Role of histone H1 in the conformation of oligonucleosomes as a function of ionic strength

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

Density functional calculations of thio effects on the in-line mechanism of methanolysis of ethylene phosphate (a reverse reaction model for RNA phosphate transesterification) are presented. A total of 12 reaction mechanisms are examined using the B3LYP functional with large basis sets, and the effects of solvation were treated using the PCM, CPCM, and SM5 solvation models. Single thio substitutions at all of the distinct phosphoryl oxygen positions (2', 3', 5', pro-R) and a double thio substitution at the nonbridging (pro-R/pro-S) positions were considered. Profiles for each reaction were calculated in the dianionic and monoanionic/monoprotic states, corresponding to reaction models under alkaline and nonalkaline conditions, respectively. These models provide insight into the mechanisms of RNA transesterification thio effects and serve as a set of high-level quantum data that can be used in the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations and linear-scaling electronic structure calculations.

In vitro chromatin self-association and its relevance to genome architecture

Chromatin in a eukaryotic nucleus is condensed through 3 hierarchies: primary, secondary, and tertiary chromatin structures. In vitro, when induced with cations, chromatin can self-associate and form large oligomers. This self-association process has been proposed to mimic processes involved in the assembly and maintenance of tertiary chromatin structures in vivo. In this article, we review 30 years of studies of chromatin self-association, with an emphasis on the evidence suggesting that this in vitro process is physiologically relevant.

NMR-Based Reappraisal of the Coordination of a Metal Ion at the Pro-Rp Oxygen of the A9/G10.1 Site in a Hammerhead Ribozyme

In the identification of a metal-binding site within enzymes, kinetic analyses based on thio-effects and Cd(2+)-rescues are widely used. In those analyses, kinetic studies using a phosphorothioate have been discussed on the premise that the substitution by a sulfur atom does not change the conformation of a ribozyme. However, our present NMR structural analysis demonstrates the change of the conformation at the metal-binding site by Rp-sulfur but not by Sp-sulfur substitution and warns against incautious interpretations of thio-effects and rescue phenomena in kinetic studies using a phosphorothioate. Our analysis further demonstrates that, in solution, a Cd(2+) ion can interact with an Rp-phosphorothioate (in support of the controversial McKay's structure, Nature 1994, 372, 68-74) and with an Sp-phosphorothioate (in support of the controversial Scott's structure, Cell 1995, 81, 991-1002) at the metal-binding A9/G10.1 site and that, in the former case, the bound Cd(2+) ion can return the ribozyme to an active conformation and rescue its enzymatic activity.

A reappraisal, based on (31)P NMR, of the direct coordination of a metal ion with the phosphoryl oxygen at the cleavage site of a hammerhead ribozyme

It has been generally accepted, on the basis of kinetic studies with phosphorothioate-containing substrates and analyses by NMR spectroscopy, that a divalent metal ion interacts directly with the pro-Rp oxygen at the cleavage site in reactions catalyzed by hammerhead ribozymes. However, results of our recent kinetic studies (Zhou, D.-M.; Kumar, P. K. R.; Zhang. L. H.; Taira, K. J. Am. Chem. Soc. 1996, 118, 8969-8970. Yoshinari, K.; Taira, K. Nucleic Acids Res. 2000, 28, 1730-1742) demonstrated that a Cd(2+) ion does not interact with the sulfur atom at the Rp position of the scissile phosphate (P1.1) in the ground state or in the transition state. Therefore, in the present study, we attempted to determine by (31)P NMR spectroscopy whether a Cd(2+) ion binds to the P1.1 phosphorothioate at the cleavage site in solution. In the case of the R32-S11S (ribozyme-substrate) complex, neither the Rp- nor the Sp-phosphorothioate signal from the S11S substrate at the cleavage site was perturbed (the change was less than 0.1 ppm) upon the addition of Cd(2+) ions (19 equiv) at pH 5.9 and 8.5. By contrast, we detected the significant perturbation of the P9 phosphorothioate signal from another known metal-binding site (the A9/G10.1 metal-binding motif). The Rp-phosphorothioate signal from A9/G10.1 was shifted by about 10 ppm in the higher field direction upon the addition of Cd(2+) ions. These observations support the results of our kinetic analysis and indicate that a Cd(2+) ion interacts with the sulfur atom of the phosphorothioate at the A9/G10.1 site (P9) but that a Cd(2+) ion does not interact with the sulfur atom at the Rp- or at the Sp-position of the scissile phosphate (P1.1) in the ground state.

What determines the folding of the chromatin fiber?

In this review, we attempt to summarize, in a critical manner, what is currently known about the processes of condensation and decondensation of chromatin fibers. We begin with a critical analysis of the possible mechanisms for condensation, considering both old and new evidence as to whether the linker DNA between nucleosomes bends or remains straight in the condensed structure. Concluding that the preponderance of evidence is for straight linkers, we ask what other fundamental process might allow condensation, and argue that there is evidence for linker histone-induced contraction of the internucleosome angle, as salt concentration is raised toward physiological levels. We also ask how certain specific regions of chromatin can become decondensed, even at physiological salt concentration, to allow transcription. We consider linker histone depletion and acetylation of the core histone tails, as possible mechanisms. On the basis of recent evidence, we suggest a unified model linking targeted acetylation of specific genomic regions to linker histone depletion, with unfolding of the condensed fiber as a consequence.

Core histone tail domains mediate oligonucleosome folding and nucleosomal DNA organization through distinct molecular mechanisms

Defined oligonucleosome model systems have been used to investigate the molecular mechanisms through which the core histone tail domains modulate chromatin structure. In low salt conditions, the tail domains function at the nucleosome level to facilitate proper organization of nucleosomal DNA, i.e. wrapping of DNA around the histone octamer. Mg2+ ions can substitute for the tail domains to yield a trypsinized oligonucleosome structure that is indistinguishable from that of an intact nucleosomal array in low salt. However, Mg(2+)-dependent formation of highly folded oligonucleosome structures absolutely requires the histone tail domains, and is associated with rearrangement of the tails to a non-nucleosomal location. We conclude that the tail domains mediate oligonucleosome folding and nucleosomal DNA organization through fundamentally different molecular mechanisms.

Microheterogeneity in H1 histones and its consequences

The extent of microheterogeneity of H1 histones in individual higher organisms, without considering post-translational modifications, is such that five to eight molecular species can be recognized. The H1 variants differ among themselves in their ability to condense DNA and chromatin fragments, and they are non-uniformly distributed in chromatin. This review assembles data that support the notion that the differences in chromatin condensation (heterochromatization) observed through the microscope are maintained by the non-uniform distribution of H1 variants, and that this pattern of chromatin condensation may determine the dynamics of chromatin during replication and may represent the commitment aspect of differentiation. The differential response of the multiple H1 variants with regard to their synthesis and turnover is consistent with this notion.

Tubulin-chromatin interactions: evidence for tubulin-binding sites on chromatin and isolated oligonucleosomes

The interaction of tubulin with chromatin has been studied using a radiolabeled tubulin binding assay and velocity sedimentation analysis on isokinetic sucrose gradients. Soluble chromatin was prepared by mild micrococcal nuclease digestion of rat liver nuclei and tubulin was purified from rat brain by temperature-dependent assembly-disassembly and phosphocellulose chromatography. The tubulin-binding assay is based on the ability of chromatin to precipitate quantitatively at physiological ionic strength allowing separation of free tubulin from chromatin-bound tubulin. The binding of tubulin to unfractionated soluble chromatin was rapid, reversible and saturable. Saturation of binding sites was obtained using tubulin concentrations ranging from 0.5 to 400 micrograms/ml, in the presence of a high concentration (2.5 mg/ml) of another acidic protein, bovine serum albumin. The Scatchard and Hill plots showed that tubulin bound to a single class of non-interacting sites and yielded values of (0.5-0.6) X 10(7) M-1 for an apparent Ka and a maximal binding capacity of 0.8 nmol tubulin/mg DNA, i.e. about 1 molecule of tubulin/10 nucleosomes. Similar binding parameters were obtained when binding experiments were performed with insoluble chromatin in 0.15 M NaCl. Velocity sedimentation analysis of tubulin-chromatin complexes revealed that tubulin bound to all classes of chromatin oligomers, irrespective of the length of the nucleosomal chain. Tubulin-trinucleosome complexes formed from isolated trinucleosome in the presence of an excess of tubulin were separated from free reactants. It was found that 10-15% of the starting oligonucleosomal species reacted with tubulin, in a stoichiometry of about 0.8 molecule of tubulin/nucleosome. Given the characteristics of the binding and the expected cellular free tubulin concentration, the tubulin-chromatin interaction could possibly take place in vivo, when the nuclear membrane breaks down during the first steps of mitosis.

Effect of exogenous histone H5 on integration of histone H1 in rat liver chromatin. Correlations with aberrant epsilon-N-methylation of histone H1

Binding modes of histones H1 and H5, and their competition for chromatin-binding sites in rat liver nuclei, were correlated with aberrant N-methylation of H1 histone lysine residues, induced by chicken erythrocyte histone H5, in order to gain more insight into the integration of lysine-rich histones in chromatin. Addition of approx. 2.5 molecules of histone H5 per nucleosome to rat liver nuclei increases the ratio of total basic residues in histones to DNA nucleotides (BR/NT) in the nuclear chromatin from 1.0 to 1.5. At this concentration, approx. 0.7 molecule of histone H5 is bound per nucleosome, and there is no displacement of histone H1 from the nuclear chromatin. If S-adenosyl[Me-3H]methionine is present in the incubation mixture, the aberrant incorporation of labeled methyl groups into histone H1 reaches a maximum at this concentration of histone H5. The radioactivity present in histone H1 from nuclei incubated with labeled AdoMet at a total BR/NT ratio of 1.5: resides mainly in a histone H1 subfraction tentatively identified by Bio-Rex 70 chromatography and acrylamide gel electrophoresis as histone H1c; presents as a single spot upon peptide mapping of tryptic hydrolysates by means of two-dimensional thin-layer chromatography; and elutes in the position of mono-N-methyllysine upon ion-exchange chromatography of histone H1 hydrolysates. Upon further increase of the BR/NT ratio, the following changes are produced: a gradual decrease in radioactive methyl uptake into histone H1; a gradual displacement of histone H1 from the chromatin; increased binding of histone H5 in chromatin, up to a maximum of 3.4 residues per nucleosome; and a slowly increasing uptake of label into histone H5. The combined data from histone H1/H5 binding and histone H1 methylation studies suggest that upon addition of exogenous histone H5 to rat liver nuclei the binding of two lysine-rich histones per nucleosome plays a significant role in the induction of specific changes in chromatin structure, which in vivo may have important functional implications in terms of chromatin condensation and suppression of transcription.

On the binding of histone H1 in chromatin

Nucleosomal subunits isolated from rabbit thymus nuclei in 0.04 M K2SO4-0.02 M Tris, pH 7.4 were devoid of histone H1, while whole chromatin prepared in the same buffer contained the full complement of histone H1. The question is asked why histone H1 dissociates from the subunits but not from the high molecular weight material. We propose that, at physiological salt concentrations, histone H1 is not bound to linker DNA as depicted in the current models; rather, alternate attachment sites, present only in the polymer, are involved.

Assembly of oligonucleosomes into a limit series of multimeric higher-order chromatin structures

Chicken erythrocyte chromatin, obtained after fragmentation with micrococcal nuclease, appears to remain folded in a stable distribution of supranucleosomal structures in buffers containing 80 mM NaCl. These supranucleosomal particles are composed of on average 25 nucleosomes. However, the integrity of the linker DNA within these particles is not required. The supranucleosomal particles have been interpreted by others as superbeads cut out of a preexisting granular nominal 30-nm chromatin fibre. We show that the same distribution of supranucleosomal structures (even those containing internal DNA scissions) can be reconstituted from unfolded nuclear chromatin extracts as present in 10 mM or 600 mM NaCl. Moreover, fractions of oligonucleosomes with mean lengths between 6 and 15 nucleosomes reassemble or aggregate into a limit series of multimeric species. The existence of an assembly barrier could be inferred as we were unable to observe a stable and soluble assembly product containing more than about 25 nucleosomes. We propose an alternative explanation for the generation and observation of a constant distribution of supranucleosomal structures in nuclear extracts, based on the assembly or aggregation property of oligonucleosomes and on the existence of an assembly barrier.

The effect of histone H1 on the compaction of oligonucleosomes. A quasielastic light scattering study

The structural properties of H1-depleted oligonucleosomes are investigated by the use of quasielastic laser light scattering, thermal denaturation and circular dichroism and compared to those of H1-containing oligomers. To obtain information on the role of histone H1 in compaction of nucleosomes, translational diffusion coefficients (D) are determined for mono-to octanucleosomes over a range of ionic strength. The linear dependences of D on the number of nucleosomes show that the conformation of stripped oligomers is very extended and does not change drastically with increasing the ionic strength while the rigidness of the chain decreases due to the folding of linker DNA. The results prove that the salt-induced condensation is much smaller for H1-depleted than for H1-containing oligomers and that histone H1 is necessary for the formation of a supercoiled structure of oligonucleosomes, already present at low ionic strength.

Time course of polynucleosome relaxation and ADP-ribosylation. Correlation between relaxation and histone H1 hyper-ADP-ribosylation

Isolated rat pancreatic polynucleosomes were poly(ADP-ribosylated) with purified calf thymus poly(ADP-ribose) polymerase. A time course study was performed using an NAD concentration of 200 microM and changes in nucleosomal structure were investigated by means of electron microscopy visualization and sedimentation velocity determinations. In parallel, analyses of histone H1 poly(ADP-ribosylation) and determinations of DNA polymerase alpha activity on ADP-ribosylated polynucleosomes were done at different time intervals. A direct kinetic correlation between ADP-ribose incorporation, polynucleosome relaxation amd histone H1 hyper-ADP-ribosylation was established. In addition, DNA polymerase alpha activity was highly stimulated on ADP-ribosylated polynucleosomes as compared to control ones, suggesting increased accessibility of DNA to enzymatic action. Because of the strong evidence implicating histone H1 in the maintenance of higher-ordered chromatin structures, the present study may provide a basis for the interpretation of the involvement of the histone H1 ADP-ribosylation reaction in DNA rearrangements during DNA repair, replication or gene expression.

Structural properties of barley nucleosomes

The structural properties of barley oligonucleosomes are investigated and compared to those of rat liver oligomers. Extraction of barley chromatin was performed using mild nuclease digestion of isolated nuclei leading to a low ionic strength soluble fraction. Oligonucleosomes were fractionated on sucrose gradients and characterized for DNA and histone content. Physico-chemical studies (sedimentation, circular dichroism and electric birefringence) showed that barley oligonucleosomes exhibit properties very close to those of the H1-depleted rat liver counterparts. Moreover, in situ, barley linker DNA was more sensitive to micrococcal nuclease digestion than that of rat liver. These results suggest that barley oligonucleosomes show a less compact structure than their rat liver counterparts and appear to be in contradiction with the very condensed organization of barley chromatin previously suggested.

Characterization of nuclear estradiol receptors released by micrococcal nuclease and deoxyribonuclease I

Interaction of estradiol receptor with chromatin was probed by nuclease digestion of receptor-chromatin complex. The complex was formed by incubating partially purified receptor with chromatin. Micrococcal nuclease digestion of the complex released a 7S form of receptor which could be converted to 2.8S form by DNAase I. Digestion of the complex with DNAase I yielded different forms of receptors ranging from 7S to 2.8S depending on the digestion time. Receptor distribution was also examined by isolating nuclei form tissue pre-incubated with radioactive estradiol. Micrococcal nuclease digestion of receptor-filled nuclei released 7S, 5.5S and 3.5S forms of receptors. Collectively, these results indicate that the 7S nuclear receptor may have an associated chromatin fragment which is sensitive to DNAase I activity. The desirable features of receptor-chromatin method over conventional methods for studies relating to receptor interaction at the gene site are discussed.

A minireview of microheterogeneity in H1 histone and its possible significance

Subtypes of H1 histone vary in primary structure, and the higher organisms that have been studied each seem to have about a half-dozen subtypes. The proportions of these subtypes vary with the progress of differentiation as seen in embryonic development, hormonally induced changes, spermatogenesis, and terminal differentiation. The H1 subtypes differ among themselves in their ability to condense DNA and small chromatin fragments. They have the potential, therefore, of causing different parts of the chromatin to be condensed to different degrees.

Nuclease digestibility of chromatin is affected by nuclei isolation procedures

Experiments using nucleases as probes of chromatin structure take place in two stages: (1) nuclei isolation, and (2) nuclease digestion. The parameters of the nuclease digestion stage are usually strictly controlled because of nuclease sensitivity to them. However, there have been no reports on whether parameters in the nuclei isolation stage affect the subsequent nuclease digestions. We have evaluated a typical nuclei isolation technique with respect to how changes in the isolation parameters affect nuclease digestion kinetics. Our observations point out that various parameters encountered in the nuclei isolation stage have a significant effect on the subsequent nuclease digestion kinetics of DNAase I. These parameters include the concentration of cells, divalent cations and phosphatase inhibitors. The pH, concentration of NaCl and concentration of detergent had little effect. Micrococcal nuclease was relatively unaffected by changes in the nuclei isolation parameters. The importance of this report lies in the demonstration that lack of control of seemingly insignificant parameters, such as cell concentration during the nuclei isolation stage, leads to subsequent irreproducible results in the DNAase I digestion. These findings indicate that great care must be exercised in the nuclei isolation stage if reproducible work is to be performed with DNAase I.

Histone H5 can increase the internucleosome spacing in dinucleosomes to nativelike values

Chicken erythrocyte chromatin was assembled with inner histones at about 60% of the ratio found in vivo and subsequently incubated with histone H5 (or H1 + H5) in a solution containing 0.1 M NaCl and poly(glutamic acid). Micrococcal nuclease digestion produced dinucleosomes of 360-390 base pair (bp) DNA content, similar to those from native chromatin and contrasting with the 270-280 bp species found in material incubated without H5. On sucrose gradients a dinucleosome sedimenting at 16 S containing 360 bp DNA was isolated. Removal of H1 + H5 after reconstitution did not change these results; H5 thus can induce rearrangements of nucleosome cores with respect to their neighbors. The results are interpreted as an H5-induced "sliding apart" of histone octamers, complementary to the "sliding together" found in native chromatin after removal of H1 + H5.

Nucleomeric organization of chromatin

In the nuclei fixed in situ, as well as in nuclei in low-ionic-strength solutions containing magnesium ions, chromatin is represented by globular nucleomeric fibrils 20-25 nm in diameter. Staphylococcal or endogenous nucleases cleave chromatin fibrils to nucleomers and multinucleomers. On removal of firmly bound magnesium, the nucleomers unfold into chains of four, six or eight nucleosomes. Mild staphylococcal nuclease digestion of nuclear chromatin releases mononucleomers, dinucleomers and trinucleomers that sediment in the sucrose density gradient in the presence of EDTA as 37-S, 47-S and 55-S particles, respectively. The mononucleomers in the sucrose density gradient with MgCl2 sediment as 45-S particles. The determination of the length of staphylococcal-nuclease-digested DNAs contained in the chromatin fragments showed that a nucleomer is composed of 8, and a dimer and trimer of 14-16 and 21-24 nucleosomes, respectively. When deprived of Mg2+ ions, the monomers lose their compactness (45 S) and become loose particles (37 S). This transition is completely reversible if nucleomers contain histone H1. Removal of this histone or dialysis of the nucleomer against EDTA at low ionic strength results in the complete unfolding of the nucleomer into a chain of nucleosomes. A structural model of a nucleomer fibril is suggested where the helicity of the nucleosome chain in a nucleomer (two turns of four nucleosomes each) is periodically discontinued. Such an organization of chromatin apparently provides additional hindrances for site-specific recognition of DNA in chromatin but permits local changes (within a single nucleomer) in chromatin when a hindrance is abolished.

Physicochemical properties of salt-soluble, unsheared chromatin. Molecular weight studies

A chromatin fraction, which can reproducibly be extracted from rat liver nuclei at moderate salt concentration (0.1 M (NH4)2SO4, 0.1 M Tris-HCl, 2 mM MnCl2, pH 7.9), was analyzed with regard to changes of its molecular weight in the range of (NH4)2SO4 concentrations between 0.1 M and 0.4 M. With the transition from 0.1 M to 0.2 M (NH4)2SO4 histone H1 is released and the molecular weight obtained from both sedimentation-viscosity and light scattering is reduced by approximately one-half. A spatial expansion of the resulting half-molecules is observed with further increasing salt concentration. On the basis of these results a double-fibrillar structure of this chromatin fraction is proposed.

The structural organization of dinucleosomes and oligonucleosomes. Electric dichroism and birefringence study

The spatial organization of nucleosomes and linker DNA in dinucleosomes and oligonucleosomes of various chain lengths has been investigated through electric dichroism, birefringence and relaxation times measurements at low ionic strengths (0.5 to 2.2 mM). From the negative dichroism observed for all the samples, it is concluded that the nucleosome subunits in the oligonucleosome chain must lie with their disc planes closely parallel to the fibre axis. The large increase of the negative dichroism of dinucleosomes upon Hl removal is interpreted by the unwinding of the DNA tails and the internucleosomal segment. All the samples displayed, under bipolar pulses, a predominantly induced orientation mechanism.

Interaction of histone H1 with superhelical DNA. Sedimentation and electron microscopical studies at low salt concentration

Complexes of histones H1 with superhelical SV40 DNA obtained by direct mixing were studied in 0.1 SSC buffer corresponding to 0.02 M Na+. Depending on the molar input ratio H1/DNA three classes of sedimenting species were observed: (1) a component sedimenting similar to superhelical DNA with a sedimentation coefficient s2o,w of 25 S observable up to 335 Mol H1/Mol DNA (w/w = 2); (2) a component with s2o,w = 120 S appearing at 135 Mol H1/Mol DNA and (3) growing amounts of heterogeneous aggregates greater than 1000 S. Electron micrographs revealed the 25 S component to consist of double-fibers formed from one DNA molecule and the 120 S component to consist of bundles of several such double-fibers. The aggregates represent cable-like structures. The addition of ethidium bromide to 25 S complexes induces the formation of bundles, if H1 is present in a quantity which alone is not sufficient to bring about this effect. This result indicates that ethidium bromide effects a redistribution of H1 molecules and that H1 is responsible for the bundle formation.

Physicochemical properties of salt-soluble, unsheared chromatin. Salt-dependent structural changes

Salt-dependent structural changes of rat liver chromatin isolated by an extraction procedure not involving shear and exogenous nucleases were investigated by sedimentation and light scattering methods. The effects observed are complex involving changes in the molecular weight and expansion. Between 0.1 M and 0.2 M (NH4)2SO4 where histone H1 is released, a fragmentation into molecules of half molecular weight is found which is accompanied by an expansion into a more extended conformation gradually increasing to 0.4 M (NH4)2SO2. The H1-free chromatin does not exhibit the reduction in molecular weight but undergoes this expansion. The original conformation is not reversible on re-decreasing the salt concentration to 0.1 M (NH4)2SO4.

Partial characterization of RNA polymerase II complex released by micrococcal nuclease digestion of rat liver nuclei

Two forms of RNA polymerase II were released from rat liver chromatin by micrococcal nuclease digestion of the nuclei. One from behaved like a free RNA polymerase II and the other like a complex with other nuclear components. Both forms of RNA polymerase II activity were recovered in the 0.16 M NaCl-soluble fraction of the nuclear digest, and the complexed from the RNA polymerase II could transcribe its endogenous template under conditions permitting only of elongation of the RNA synthesis. The RNA polymerase II complex was further purified by gel filtration chromatography and column electrophoresis. Analysis of protein and DNA of the partially purified complex suggested that the RNA polymerase II was bound to mono- or dinucleosomes carrying some characteristic nonhistone proteins. Furthermore, in experiments on tissues from starved rats, the two forms of RNA polymerase II were found to originate from different functional states of the chromatin-bound enzyme in vivo.

Cross-linking of histone H1 in chromatin

Arrays of neighbouring histone H1 molecules are present in rat liver chromatin, and can be cross-linked to each other by bisimidoesters. The product, poly(H1), can be extracted from cross-linked chromatin in high yield with 5% perchloric acid and thus distinguished from cross-linked oligomers of the core histones. On analysis in dodecyl sulphate/polyacrylamide gels poly(H1) gives a striking pattern of alternating strong and weak bands which have been shown, by the use of cleavable cross-linked reagents and two-dimensional gel electrophoresis, to arise respectively from H1 homopolymers and H1 polymers linked to the nucleosome core histones. H1-H1 proximities as measured by cross-linking exist both at low ionic strength where the nucleosome filament is extended, and at higher ionic strengths at which it is folded into a 30-nm-diameter fibre, probably in the form of a solenoid, although some additional H1-H1 contacts seem to occur in the folded form. A similar pattern of H1-H1 cross-linking is observed for nucleosome oligomers too short to form a complete turn of a solenoid. The lack of any strong dependence of the H1 cross-linking pattern on ionic strength, and the results for short oligomers, suggest that in a solenoid the major H1-H1 interactions are lateral (i.e. they occur between neighbouring nucleosomes along a turn) although additional vertical contacts (between successive turns) are not excluded. For a short nucleosome oligomer containing n nucleosomes, the number of H1 molecules that may be cross-linked into an array at low ionic strength (approximately 15 mM) is n, consistent with the presence of one H1 per nucleosome. H1-H1 cross-linking occurs only within the chromatin framework; when cross-linking is carried out in 0.5 M NaCl so that H1 is dissociated from chromatin, no poly(H1) is formed. When H1 which has been dissociated in 0.5 M NaCl is allowed to reassociate by gradual lowering of the ionic strength, the poly(H1) is identical with that in native chromatin, suggesting faithful rebinding of H1 molecules. H1-H1 proximities do not seem to be mediated by the presence of bound high-mobility-group non-histone proteins because the poly(H1) pattern persists when cross-linking is carried out at 365 mM ionic strength, when these high-mobility-group proteins are dissociated from chromatin. The H1 cross-linking pattern described here could prove to be a useful assay for the native arrangement of H1 molecules in reconstituted chromatin and for changes in H1-H1 contacts that might result from cell-cycle modifications (e.g phosphorylation) of H1. It may not prove a good assay for higher-order structure because of the relative insensitivity to ionic strength of the poly(H1) pattern as studied here. A detailed analysis will be necessary to determine whether there are any subtle differences in the interactions between H1 molecules in the folded and extended nucleosome filament.

Conformation of nucleosome core particles and chromatin in high salt concentration

The conformation of nucleosome core particles and chromatin under different ionic strength conditions has been studied by electron microscopic, hydrodynamic, and spectroscopic techniques. In the range of ionic strength used (6--600 mM), all four core histones were bound to the DNA. The sedimentation coefficient of the core particle decreases from 11.3 in 6 mM NaCl to 9.4 in 600 mM NaCl, and an alteration of the circular dichroic spectrum was observed when the ionic strength was increased. Direct evidence for the alteration of the chromatin structure in high salt was obtained by electron microscopy where a very extended conformation of the nucleosome was observed. The protein cross-linking agent dimethylsuberimidate was used to study the histone--histone proximities in the core particles; our experiments reveal that the same histones are in contact in the extended particles and in the compact native particles.

Expression of H1 histone genes in mouse-human somatic cell hybrids

The synthesis of H1 histones was studied in nine mouse-human somatic cell hybrid clones containing reduced numbers of human chromosomes. The entire human genome could be accounted for karyologically and by the use of functional assays for specific enzyme markers encoded by human chromosomes. Chromatographic resolution and peptide mapping of species-specific H1 histones failed to reveal human H1 histones to a level of about 1% of total in the nine clones. In addition to the species-specific extinction of human H1 histones, effects were seen on the quantity of mouse H1 histone subtypes produced in four of the nine clones. The remaining five clones produced H1 histones qualitatively and quantitatively identical with those of the mouse parent, which was common to all nine clones. The results suggest at least two levels of control for H1 histone gene expression.