely to contact DNA more strongly than the major groove conformer, and the H2A N-tail reduces contact with DNA in the major groove when the H2B N-tail is located in the entry/exit side.