Studies on the role of histones HI (f1) and H5 (f2c) in chromatin structure

The perichromatin region: a functional compartment in the nucleus that determines large-scale chromatin folding

The perichromatin region has emerged as an important functional domain of the interphase nucleus. Major nuclear functions, such as DNA replication and transcription, as well as different RNA processing factors, occur within this domain. In this review, we summarize in situ observations regarding chromatin structure analysed by transmission electron microscopy and compare results to data obtained by other methods. In particular, we address the functional architecture of the perichromatin region and the way chromatin may be folded within this nucleoplasmic domain.

Trypanosoma cruzi: flow cytometric analysis of developmental stage differences in DNA

Flow cytometry and DNA binding-specific fluorescent reagents were used to compare the total DNA, G-C, and A-T content of the epimastigote and trypomastigote stages of Trypanosoma cruzi stocks. Significant total DNA differences of 2-12% between epimastigotes and trypomastigotes were found in three of six stocks studied. The epimastigote G-C content of five of six stocks was 4-8% higher than trypomastigotes, whereas the trypomastigote A-T content was 2.5-13% higher than the epimastigote A-T content. Although no obvious developmental stage association between total DNA and base composition was found, intrastage associations do exist. These observations were unaffected by nucleoprotein extraction implying that the observed differences between trypomastigotes and epimastigotes are not a consequence of nucleoprotein interference with DNA-binding fluorochromes. The nuclei and kinetoplasts of four T. cruzi stocks were isolated and analyzed. Developmental stage differences in nuclear and kinetoplast DNA are stock-dependent and base composition-dependent; both organelles contribute to the observed differences in DNA of intact cells. We found a nearly linear association between the percentage of total kinetoplast DNA, G-C, and A-T content. During metacyclogenesis, the G-C content decreases by approximately 7% as epimastigotes transform into metacyclic trypomastigotes. The decrease in G-C content precedes changes in morphology or in complement resistance. If the DNA changes are causally connected to developmental stage transformations in T. cruzi remains to be determined. However, our results could facilitate studies of the molecular genetic processes the parasite uses to successfully complete various phases of its life cycle and, consequently, the disease process it evokes.

Cooperative interaction of the C-terminal domain of histone H1 with DNA

We have studied the interaction of the isolated C-terminal domain of histone H1 with linear DNA using precipitation curves and electron microscopy. The C-terminal domain shows a salt-dependent transition towards cooperative binding, which reaches completion at 60 mM NaCl. At this salt concentration, the C-terminal domain binds to some of the DNA molecules, leaving the rest free. A binding site of 22 base-pairs can be calculated from the stoichiometry of the precipitated fractions. The C-terminal domain condenses the DNA in toroidal particles. The average inner radius of the particles is of the order of 195 A. Consideration of the value of the inner radius of the toroids in the light of counterion condensation theory suggests that in these complexes the isolated C-terminal domain is capable of nearly full electrostatic neutralization of the DNA phosphate charge.

Flow cytometric evaluation of DNA stainability with propidium iodide after histone H1 extraction

A flow cytometric evaluation of the effect of the histone H1 extraction on DNA stainability with propidium iodide was performed on isolated HeLa nuclei. Selective removal of the lysine-rich protein was attained by using two established techniques involving treatment with 0.7 M NaCl or low pH. DNA stainability was monitored at different dye/DNA-P ratios, varying from low to high saturating concentrations. Depletion of the histone H1from nuclei results in the transition from low to high affinity of a portion of binding sites, as shown by 1) the increase in fluorescence intensity after staining with the dye at low saturating concentrations and 2) the higher value of the fluorescence intensity ratio (FI5/FI50) exhibited by H1-depleted nuclei stained with a low (5 micrograms/ml) vs. a high (50 micrograms/ml) concentration, as compared with control samples.

A flow cytometric study of DNA staining in situ in exponentially growing and stationary Euglena gracilis

DNA stainability by different fluorochromes has been compared in exponentially dividing and stationary Euglena cells. With the intercalating fluorochromes, ethidium bromide, acridine orange and DAPI, a decrease of fluorescence intensity of the G1 cells is observed when cells enter stationary stage. However this decrease of fluorescence is not obtained with the nonintercalating fluorochrome Hoechst 33258. If nuclear basic proteins are extracted, however, the intensity of staining by either Hoechst 33258 or ethidium-bromide is comparable in stationary and dividing cells. Therefore, the decrease of fluorescence intensity of the G1 cells observed during the transition from exponential to stationary phase is not due to a loss of DNA but is related to the exposure of chromatin binding sites for ethidium bromide. In Euglena cells, DNA accessibility for intercalating fluorochromes depends upon chromatin structure and consequently upon cell age.

Effects of osmotic shocks on the ultrastructure of different tissues and cell types

This study deals with the effects of hyper- and hypo-osmotic media on the ultrastructure of four different types of cells and tissues: rat pheochromocytoma cells of line PC12, mouse Ehrlich ascites tumor cells, rat kidney cortex and intestine. Application of hyper-osmotic conditions induces in the nuclear compartment of the tested cell types a condensation of chromatin, a ruffling of the nuclear envelope with loosening of condensed chromatin from the lamina, and an apparent loss of nucleolar fibrillar component which disappears in a background of diffuse granular material. In hypo-osmotic media, there is a marked decondensation of chromatin and a fragmentation of the granular material of the nucleolus. As far as the cytoplasmic compartment is concerned, the electron density of the cytosol is markedly increasing when going from hypo- to hyper-osmotic conditions and there is no vacuolization in hypo-osmotic media. In kidney cortex slices, application of hypo-osmotic shocks further results in a marked reduction of the extracellular space delimited by the infoldings of the tubular cells plasma membranes. These modifications are discussed in relation to the volume regulation process and the changes in ion concentration that occur in cells submitted to anisosmotic media.

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.

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.

Involvement of the globular domain of histone H1 in the higher order structures of chromatin

We have attacked H1-containing soluble chromatin by alpha-chymotrypsin under conditions where chromatin adopts different structures. Soluble rat liver chromatin fragments depleted of non-histone components were digested with alpha-chymotrypsin in NaCl concentrations between 0 mM and 500 mM, at pH 7, or at pH 10, or at pH 7 in the presence of 4 M-urea. alpha-Chymotrypsin cleaves purified rat liver histone H1 at a specific initial site (CT) located in the globular domain and produces an N-terminal half (CT-N) which contains most of the globular domain and the N-terminal tail, and a C-terminal half (CT-C) which contains the C-terminal tail and a small part of the globular domain. Since in sodium dodecyl sulfate/polyacrylamide-gel electrophoresis CT-C migrates between the core histones and H1, cleavage of chromatin-bound H1 by alpha-chymotrypsin can be easily monitored. The CT-C fragment was detected under conditions where chromatin fibers were unfolded or distorted: under conditions of H1 dissociation at 400 mM and 500 mM-NaCl (pH 7 and 10); at very low ionic strength where chromatin is unfolded into a filament with well-separated nucleosomes; at pH 10 independent of the ionic strength where chromatin never assumes higher order structures; in the presence of 4 M-urea (pH 7), again independent of the ionic strength. However, hardly any CT-C fragment was detected under conditions where fibers are observed in the electron microscope at pH 7 between 20 mM and 300 mM-NaCl. Under these conditions H1 is degraded by alpha-chymotrypsin into unstable fragments with a molecular weight higher than that of CT-C. Thus, the data show that there are at least two different modes of interaction of H1 in chromatin which correlate with the physical state of the chromatin. Since the condensation of chromatin into structurally organized fibers upon raising the ionic strength starts by internucleosomal contacts in the fiber axis (zig-zag-shaped fiber), where H1 appears to be localized, it is likely that in chromatin fibers the preferential cleavage site for alpha-chymotrypsin is protected because of H1-H1 contacts. The data suggest that the globular part of H1 is involved in these contacts close to the fiber axis. They appear to be hydrophobic and to be essential for the structural organization of the chromatin fibers.(ABSTRACT TRUNCATED AT 400 WORDS)

Structural function of the basic nuclear proteins in ram spermatids

The function of the cysteine-containing spermatidal proteins and of protamine in the packaging and stabilization of chromatin during ram spermiogenesis was investigated. Extractions of the histones and spermatidal proteins from the nonround spermatid nuclei decreases the nuclear stability (sonication resistance), decondenses the chromatin, and reduces the diameter of the largest chromatin threads (100-200 A vs. 380 A in the control nuclei). Extractions by acid, salt, or heparin have no effect on the protamine-containing electron-opaque chromatin. In contrast, treatment by dithiothreitol alone decondenses all the nonround spermatid nuclei at a rate which decreases with the maturation state of the nuclei. The electron-opaque chromatin is then resolved in 35-A-thick filaments. Experimentally induced fluctuations of the level of SS bonding appear to influence the chromatin stabilization and ultrastructure in most of the nonround spermatid nuclei. These data evidence that noncovalent interactions play a main structural role at the beginning of chromatin reorganization, and SS bonding between spermatidal proteins and then between protamine molecules increases progressively and becomes mainly responsible for the chromatin stabilization in the protamine-containing nuclei.

Involvement of the domains of histones H1 and H5 in the structural organization of soluble chromatin

We have studied in reconstitution experiments the conditions under which peptides derived from histones H1 and H5 are bound in chromatin and to what extent they are involved in the organization of chromatin fibers. The fragments of rat liver histone H1 (rH1) and chicken erythrocytes H1 (cH1) and H5 (cH5) used were the globular domains (rG-H1, cG-H1, cG-H5), the globular domain and the N-terminal tail (rCT-N), about half of the globular domain and the C-terminal tail (rNBS-C) and the C-terminal tail (rCT-C). Fragments containing the C-terminal tail (rNBS-C and rCT-C) dissociate from H1-depleted rat liver chromatin at 300 mM-NaCl and above (similar to uncleaved H1) and fragments lacking the C-terminal tail (rG-H1 and rCT-N) dissociate between 100 and 200 mM-NaCl. This suggests that at putative physiological ionic strengths the binding of rH1 is dominated by its C-terminal tail, whereas the globular region and the N-terminal tail might only be loosely bound or not bound at all and by this modulate chromatin structure. The globular domain of cH5 binds more tightly than that of the chicken and rat H1 and is only partially released at 200 mM. Since in the transcriptionally silent erythrocytes of birds H5 replaces H1 to a large extent, we suggest that the globular domain of H1 serves as a temporary seal and that of H5 as a permanent seal of the nucleosome. All the H1 and H5 peptides tested condensed and precipitated chromatin and H1-depleted chromatin: rNBS-C and rCT-C at lower peptide per nucleosome ratios than rG-H1, cG-H1 and rCT-N. At about one peptide per nucleosome none of the H1 fragments induced condensation similar to that of native chromatin. At a peptide per nucleosome ratio close to the point of precipitation, all H1 fragments, but not poly-L-lysine, induced similar compact forms which were fiberlike, although more irregular than the compact fibers of native chromatin. These reconstitution experiments suggest that both halves of H1 as well as the globular domain by itself are involved and capable in forming higher-order chromatin structures. Details of these structures are not known.

Low angle x-ray diffraction studies of chromatin structure in vivo and in isolated nuclei and metaphase chromosomes

Diffraction of x-rays from living cells, isolated nuclei, and metaphase chromosomes gives rise to several major low angle reflections characteristic of a highly conserved pattern of nucleosome packing within the chromatin fibers. We answer three questions about the x-ray data: Which reflections are characteristic of chromosomes in vivo? How can these reflections be preserved in vitro? What chromosome structures give rise to the reflections? Our consistent observation of diffraction peaks at 11.0, 6.0, 3.8, 2.7 and 2.1 nm from a variety of living cells, isolated nuclei, and metaphase chromosomes establishes these periodicities as characteristic of eukaryotic chromosomes in vivo. In addition, a 30-40- nm peak is observed from all somatic cells that have substantial amounts of condensed chromatin, and a weak 18-nm reflection is observed from nucleated erythrocytes. These observations provide a standard for judging the structural integrity of isolated nuclei, chromosomes, and chromatin, and thus resolve long standing controversy about the "tru" nature of chromosome diffraction. All of the reflection seen in vivo can be preserved in vitro provided that the proper ionic conditions are maintained. Our results show clearly that the 30-40-nm maximum is a packing reflection. The packing we observe in vivo is directly correlated to the side-by-side arrangement of 20- 30-nm fibers observed in thin sections of fixed and dehydrated cells and isolated chromosomes. This confirms that such packing is present in living cells and is not merely an artifact of electron microscopy. As expected, the packing reflection is shifted to longer spacings when the fibers are spread apart by reducing the concentration of divalent cations in vitro. Because the 18-, 11.0-, 6.0-, 3.8-, 2.7-, and 2.1-nm reflections are not affected by the decondensation caused by removal of divalent cations, these periodicities must reflect the internal structure of the chromaticn fibers.

Higher order folding of two different classes of chromatin isolated from chicken erythrocyte nuclei. A light scattering study

Bulk chromatin fragments were excised from chicken erythrocyte nuclei by digestion with micrococcal nuclease. Fractionation into S chromatin (soluble at physiological ionic strengths) and I chromatin (insoluble at physiological ionic strengths) was achieved by dialysis against buffers containing 0.15 M NaCl. The effects of NaCl concentration on the molecular dimensions of S and I chromatins were determined by dynamic and static light scattering. Series of fragment lengths were obtained by gel filtration of S and I chromatins under ionic conditions which lead to maximal intramolecular compaction. Hydrodynamic radii and radii of gyration were determined for fragment lengths ranging from 8 to 53 nucleosomes. These data are in excellent agreement with calculations for extended helical structures. Close-packed solenoidal or superbead structures are not compatible with these data. Comparisons of molecular dimensions derived from light scattering and electron microscopy indicate that considerable shrinkage of chromatin fragments can occur when common methods of sample preparation are used for microscopy.

Propidium iodide as a probe for the study of chromatin thermal denaturation in situ

The possibility of using propidium iodide, a phenanthridinic fluorochrome specific for double-stranded nucleic acids, for the study of chromatin thermal denaturation in situ has been examined. Smears of lymphocytes and hepatocyte nuclei from 15-day-old rats were fixed in acetic acid--ethanol (1:3 v/v), treated with RNAse and submitted to different protein extraction procedures, namely, incubation with pepsin, trypsin and sodium chloride. Denaturation experiments were performed in Sörensen buffer at pH 7.4 containing 10% formamide at temperatures between 27 and 95 degrees C. The samples were stained with propidium iodide and mounted in buffer or glycerol. Measurements were performed with a microfluorometer at a wavelength of 446 nm. The results indicate a higher thermostability of lymphocytes as compared to hepatocytes. The denaturation pattern suggests a certain organization complexity of chromatin, better emphasized by the derivative curves which show the presence of at least three fractions with different melting points. After protein extraction, the denaturation curves exhibit a somewhat simplified pattern, with the disappearance of the most stable peak in the derivative curves. The samples mounted in glycerine exhibit a better stability of staining with time, and an increased quantum efficiency of the fluorochrome with regard to those mounted in buffer. These data confirm the importance of protein--DNA interactions in the organization of chromatin and point to some differences, depending on the cell type and on functional activity.

The binding of histones H1 and H5 to chromatin in chicken erythrocyte nuclei

The binding curves of histones H1 and H5 to chromatin in nuclei have been determined by a novel method which utilises the differential properties of free and bound histones on cross-linking with formaldehyde. The dissociation is thermodynamically reversible as a function of [NaCl]. The binding curves are independent of temperature over the range 4 degrees - 37 degrees C and independent of pH over the range 5.0 to 9.0. The curves are sigmoid, indicating co-operative dissociation with NaCl. The standard free energy of dissociation in 1 M NaCl for H1 is 0.5 Kcals/mole and for H5 is 3.5 Kcals/mole.

The chemistry of the retina: Function, renewal, rhythms, and the nucleus

Investigation of the chemical activities of retinal cells began with functional chemistry, an origin which can be traced to the pioneering studies of Kühne and Wald. Next to develop was renewal chemistry, which is concerned with the continued replacement of retinal cell structure. A third field of retinal chemistry, more recently evolved, is the analysis of chemical change associated with daily rhythms. In the living cell, all such groups of chemical reactions are merged into a single, integrated metabolism which ultimately is regulated by molecular systems sequestered within the nucleus. Although nuclear chemistry has so far been neglected in vision research, a theory of nuclear metabolism has been maturing in other fields of biological chemistry. One salient aspect of the theory is the temporal stability of the fundamental constituents of the chromosomes: DNA and histone. Alone among all cellular molecules, they may persist indefinitely. Nuclear theory has proved to have important predictive value in preliminary applications to analysis of the mammalian retina. Evidence is presented in the following report which indicates that retinal cells can repair DNA lesions provoked by UV radiation. Other experiments suggest that in retinal nuclei there is a reversible acetylation of histones and non-histone chromosomal proteins-a process which is implicated in gene regulation.

Chromatin substructure: an electron microscopic study of thin-sectioned chromatin subjected to sequential protein extraction and water swelling procedures

Electron microscopic observations and measurements were made on thin-sectioned chromatin fibers and fibrils obtained from nuclei of mature chicken erythrocytes. The nuclei were isolated in low ionic strength gum arabic and octanol then extracted sequentially with (1) 0.14 M NaCl, (2) 0.25 N HCl, (3) buffer saturated phenol, (4) hot 5% SDS and 0.14 M 2-mercaptoethanol and, (5) 0.4 N NaOH. The amount of nuclear protein removed at each of the first four extraction steps was 1, 86, 3 and 11% of the total, respectively. Each extract was characterized by electrophoretic profiles. At each extraction the chromatin was fixed by adding large quantities of a mixture of equal volumes of sodium cacodylate buffered 8% (w/v) glutaraldehyde (pH 6.8) and 2% OsO4 (w/v), directly into (1) an aliquot of the chromatin in extraction fluid, and (2) an aliquot of the chromatin after water washing and swelling. Three size classes of chromatin structure were seen in thin sections prepared for high resolution transmission electron microscopy and stained with uranyl acetate and lead citrate. A thick fiber of about 25 + nm diameter was the predominant large fiber seen in freshly isolated nuclei or in nuclei after salt extraction. This 25 + nm fiber has a substructure consisting of 3.2-5.2 nm diameter fibrils. After water swelling of such freshly isolated or salt extracted nuclei a fiber of about 10 nm diameter was the predominant large fiber instead of the 25 nm diameter fiber. The HCl extraction step which is known to remove histones, caused the disappearance of both the 25 nm and the 10 nm fibers. High magnification (600,000 x) micrographs of the chromatin at all procedural steps, except the last NaOH step, reveal the fibril to be omnipresent. This fibril tends to decrease somewhat in diameter during the protein extraction steps to a 2.5 nm diameter fibril after the hot SDS extraction. A fibril of 2.5 nm diameter is expected of naked double helical DNA stained with a positive stain. The NaOH, which is known to denature DNA, completely destroyed the remaining fibril. We inerpret our results to indicate that the larger chromatin fiber seen in micrographs of thin-sectioned chromatin has a fibrillar substructure which probably represents a double coil of native DNA which may have a thin protein coating of its own. The latter fibril may in turn be wrapped around a hydrophobic histone domain, perhaps reflected in the 10 nm diameter fiber which is seen upon swelling of the chromatin. This 10 nm diameter fiber is thought to be further packaged by folding into the 25 + nm diameter chromatin fiber most frequently reported in thin sections of eukaryotic cell nuclei in situ.

Higher order structure of simian virus 40 chromatin

Simian virus 40 nucleoprotein complexes undergo an ionic strength-dependent structural transition. At moderate ionic strength they contain histone H1 as well as the nucleosomal histones and have a compact conformation with globular subunits 190 angstroms in diameter. At high ionic strength histone H1 is released, and the structure unfolds into chains with an average of 24 nucleosomes. The extended viral chromatin converts to the compact form by the addition of histone H1. Transcriptionally active simian virus 40 chromatin undergoes the same structural transitions. The higher order structure of viral chromatin may be analogous to the compact state of cellular chromatin fibers observed at physiological ionic strength.

The organization, composition and matrix of hepatocyte nuclei exposed to alpha-amanitin

Alterations in the structure and molecular composition of avian hepatocyte nuclei were compared following administration in vivo of lethal and sub-lethal doses of alpha-amanitin. This toxin interferes with extranucleolar transcription by direct inhibition of RNA polymerase II activity. the resultant effects include: extensive condensation of chromatin, displacement of nucleoplasmic contents and fragmentation of nucleoli. Changes in nuclear morphology were quantitated by stereometry and related to variations in RNA and residual, non-histone proteins (NHP). Gross alterations in nuclear structure and depletion of RNA and NHP levels were of similar magnitude with both doses of amanitin. The effects were fully reversible, however, with a minimal dose but terminal with a lethal dose. DNA and histone protein levels remained unchanged at all stages. These results imply that the process of transciption may itself keep and/or maintain chromatin in a dispersed state, and that in the absence of transcription chromatin naturally condenses. Modification of nuclear proteins may be necessary only to maintain chromatin compacted permanently or for extended periods of time. A model of nuclear organization is proposed to incorporate these considerations and to identify the probable location of the nuclear matrix in situ.

Influence of histone H1 on chromatin structure

Removal of histone H1 produces a transition in the structure of chromatin fibers as observed by electron microscopy. Chromatin containing all histone proteins appears as fibers with a diameter of about 250 A. The nucleosomes within these fibers are closely packed. If histone H1 is selectively removed with 50-100 mM NaCl in 50 mM sodium phosphate buffer (pH 7.0) in the presence of the ion-exchange resin AG 50 W - X2, chromatin appears as "beads-on-a-string" with the nucleosomes separated from each other by distances of about 150-200 A. If chromatin is treated in the presence of the resin with NaCl at concentrations of 650 mM or more, the structural organization of the chromatin is decreased, yielding fibers of irregular appearance.

The chromosome fiber: evidence for an ordered superstructure of nucleosomes

Chromosome fibers isolated from lymphocyte nuclei and prepared for electron microscopy by techniques designed to preserve their native structure have a distinctly knobby appearance, suggesting that DNA and protein are not distributed evenly along the fiber axis. Individual knobs (superbeads) are arranged in tandem and have an average diameter of about 200 A. Mild nuclease digestion of isolated nuclei releases apparent monomer superbeads that are composed of nucleohistone particles with the properties of nucleosomes. The kinetics of digestion indicate that the superbead is a discrete structural unit containing, on the average, about eight nucleosomes.