组蛋白变体及组蛋白替换

组蛋白作为核小体的基本组分,是染色质的结构和功能必需的。对于不同状态的染色质,核小体中会组装入相应的组蛋白变体,并且各种组蛋白变体的尾部也能发生多种修饰。这些变体通过改变核小体的空间构象和稳定性,决定基因转录的激活或沉默,DNA的修复,染色体的异染色化等。在组蛋白替换过程中,组蛋白变体是通过相应的染色质重构复合物组装入核小体,不同的变体有着不同的组装途径。对组蛋白变体的研究是近年来表观遗传学新的研究热点,也是对“组蛋白密码”的新的诠释。并且,组蛋白替换揭示了DNA-组蛋白相互作用变化的一种新的机制。

     

The effect of poly(ADP-ribose) on interactions of DNA with histones H1, H3 and H4

The competition between poly(ADP-ribose) and DNA for binding of the histones H1, H3 and H4 was studied, using a membrane filter-binding test. Poly(ADP-ribose) differently affected the interaction between DNA and the individual histones. While poly(ADP-ribose) effectively competed with DNA for binding of histone H4, it equally competed with DNA for binding of histone H3 and only inefficiently competed with DNA for binding of histone H1. Moreover, preformed complexes were correspondingly affected by the addition of competing polynucleotides, thereby also indicating the reversibility of complex formation. The competition capacity of DNA for histone H4 binding did not depend on DNA size. Competition experiments with poly(A) also indicated that poly(ADP-ribose) preferentially affected DNA-histone H4 interaction. The significance of the differing binding properties is discussed with regard to the possible molecular function of poly(ADP-ribose), especially with regard to its potential effect on nucleosome structure.     

The nature of interactions responsible for the differences in the affinities of histones for DNA

Electrophoretic studies on the sequential binding of histones to DNA and to polyphosphate in low ionic strength solution have shown that the affinities of histones for both the polyanions decreases in the same order: H4 ～ H3 > H2A > H2B>H1. This permits to suggest that hydrophobic DNA-histone interactions do not determine the relative affinity of histones for DNA. Non-ionic interactions within and between histone molecules participate in determining the histone affinity for DNA affecting electrostatic DNA-histone interactions.     

ANTIGEN-INDUCED CHANGES IN LYMPHOID CELL HISTONES : III. In Vitro and in Extract

Previous papers in this series have reported an acute, transitory effect of antigens on lymphoid cell nuclei. In the previous reports the effect was related to a change in ammoniacal silver (A-S) stainability of smears and cryostat sections. The variable substrate was identified as histone. This paper reports the results of an extended series of studies of histone and chromatin extracts from thymus glands exposed to antigen in vivo and in vitro. The antigen effect on A-S stainability is demonstrable not only in vitro but also in chromatin fibers representing a DNA-histone complex. However, it is not demonstrable in isolated histone fractions. The inference is drawn that the antigen-induced alteration in A-S stainability is brought about not by any quantitative change in histone, but by a biologically significant shift in histone binding, perhaps to DNA. It is suggested that alteration in DNA-histone binding during gene activation may alter A-S stainability of histones.     

An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants

Chromatin immunoprecipitation (ChIP) is a powerful tool for the characterization of covalent histone modifications and DNA-histone interactions in vivo. The procedure includes DNA-histone cross-linking in chromatin, shearing DNA into smaller fragments, immunoprecipitation with antibodies against the histone modifications of interest, followed by PCR identification of associated DNA sequences. In this protocol, we describe a simplified and optimized version of ChIP assay by reducing the number of experimental steps and isolation solutions and shortening preparation times. We include a nuclear isolation step before chromatin shearing, which provides a good yield of high-quality DNA resulting in at least 15 mug of DNA from each immunoprecipitated sample (from 0.2 to 0.4 g of starting tissue material) sufficient to test > or =25 genes of interest. This simpler and cost-efficient protocol has been applied for histone-modification studies of various Arabidopsis thaliana tissues and is easy to adapt for other systems as well.     

Effect of Organic Effectors on Chromatin Solubility,DNA-Histone H1 Interactions,DNA and Histone HI Structures

Abstract

We have extended our previous investigations on the effect of organic osmolytes (glycine, proline, taurine, mannitol, sorbitol and trimethylammonium oxide (TMAO)) on chromatin solubility, to the study of their influence on DNA stability and DNA-histone interactions. Our aim was to understand the molecular origin of the protection effects observed.

To this end, we determined the amount of histone H1 required to precipitate DNA or H1-depleted chromatin, at various salt concentrations, in the presence of the above mentioned organic compounds. We found a shift of the H1/DNA ratio required to reach 50% precipitation, towards higher values. Taurine was the most efficient compound followed by mannitol and glycine, then sorbitol and proline. On the contrary, TMAO favoured the precipitation process. We attempted to interpret these results on the basis of Manning's counterion condensation theory.

Changes in histone H1 structure folding and in DNA melting temperature T_m were also analyzed. Glycine, taurine, sorbitol and TMAO increased the degree of secondary structure folding of the protein while mannitol and sorbitol had no effect. Taurine, glycine and proline decreased the T_m of DNA TMAO largely destabilized DNA but mannitol and sorbitol had no effect

Measurements of NaC1 activity in the presence of organic osmolytes did not reveal sufficiently large changes to account for their protection effect against chromatin precipitation. The osmotic coefficient j of the organic effectors solutions increased in the order : taurine < glycine < sorbitol < mannitol < proline ? TMAO. For the two latter compounds, the j values increased above 1 at high concentration.

We consider that the organic compounds investigated maybe classified into three categories : (i) class I (zwitterionic compounds : glycine, proline, taurine) would produce sodium ions release from the DNA surface; (ii) class II (the very polar molecule TMAO) would increase sodium counterions condensation on DNA together with histone HI folding; (iii) class III compounds (mannitol and sorbitol) would possibly produce a modification of NaCl activity but no definite explanation could be found for the complex behavior of these compounds.     

A contribution of nonhistone proteins to the conformation of chromatin.

1. Changes in circular dichroism (CD) spectra and thermal melting profiles of guinea pigliver DNA reassociated with histones and/or nonhistone proteins from the cerebral of liver chromatin are described. 2. In the DNA-histone complex, positive ellipiticity in the CD spectrum at 260-300 nm is progressively lod by a red-shift of the crossover point at around 260 nm. DNA in this complex is thermally stabilised to a considerable extent, but not to such a full extent as is shown with DNA in native chromatin. 3. DNA-nonhistone complex in 0.14 M NaCl is, in contrast to DNA-histone complex, not precipitable by centrifugation at 20 000 X g. DNA in this complex shows only a slight reduction in ellipticity at 260-300 nm, and a very weak thermal stabilisation. 4. Characteristics in the CD spectrum of the native chromatin are most satisfactorily reproduced in the DNA-histone-nonhistone complex. These include a large decrease in ellipticity at 260-300 nm, a red-shift of the crossover point at around 260 nm, and a slight negative band at around 305 nm. Also, DNA in this complex is thermally stabilised to the extent comparable with DNA in the native chromatin. 5. Addition of nonhistone proteins to the preformed DNA-histone complex in 3 M urea renders a half of the complex, named DNA-histone(-nonhistone), unprecipitable upon centrifugation at 20 000 X g in 0.14 M NaCl. CD spectrum and thermal melting profile of the precipitable DNA-histone(-nonhistone) complex are similar to those of the DNA-histone-nonhistone complex, while in the unprecipitable DNA-histone(-nonhistone) comples, the ellipticity at 260-300 nm is significantly elevated and the highest melting transition (at 80 degrees C) is lacking. 6. The CD spectrum of native cerebral chromatin closely resembles that of unprecipitable DNA-histone(-nonhistone) complex, while in liver chromatin, the spec.trum is an intermediate between those of the unprecipitable and pn of chromatin by nonhistone proteins. Cerebral nonhistone proteins bind to DNA and to the DNA-histone complex more extensively than liver nonhistone proteins. 7. It is concluded that, although the basic conformation of DNA in native chromatin is determined largely by histones, nonhistone proteins also play an individual role. There is also an indication that nonhistone proteins exert an organ-specific modification of chromatin superstructure.     

DNA chain flexibility and the structure of chromatin nu-bodies.

The persistence length of high-molecular-weight, monodisperse-bihelical DNA has been evaluated from low-shear flow birefingence and viscosity data at several temperatures in 2.0 M Nacl neutral pH buffer. At these solvent conditions, both the DNA and histone components of chromatin nu-bodies have structural features similar to those in the intact nucleohistone complex at low ionic strength. The theory of Landau and Lifshitz is used to relate the experimental result to the thermodynamic functions for bending 140 nucleotide pairs of DNA into a plausible model structure: per nu-body, delta Gb=43.8 +/- 5.3 kcal/mole, delta Hb= 45.7 +/- 3.7 kcal/mole, and delta Sb = 6.2 +/- 12.4 entropy units. This bending free energy is comparable to or less than that estimated to be required for a kinked DNA configuration and appears to be well within the range of estimated electrostatic free energies available from DNA-histone interactions in a nu-body assembly.     

Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping

The nucleosome complex of DNA wrapped around a histone protein octamer organizes the genome of eukaryotes and regulates the access of protein factors to the DNA. We performed molecular dynamics simulations of the nucleosome in explicit water to study the dynamics of its histone-DNA interactions. A high-resolution histone-DNA interaction map was derived that revealed a five-nucleotide periodicity, in which the two DNA strands of the double helix made alternating contacts. On the 100-ns timescale, the histone tails mostly maintained their initial positions relative to the DNA, and the spontaneous unwrapping of DNA was limited to 1–2 basepairs. In steered molecular dynamics simulations, external forces were applied to the linker DNA to investigate the unwrapping pathway of the nucleosomal DNA. In comparison with a nucleosome without the unstructured N-terminal histone tails, the following findings were obtained: 1), Two main barriers during unwrapping were identified at DNA position ±70 and ±45 basepairs relative to the central DNA basepair at the dyad axis. 2), DNA interactions of the histone H3 N-terminus and the histone H2A C-terminus opposed the initiation of unwrapping. 3), The N-terminal tails of H2A, H2B, and H4 counteracted the unwrapping process at later stages and were essential determinants of nucleosome dynamics. Our detailed analysis of DNA-histone interactions revealed molecular mechanisms for modulating access to nucleosomal DNA via conformational rearrangements of its structure.     

ATP-dependent chromatosome remodeling

Chromatin serves to package, protect and organize the complex eukaryotic genomes to assure their stable inheritance over many cell generations. At the same time, chromatin must be dynamic to allow continued use of DNA during a cell's lifetime. One important principle that endows chromatin with flexibility involves ATP-dependent 'remodeling' factors, which alter DNA-histone interactions to form, disrupt or move nucleosomes. Remodeling is well documented at the nucleosomal level, but little is known about the action of remodeling factors in a more physiological chromatin environment. Recent findings suggest that some remodeling machines can reorganize even folded chromatin fibers containing the linker histone H1, extending the potential scope of remodeling reactions to the bulk of euchromatin.     

Structural effects of cobalt-amine compounds on DNA condensation.

Light scattering and electron microscopy have been used to investigate the structural effects of the trivalent complexes hexaammine cobalt (III) chloride (Cohex), tris(ethylenediamine) cobalt(III) chloride (Coen), and cobalt(III) sepulchrate chloride (Cosep) on DNA condensation. These cobalt-amine compounds have similar ligand coordination geometries but differ slightly in size. Their hydrophobicity is in the order Cosep > Coen > Cohex, according to the numbers of methylene groups in these ligands. All of these compounds effectively precipitate DNA at high concentrations; but despite a lower surface charge density, Cosep condenses DNA twice as effectively as Coen or Cohex. UV and CD measurements of the supernatants of cobalt-amine/DNA solutions reveal a preferential binding of Delta-Coen over Lambda-Coen to the precipitated DNA, but there is no chiral selectivity for Cosep. Competition experiments show that the binding strengths of these three cobalt-amine compounds to aggregated DNA are comparable. A charge neutralization of 88-90% is required for DNA condensation. Our data indicate that 1) electrostatic interaction is the main driving force for binding of multivalent cations to DNA; 2) DNA condensation is dependent on the structure of the condensing agent; and 3) the hydration pattern or polarization of water molecules on the surface of condensing agents plays an important role in DNA condensation and chiral recognition.     

The effect of superhelicity on the interaction of histone f1 with closed circular duplex DNA.

A set of covalently closed circular duplex simian virus 40 DNA preparations of varying superhelical densities was prepared by closure of nicked duplex DNA with polynucleotide ligase in the presence of varying amounts of ethidium. The resulting molecules were tested for complex formation with the lysine-rich histone f1. The results confirmed earlier experiments in demonstrating that f1 histone reacts preferentially with superhelical DNA compared to relaxed circular DNA. Furthermore, the extent of the reaction is demonstrated to depend on the superhelical density. At the relatively low ratios of histone to DNA used in these experiments, the product of the interaction of f1 histone with superhelical DNA does not precipitate. At higher ratios of histone to DNA, an insoluble aggregate is formed.     

Thermodynamics of nucleosomal core particles

In this paper, a numerically detailed thermodynamic investigation of nucleosomal core particles is presented. The nonlinear Poisson-Boltzmann equation governs the electrostatic properties of both the DNA and histone protein. Brownian dynamics is used as the leading method, in combination with the analysis of the electrical features of the nucleosome. At elevated temperature, the structure of the nucleosome is destabilized by the decrease in electrical interactions of DNA-histone complexes, which can be explained with the EDL theory. Two obvious unwrapping transitions can be found, occurring within the temperature ranges 43-52 and 65-80 degrees C. The first transition is characterized by the melting of DNA terminal domains, and the feature of the second transition is the massive unwrapping of the DNA middle domain. It can be concluded that the nucleosomal DNA consists of two distinct structures, where the DNA terminal domains are less tightly bound to the histone than the DNA middle domain.     

Preferential nucleosome placement on pBR322 restriction fragments

Two restriction fragments of DNA containing the regulatory feature GTG/CAC were experimentally associated with core histones. The reconstituted DNA-histone complexes consisted of different forms of mononucleosomes. Lambda exonuclease and Fnu4HI were used to probe the structure of each distinct nucleoprotein complex. For each of the DNA fragments, one form of particle was produced that showed preferred placement of the core octamer on the DNA. The GTG/CAC base triplets may play some role in determining the final histone core positions in these reconstitutes.     

Poly(ADP-ribose) effectively competes with DNA for histone H4 binding

The effect of poly(ADP-ribose) on DNA-histone H4 interaction was studied using a nitrocellulose filter binding assay. Poly-(ADP-ribose) was found to form poly(ADP-ribose)-histone H4 complexes at physiological salt concentrations. The homopolymer effectively competed with DNA for histone H4 binding. Poly(ADP-ribose) was also capable of displacing DNA from preformed DNA-histone H4 complexes. Our hypothesis is that poly(ADP-ribose), locally and transiently formed at the site of DNA damage, causes dissociation of DNA from the nucleosome particle or nucleosome unfolding.     

Studies on the role of polyamines associated with the ribosomes from Bacillus stearothermophilus

1. Spermine and spermidine were the main polyamines detectable in Bacillus stearothermophilus. 2. When grown at 65 degrees B. stearothermophilus contained lower concentrations of polyamines per mg. of RNA than when grown at 45 degrees or at 55 degrees . 3. Ribosomes isolated from B. stearothermophilus in 0.01m-tris-hydrochloric acid buffer (pH7.4)-0.01m-magnesium chloride contained sufficient polyamines to neutralize between 4% and 9% of their RNA phosphorus. 4. Removal of polyamines from the ribosomes by dialysis against m-potassium chloride did not appreciably alter the hypochromicity or thermal denaturation profiles of the ribosomes when measured in 0.01m-tris-hydrochloric acid buffer (pH7.4)-0.01m-magnesium chloride, though it did cause a loss of ribosome particles sedimenting at greater than 78s. 5. When ribosomes were dialysed against acridine orange solutions acridine orange bound to the ribosomes and did not displace spermine, but when a mixture of ribosomal RNA and spermine was dialysed against acridine orange the acridine orange displaced the spermine. It is concluded that polyamines in the ribosomes are less accessible for displacement by acridine orange than when polyamines are bound to ribosomal RNA.     

The use of proteolytic enzymes to determine the location of histones in chromosomal substructures

We have observed that three proteolytic enzymes with widely different specificities produce a very similar pattern in terms of the order of digestion of the various histone fractions in chromatin. Histone H2A is most resistant to proteolytic attack by trypsin, chymotrypsin, or Pronase. H2B is next most resistant, followed by H3. Histone H1 is least resistant and is rapidly hydrolyzed by each of these enzymes. The behavior of histone H4 differs for the various enzymes. It is as resistant as H2A to digestion by trypsin and chymotrypsin but is readily hydrolyzed by Pronase. A comparison of the rates of digestion of the various histone fractions in chromatin with the rates in a DNA-free histone mixture and a study of the degradation products which result from digestion indicate that histone conformation and histone-histone and DNA-histone interactions are all involved in protecting histones from attack by proteolytic enzymes. From the results of our studies we have concluded that histones H1 and H3 are located in superficial positions of the chromosomal substructures (or nu bodies) while H2A is buried inside. Since histone H2B is relatively resistant to digestion but more readily degraded in chromatin than in a DNA-free histone mixture, it is difficult to determine its chromosomal location. Histone H4 behaves as if a large portion of the molecule is located in the major groove of the DNA helix.     

Coordinate regulation of histone mRNA metabolism and DNA replication

S phase is characterized by the replication of DNA and assembly of chromatin. This requires the synthesis of large amounts of histone proteins to package the newly replicated DNA. Histone mRNAs are the only mRNAs that do not have polyA tails, ending instead in a conserved stemloop sequence. The stemloop binding protein (SLBP) that binds the 3' end of histone mRNA is cell cycle regulated and SLBP is required in all steps of histone mRNA metabolism. Activation of cyclin E/cdk2 prior to entry into S phase is critical for initiation of DNA replication and histone mRNA accumulation. At the end of S phase SLBP is rapidly degraded as a result of phosphorylation of SLBP by cyclin A/cdk1 and CK2 effectively shutting off histone mRNA biosynthesis. E2F1, which is required for expression of many S-phase genes, is regulated in parallel with SLBP and its degradation also requires a cyclin binding site, suggesting that it may also be regulated by the same pathway. It is likely that activation of cyclin A/cdk1 so helps inhibit both DNA replication and histone mRNA accumulation, marking the end of S phase and entry into G2 phase.     

Interaction of basic oligo-L-amino acids with deoxyribonucleic acids. Oligo-L-arginines of various chain lengths and herring sperm DNA

The interaction of DNA and oligo-L-arginines having definite chain lengths of 1-17 residues was studied by precipitate formation and thermal denaturation of the complexes in order to obtain a better understanding of the roles of nuclear basic proteins. The results can be summarized as follows. 1. Those oligo-L-arginines, (Arg)n, in which n greater than or larger than 4 can bind with DNA irreversibly to form precipitates of the complexes. Among them, oligomers larger than (Arg)5 precipitate DNA completely in Arg/P input ratios below 1. The Arg/P ratios in the precipitates are between 0.6-0.8. 2. The thermal stability of the complexes depends on the method of complex formation, and complexes formed by the dialysis method are more stable than those formed by the mixing method. 3. The binding of (Arg)n to DNA was found to be reversible and in a equilibrium for n less than or equal to 6. In general, the longer the oligomer, the higher the stability of the complex at a definite Arg/P ratio. 4. For (Arg)7-10, three kinds of complexes with different stabilities are formed between DNA and oligopeptides. 5. For (Arg)14-17, only a restricted type of complexes can be formed between DNA and oligomers, as in the case with poly-L-arginine or protamines. 6. The interaction between basic nuclear proteins and DNA is discussed in the light of the basic region in protamine and histone molecules.