Chromatin architecture: investigation of a subunit of chromatin by dark field electron microscopy

Higher Order Structures in Chromosomes

Chromosomes are units of the genom in eukaryotes containing a specific fraction of the DNA characteristic for the species. This DNA forms the backbone of the chromosome and usually is represented by a single DNA double helix stretching from one end of the chromosome to the other. Relative to the size of most nuclei the length of the DNA is considerable. In humans for instance the haploid set of DNA is about 1 m long and in certain amphibia can measure many meters. The analysis of chromosome structure is mainly concerned with the various levels of folding or coiling by which this DNA is compacted in a regular way into chromosomes of interphase and mitotic stages.

The electron microscope has played an important role in the discovery of chromosome organization. The 20 nm fiber was first described in 1956 as a unit of interphase chromatin (Ris, 1956). Later the 10 nm fiber was recognized as the component of chromatin dispersed in the presence of chelating agents for biochemical studies (Ris, 1961).

Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems.

Direct imaging in a water layer of human chromosome fibres composed of nucleosomes and their higher-order structures by laser-plasma X-ray contact microscopy

X-ray contact microscopy with a 300-ps-duration laser-plasma X-ray source has been used to image hydrated human chromosomes. Clearly imaged are individual nucleosomes and their higher-order particles (superbeads), elementary chromatin fibrils. c. 30 nm in diameter and their higher-order fibres of various sizes up to c. 120 nm in diameter. The results demonstrate that X-ray microscopy is now capable of opening a new path of investigation into the detailed structures of hydrated chromosome fibres in their natural state.

Ultrastructure of transcriptionally competent chromatin

We have examined a salt-soluble, transcriptionally competent gene-enriched fraction of chicken erythrocyte chromatin and compared it to bulk chromatin using the unique microanalytical capabilities of Electron Spectroscopic Imaging (ESI). The salt-soluble fraction is enriched 48 fold in beta-globin gene sequences and is also enriched in histones that are post-synthetically modified, including acetylation and ubiquitination. Differences between the two fractions are also apparent in the distribution of the two major forms of nucleoprotein structures, including (1) particles which present a circular profile and possess protein and DNA content nearly identical to that of the canonical nucleosome and account for 89% of particles in the bulk fraction but account for only 66% of the particles in the competent fraction, and (2) u-shaped particles which possess about 20% less protein mass than particles of circular profile and are about 10x more prevalent in the transcriptionally competent fraction than in the bulk. Additionally, elongated particles with protein and DNA content similar to the u-shaped objects are also seen in the competent fraction.

The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin

The diameters of chromatin fibers from Thyone briareus (sea cucumber) sperm (DNA linker length, n = 87 bp) and Necturus maculosus (mudpuppy) erythrocytes (n = 48 bp) were investigated. Soluble fibers were frozen into vitrified aqueous solutions of physiological ionic strength (124 mM), imaged by cryo-EM, and measured interactively using quantitative computer image-processing techniques. Frozen-hydrated Thyone and Necturus fibers had significantly different mean diameters of 43.5 nm (SD = 4.2 nm; SEM = 0.61 nm) and 32.0 nm (SD = 3.0 nm; SEM = 0.36 nm), respectively. Evaluation of previously published EM data shows that the diameters of chromatin from a large number of sources are proportional to linker length. In addition, the inherent variability in fiber diameter suggests a relationship between fiber structure and the heterogeneity of linker length. The cryo-EM data were in quantitative agreement with space-filling double-helical crossed-linker models of Thyone and Necturus chromatin. The data, however, do not support solenoid or twisted-ribbon models for chromatin that specify a constant 30 nm diameter. To reconcile the concept of solenoidal packing with the data, we propose a variable-diameter solid-solenoid model with a fiber diameter that increases with linker length. In principle, each of the variable diameter models for chromatin can be reconciled with local variations in linker length.

Fine structure of unstained human chromosome fibres dried with no fixative as observed by X-ray contact microscopy

X-ray contact microscopy was used to examine unstained human chromosomes dried without any fixative. This is the first report of the observation of single human chromosome fibres at high resolution without any modification(s) such as staining or fixation. The 'beads-on-a-string' structure was observed in stretched portions of chromosome fibres. The diameters of the thin filaments and small particles were 7-15 nm (mean +/- SD of 12.2 +/- 2.1 nm) and 16-69 nm (31.4 +/- 13.2 nm), respectively. These sizes correspond to those of fibres composed of nucleosomes (10-15 nm in diameter) and particle units (15-50 nm in diameter) called superbeads (unit structures composed of a multiple association of nucleosomes). These results are in good agreement with the current nucleosome and superbead model for chromosome fibre structure.

Calibration methods for quantitative image processing in electron microscopy

An image can be represented digitally as a matrix of numbers. When those numbers are linearly related to a property of the object, such as mass per unit area, a simple integration of an image area leads to a total of that property, such as the mass of a particle that is represented in a selected area. Following techniques pioneered by Bahr and Zeitler, we illustrate the use of photographic densitometry of films exposed in an electron microscope to measure electron scattering. The transmission of an electron micrograph will be linear with respect to mass thickness for a particular value of background brightfield density, hence allowing determination of the mass of microscopic particles. We show here a digital computer method for conveniently establishing the linear condition by quantitative image processing using micrographs of polystyrene spheres. The method also serves to produce calibration curves for cases where the transfer from transmission to mass thickness is not linear. We also illustrate how an inexpensive computer is used to display and integrate regions of micrographs to determine particle mass.

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.

Mass mapping of a protein complex with the scanning transmission electron microscope

A mass map of the hexagonally packed intermediate layer (HPI-layer), a regular protein monolayer from the cell envelope of Micrococcus radiodurans, has been obtained by scanning transmission electron microscopy. Samples were freeze-dried within the microscope, and low-dose images were recorded in the dark-field mode directly in digital form and processed by correlation averaging. The averaged projection of the unstained structure--i.e., the mass map--thus calculated shows a resolution to 3-nm period and reveals morphological features consistent with those obtained by negative staining. The mass of individual morphological domains was extracted by using variously the mass map itself or an average from a negatively stained HPI layer to define the domain boundaries. Protrusions as small as 1,300 daltons could be measured reproducibly within the unit cell of 655,000 daltons. The method developed opens an avenue to identify molecular species in situ and to correlate topographic information with biochemical data.

Cytophotometric determinations of DNA, histone, arginine, lysine, and their concentrations in eu- and heterochromatin of the cell nucleus of dysplasias, carcinoma in situ, and carcinoma of the human cervix uteri

In the cell nuclei of dysplasias, carcinoma in situ, and carcinoma the amount of DNA, histone, arginine, lysine, and their condensed areas were determined by cytophotometry. Moreover their concentrations in the euchromatic and heterochromatic areas of the nuclei were measured. Statistical analysis showed that the quantitative relations between parameters did not change during carcinogenesis. The significantly increased amount of lysine underlines the role of the lysine-rich histones in producing denser coiling of the chromatin fibril in heterochromatin.

Composition of native and reconstituted chromatin particles: direct mass determination by scanning transmission electron microscopy

Chromatin particles reconstituted from 145-base-pair lengths of DNA and either the arginine-rich histones H3 and H4 only or all four nucleosomal core histones have been compared with native nucleosomes in terms of their ultrastructure and mass distribution, as determined by scanning transmission electron microscopy (STEM). The mass of the nucleosome derived from STEM analysis was very close to that calculated for its DNA and histone components. The reconstituted particles showed a broader mass distribution, but it was clear that the majority contained at least eight histone molecules. This was to be expected for structures reconstituted from all four core histones, but in the case of H3H4-DNA complexes clearly showed that an octamer rather than tetramer of these histones was required to fold nucleosomal DNA into a stable compact particle. The significance of the H3H4 octamer complex with respect to nucleosomal structure is discussed, and the evidence that nucleosomal DNA can accept even greater numbers of histones is considered.

Properties of condensed chromatin in barley nuclei

A method for isolation and purification of intact nuclei from barley leaves was developed and several properties of the chromatin were studied. The dense structure of the main part of the chromatin does not alter the accessibility of the DNA to nucleases. 60% of the nuclear DNA can be degraded by micrococcal endonuclease. Nevertheless the solubility of the chromatin fragments depends on the extent of nuclease digestion; solubilisation occurring only when the major part of the internucleosomal DNA was degraded (≃30% of digestion). Electron microscopic observations suggest that this was due to particularly dense organization of the chromatin "in situ". The possible physiological meaning of some of these properties are discussed.

Nucleosomes structure and its dynamic transitions

The discovery of nucleosomes as a basic repeating unit of the chromatin structure organizing the major part of eukaryotic DNA greatly catalyzes the expansion of our knowledge on chromatin. Several lines of experimental evidence have led to the formulation of the nucleosome conception: the observation of chains of globular particles in electron micrographs of chromatin (Olins & Olins, 1974); the demonstration that DNA is released as a set of discrete sizes upon digestion of chromatin with endogenous nucleases (Hewish & Burgoyne, 1973); the isolation of discrete nucleoprotein particles upon digestion of chromatin with micrococcal nuclease (Rill & Van Holde, 1973).

Chromatin freeze fracture electron microscopy: a comparative study of core particles, chromatin, metaphase chromosomes, and nuclei

Chromatin gels, metaphase chromosomes, and intact nuclei were studied by freeze fracturing followed by electron microscopy. The results complement and extend those obtained by classical electron microscopy techniques as they are obtained without fixation or dehydration. The freeze fracturing technique permits a determination of the hydrated diameters of nucleosomes in chromatin and in nuclei to be 13 nm by comparing to simultaneously studied test objects. Nucleosomes in chromatin fibers are closely spaced but are discrete particles in all conditions studied. In the presence of divalent ions, most chromatin in solution, chromosomes, and nuclei is organized into fibers whose thickness is larger than 40 nm. The images are not at all compatible with a super bead organization of the nucleofilament. Freeze fractures of intact nuclei provides information on the distribution of chromatin in a hydrated unfixed state. The images suggest that most of the chromatin is localized in large domains in contact with the inner nuclear membrane.

Self-assembly of single and closely spaced nucleosome core particles

Self-assembly of DNA with the four core histones but in the absence of H1 generates nucleosome core particles which are spaced randomly over large distances. Closely spaced core particles, however, exhibit a preferred short linkage which is not a multiple of 10 base pairs. They bind about 140 base pairs whereas apparently shorter DNA lengths per nucleosome observed after digestion with micrococcal nuclease are the result of degradation from the ends. The DNA length of one superhelical turn in the core particle is 83 +/- 4 base pairs. Single core particles may bind more DNA than closely spaced core particles but probably less than two full turns of 168 base pairs. The internal structures of single and of native core particles are very similar as judged by their amount of DNA, sedimentation coefficient, appearance in the electron microscope, and digestion with DNase I. In addition to core particles, a particle is described which sediments at 9 S and consists of 108 base pairs of DNA bound to the histone octamer. It appears to be the smallest stable "core particle" but it is not a degradation product of the 146-base-pair core particle. Digestion of end-labeled 9 S and nucleosome core particles with DNase I shows distinct differences.

Points of contact between histone H1 and the histone octamer

The topography of the interaction between histone H1 and the histone octamer has been investigated. Bovine thymus nuclei or enzymatically fragmented chromatin were treated 1-ethyl-3(3-dimethylaminopropyl)carbodiimide, which catalyzes the formation of covalent bonds between residues of proteins in electrostatic contact. Histone H1-core histone dimers were identified and the segments of molecules participating in crosslinking were elucidated. The results demonstrate that the major histone H1-core histone dimer generated upon carbodiimide crosslinking of intact nuclei, chromatin, or mononucleosomes consists of the segment of histone H1 containing amino acids 74-106 crosslinked to the segment of histone H2A containing amino acids 58-129. Thus, the central globular region of histone H1 intimately contacts the histone octamer. Besides histone H1-H2 dimers, two other histone H1-containing crosslinked products were detected. In these instances, the segments of histone H1 molecules containing amino acids 1-72 were shown to participate in crosslinking. The histone H1 contact points defined here all occur within mononucleosomes and not between nucleosomes. These results permit the formulation of a testable model for the arrangement of histone H1 along polynucleosome chains.

Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin

We describe the results of a systematic study, using electron microscopy, of the effects of ionic strength on the morphology of chromatin and of H1-depleted chromatin. With increasing ionic strength, chromatin folds up progressively from a filament of nucleosomes at approximately 1 mM monovalent salt through some intermediate higher-order helical structures (Thoma, F., and T. Koller, 1977, Cell 12:101-107) with a fairly constant pitch but increasing numbers of nucleosomes per turn, until finally at 60 mM (or else in approximately 0.3 mM Mg++) a thick fiber of 250 A diameter is formed, corresponding to a structurally well-organized but not perfectly regular superhelix or solenoid of pitch approximately 110 A as described by Finch and Klug (1976, Proc. Natl. Acad. Sci. U.S.A. 73:1897-1901). The numbers of nucleosomes per turn of the helical structures agree well with those which can be calculated from the light-scattering data of Campbell et al. (1978, Nucleic Acids Res. 5:1571-1580). H1-depleted chromatin also condenses with increasing ionic strength but not so densely as chromatin and not into a definite structure with a well-defined fiber direction. At very low ionic strengths, nucleosomes are present in chromatin but not in H1-depleted chromatin which has the form of an unravelled filament. At somewhat higher ionic strengths (greater than 5 mM triethanolamine chloride), nucleosomes are visible in both types of specimen but the fine details are different. In chromatin containing H1, the DNA enters and leaves the nucleosome on the same side but in chromatin depleted of H1 the entrance and exit points are much more random and more or less on opposite sides of the nucleosome. We conclude that H1 stabilizes the nucleosome and is located in the region of the exit and entry points of the DNA. This result is correlated with biochemical and x-ray crystallographic results on the internal structure of the nucleosome core to give a picture of a nucleosome in which H1 is bound to the unique region on a complete two-turn, 166 base pair particle (Fig. 15). In the formation of higher-order structures, these regions on neighboring nucleosomes come closer together so that an H1 polymer may be formed in the center of the superhelical structures.

Superstructures of wet inactive chromatin and the chromosome surface

Superpacking of chromatin and the surface features of metaphase chromosomes have been studied by SiO replication of wet, unstained, and unfixed specimens in an exceedingly thin (less than or equal to nm) aqueous layer, keeping them wet. Hydrophilic Formvar substrates allow controlled thinning of the aqueous layer covering the wet specimens. Whole mounts of chromatin and chromosomes were prepared by applying a microsurface spreading method to swollen nuclei and mitotic cells at metaphase. The highest level of nucleosome folding of the inactive chromatin in chicken erythrocytes and rat liver nuclei is basically a second-order superhelical organization (width 150--200 nm, pitch distance 50--150 nm) of the elementary nucleosome filament. In unfavorable environments (as determined by ionic agents, fixative, and dehydrating agetns) this superstructure collapses into chains of superbeads and beads. Formalin (10%) apparently attacks at discrete sites of chromatin, which are then separated into superbeads. The latter consist of 4--6 nucleosomes and seemingly correspond to successive turns of an original solenoidal coil (width 30--35 nm), which forms the superhilical organization. When this organization is unfolded, eg, in 1--2 mM EDTA, DNAse-sensitive filaments (diameter 1.7 nm) are seen to be wrapped around the nucleosomes. The wet chromosomes in each metaphase spread are held to each other by smooth microtubular fibers, 20--20 nm in diameter. Before they enter into a chromsome, these fibers branch into 9--13 protofilaments, each 5 nm wide. The chromosome surface contains a dense distribution of subunits about 10--25 nm in diameter. This size distribution corresponds to that of nucleosomes and their superbeads. Distinct from this beaded chromosome surface are several smooth, 23--30-nm-diameter fibers, which are longitudinal at the centromere and seem to continue into the chromatid structure. The surface replicas of dried chromosomes do not show these features, which are revealed only in wet chromosomes.

Higher order structure in metaphase chromosomes. I. The 250 A fiber

Metaphase chromosomes released from cells in the presence of Joklik's suspension media by vortex-mixing with 0.5 mm glass beads have been analyzed by electron microscopy. In these preparations the chromosomes are composed of series of loops (200-300 A in diameter) which are, in turn, composed of closely-apposed arrays of nucleosomes. Negative-staining of these preparations has allowed the identification of several distinct patterns within the loop which appear to arise from variations in nucleosome packing. Analogous patterns are also observed in chromatin fragments generated by brief micrococcal nuclease digestion. From these data we have deduced certain features of nucleosome-nucleosome interactions in higher-ordered chromatin fibers.

Nucleosomes arrangement in chromatin

The spatial arrangement of nucleosomes in rat liver chromatin has been examined using the electric birefringence technique. All chromatin subunits studied (up to 9 consecutive nucleosomes) contain their full complement of the five histone types associated with about 200 base pairs repeat length DNA. From the relaxation times and the orientation mechanisms, the nucleosome may be assimilated to an oblate ellipsoid of dimensions about 140 x 140 x 70 A, and the DNA superhelical axis is parallel to its shorter axis. The most important result is a sharp transition in the electro-optical properties of subunits when the number of nucleosomes in the chain is greater than 6 : the initial negative birefringence, as for DNA, becomes positive and the relaxation time is multiplied by ten. The hexanucleosome, which presents no birefringence, has an helical symmetrical structure without preferential orientation axis. This structure is approximatively spherical of about 250 A diameter and the chromatin appears as a periodic array of such a structure.

Nucleosome arcs and helices

Crystals and other regular arrangements of nucleosome cores have been obtained and analyzed in the electron microscope. Two types of regular structures have been studied in detail, the nucleosome arcs and cylinders. The latter are composed of concentric cylindrical layers of intertwined right-handed helices of nucleosome cores. These studies lead to the following conclusions and concepts. The overall structure of the nucleosome core is a short, wedge-shaped cylinder measuring about 110 by 110 by 60 angstroms. Nucleosome cores interact primarily between top and bottom planes. Nucleosome cores exhibit large conformational variability. A pivot allowing two degrees of rotational freedom is postulated in the region of the 70th base pair to account for this property of the nucleosome.

Transient electric dichroism studies of nucleosomal particles

We report transient electric dichroism experiments on nucleosomal core particles containing 140 and 175 base pairs of DNA, and on spacerless dinucleosomes. The results indicate that all particles posses a permanent dipole moment. The orientation time of 140 base pair nucleosomes implies an estimated maximum dimension of a = 130 A (a must be at least 111 A), consistent with the disk model. The maximum dimension of the spacerless dinucleosome is estimated to be about 290 A (at least 180 A), ruling out a structure in which two disks are stacked directly on top of each other. The reduced dichroism amplitude indicate that the DNA superhelix axis in nucleosomes aligns perpendicular to the electric field, as expected for a dipole moment directed along a C2 symmetry axis across the disk diameter. Nucleosomes containing 175 base pairs of DNA show a substantially larger dichroism amplitude that do 140 base pair nucleosomes. In the context of the disk model, this result is shown to be consistent with 100 base pairs of DNA per superhelical turn, but not with 80 base pairs per turn.

Transcription of nucleosomes from human chromatin

Nucleosomes (chromatin subunits) prepared by micrococcal nuclease digestion of human nuclei are similar in histone content but substantially reduced in non-histone proteins as compared to undigested chromatin. Chromatin transcription experiments indicate that the DNA in the nucleosomes is accessible to DNA-dependent RNA polymerase in vitro. The template capacities of chromatin and nucleosomes are 1.5 and 10%, respectively, relative to high molecular weight DNA, with intermediate values for oligonucleosomes. Three distinct sizes of transcripts, 150, 120 and 95 nucleotides in length, are obtained when nucleosomes are used as templates. However, when nucleosomal DNA is used as a template, the predominant size of transcripts is 150 nucleotides. When oligonucleosomes are used as templates longer transcripts are obtained. This indicates that RNA polymerase can transcribe the DNA contained in the nucleosomes.

Alteration in nucleosome structure induced by thermal denaturation

Mononucleosomes prepared from goose erythrocyte nuclei exhibited limited heterogeneity with respect to number of electrophoretic components, histones and DNA composition. The components differ slightly in ionic strength induced self-association. Thermal denaturation of each component gave only two dominant, highly cooperative, melting transitions, T" and T"'. Urea and trypsin were used to establish the differential lability of these two transitions. Comparison of the morphologies of the mononucleosomes at various stages throughout the melting profile indicated that the 13.3 +/- 1.5 nm diameter mononucleosomes start to disrupt only in the latter half of transition T" and do not unfold until after reaching T"'. The resultant, open ended (17.4 +/- 2.2 nm diameter) toroids are still largely negatively staining and much more uniform in shape if fixed simultaneously with gluteraldehyde.

The helical model of the nucleosome core

A model of the nucleosome core is proposed based on a topologically linear array of histones attached sequentially to DNA. The linear complex folds helically forming a spring-like particle. Different variants of the particle are discussed (cylindrical springs with and without histone-histone contacts between turns of the helix, solenoidal spring). The model is consistent with known data about the nucleosome structure. Histones H3 and H4 have a special role in the model which is related also to the superstructure of chromatin.

Characterization of the histone core complex

A stable histone core complex containing equimolar ratios of H2A, H2B, H3, and H4 has been isolated from chicken erythrocyte chromatin in high salt. This complex has been characterized by sedimentation and chemical cross-linking studies. In velocity ultracentrifugation, only one single sharp sedimentation boundary has been observed with sedimentation coefficient S020,w = 3.8 +/- 0.1. The molecular weight of the histone core complex has been investigated by low-speed sedimentation equilibrium studies over a wide range of protein concentration. Analysis of the apparent weight-average molecular weight as a function of concentration indicates that the histone core complex in 2 M NaCl, pH 9.0, is in equilibrium between a tetramer (H2A)(H2B)(H3)(H4) and an octamer [(H2A)(H2B)(H3)(H4)]2 species with a tetramer molecular weight of 55,000. The equilibrium constant K is approximately 1.2 X 10(-5) liter per mol at 10 degrees. Evidence of such a tetramer-octamer equilibrium in solution is also supported by the results of our chemical crosslinking experiments on the histone core complex.

Conformational changes of the chromatin subunit

Hydrodynamic studies on monomer chromatin subunits (v1) as a function of ionic strength (0.7 mM to 100 mM KCl) indicate two salt-dependent conformational transitions. An abrupt transition occurs at about 7.5 mM ionic strength. Decreasing the ionic strength from 10 to 5 mM results in a decrease in s20,w of the v1 from 11.1 to 9.9 S. The diffusion coefficient D20,w decreases from 3.3 to 2.7 X 10(-7) cm2 sec--1. The v1 crosslinked with formaldehyde at 10 mM ionic strength do not undergo a similar salt-dependent change in s20,w. Another transition is observed at about 1 mM ionic strength; s20,w decreases to 9.4 S and D20,w decreases to 2.2 X 10(-7) cm2 sec--1. Throughout the entire salt range the molecular weight of the v1 remains reasonably constant, implying that salt-dependent changes in the frictional coefficient are being observed. Various hydrodynamic models are considered as possible interpretations of the observed changes in the frictional coefficient.

Chromatin

The approximate shape of the chromatin subunit called the nucleosome is now known, but its internal architecture is not well understood. Recent studies reveal details of the organisation of DNA within the nucleosome, and show that the arginine-rich histones are essential to DNA folding. Nucleosomes or structures related to them seem to be present at points of DNA replication and transcription; interactions within and between nucleosomes are likely to play a critical part in these processes.

A low resolution model for the chromatin core particle by neutron scattering

Neutron scattering studies have been applied to chromatin core particles in solution, using the contrast variation technique. On the basis of the contrast dependance of the radius of gyration and the radial distribution function it is shown that the core particle consists of a core containing most of the histone around which is wound the DNA helix,following a path with a mean radius of 4.5 nm,in association with a small proportion of the histones. Separation of the shape from the internal structure, followed by model calculations shows that the overall shape of the particle is that of a flat cylinder with dimensions ca. 11x11x6 nm. Further details of the precise folding of the DNA cannot be deduced from the data, but detailed model calculations support concurrent results from crystallographic studies(25).Images

Structure of nucleosome core particles of chromatin

Cystals have been obtained on nucleosome cores and analysed by X-ray diffraction and electron microscopy. The core is a flat particle of dimensions about 110 X 110 X 57 A, somewhat wedge shaped, and strongly divided into two 'layers', consistent with the DNA being wound into about 1 3/4 turns of a flat superhelix of a pitch about 28 A. The organisation of the DNA can be correlated with the results to enzyme digestion studies. A change in the screw of the DNA double helix on nucleosome formation can be deduced.

The structure of the chromatin core particle in solution

The shape and size of the nucleosomal core particle from chromatin has been examined by analysis of neutron and X-ray scattering data from dilute solutions. Calculations of scattering for many different models have been made and only one model was able to account for both the X-ray and neutron profiles. This model is an oblate structure with height about 50A and diameter 110A. The DNA is mainly confined to two annuli located at the top and bottom respectively of the core particle positioned on the outside of a compact protein core which has a height of about 40A and diameter about 73A.

Hydrodynamic evidence in support of spacer regions in chromatin

Quasi-elastic light scattering and sedimentation velocity methods were used to study the hydrodynamic properties of purified dimer subunits obtained from partial digestion of chicken erythrocyte chromatin with staphylococcal nuclease. The experimental value of 1.87 +/- 0.08 X 10(-7) gram per second for the friction factor of these dimer subunits in low ionic strength buffer cannot be reasonably interpreted in terms of a contiguous sphere model. Analysis by means of an equivalent dimer method suggests that the spacer region accounts for a maximum of 19 percent of the friction properties of the dimer.

The chromosomes of man--clinical and biologic significance. A review

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Chromatin nu bodies: isolation, subfractionation and physical characterization

Monomer chromatin subunit particles (nu1) have been isolated in gram quantities by large-scale zonal centrifugation of micrococcal nuclease digests of chicken erythrocyte nuclei. nu1 can be stored, apparently indefinitely, frozen in 0.2 mM EDTA (pH 7.0) at less than or equal to 25 degrees C. Aliquots of the stored monomers have been subfractionated by dialysis against 0.1 M KCl buffers into a soluble fraction containing equimolar amounts of H4, H3, H2A, H2B associated with a DNA fragment of approximately 130-140 nucleotide pairs, and a precipitated fraction containing all of the histones including H5 and H1 associated with DNA fragments. The total nu1 and the KCl-soluble fraction of nu1 have been examined by sedimentation, diffusion, sedimentation equilibrium ultracentrifugation, low-angle X-ray diffraction, and electron microscopy. Physical parameters from all of these techniques are presented and correlated in this study.

Relaxation of chromatin structure by ethidium bromide binding: determined by viscometry and histone dissociation studies

The effects of ethidium bromide intercalation on chromatin structure were monitored by viscometry and analysis of histone dissociation. Investigation of the NaCl concentration dependence of chromatin viscosity showed that the reduced viscosity (etared) was very low up to 0.4 M NaCl and increased gradually when the salt concentration was raised further. In chromatin intercalated by ethidium bromide, etared was not significantly different at low salt concentrations (up to 0.2 M NaCl). However, when the salt concentration was raised further, the viscosity response curve increased sharply to reach viscosities about 4-5 times higher than those for nonintercalated chromatin. The increase in viscosity was proportional to the increase in fluorescence intensity, when the ratio of ethidium bromide to DNA mucleotide was raised. The transition of intercalated chromatin into the relaxed form was reversible, dependent on the nature of the electrolyte and cooperative, as indicated by the small increase in salt concentration required to obtain chromatin relaxation. Investigation of the NaCl concentration dependence of histone dissociation revealed that total histones and each individual histone fraction were released from intercalated chromatin at much reduced NaCl concentrations. The midpoints of the dissociation curves of the individual histones ranged from 0.30 to 0.45 M NaCl and fell within the same range where the drastic viscosity change occurred. These results indicate that intercalation of ethidium bromide labilizes chromatin structure to relaxation by moderately elevated salt concentrations. It is suggested that the labilization is caused by changes in the DNA helix conformation due to dye intercalation decreasing the stability of histone-DNA interactions.

Analysis of chromatin-associated fiber arrays

Electron microscopic examination of chromatin from embryonic nuclei of Oncopeltus fasciatus and Drosophila melanogaster reveals arrays of chromatin associated fibers. The lengths and spacings of these fibers were analyzed to provide a basis for defining and interpreting regions of transcriptionally active chromatin. The results of the analysis are consistent with the interpretation of some fibers as nascent RNA with associated protein (RNP). The chromatin segments underlying these fiber arrays were classified as ribosomal or non-ribosomal transcription units according to definitions and criteria described by Foe et al. (1976). Nascent fibers on active ribosomal transcription units were analyzed and compared for Drosophila melanogaster, Triturus viridescens, and Oncopeltus fasciatus. A common feature of the fiber patterns on ribosomal TUs is that origin-distal fibers exhibit greater length variability and a lower slope relative to proximal fibers. The region of increased variability in fiber lengths is correlated with the expected location of 28S ribosomal RNA sequences in the distal half of each ribosomal transcription unit. Because 28S ribosomal RNA appears to contain more extensive regions of base sequence complementarity, we suggest that the length of ribosomal RNP fibers is influenced under our spreading conditions by the secondary structure of the nascent RNA. In order to calculate the RNA content of RNP fibers, chromatin morphology was used to estimate lengths of transcribed DNA. The packing ratio of DNA in chromatin, which we express as the length of B-structure DNA divided by length of chromatin, is 1.1-1.2 and 1.6 for the DNA in active ribosomal and non-ribosomal chromatins, respectively. These DNA packing ratios are used to determine the extent to which nascent RNP fibers are shorter than the transcribed DNA (expressed as DNA/RNP length ratio). For non-ribosomal transcription units and for proximal fibers of ribosomal transcription units. DNA/RNP length ratios are relatively constant within each array. However, considerable variability in this ratio (4-23) is observed for different arrays of fibers. Possible sources of this variability are considered by comparing ratios derived from the presumably identical ribosomal transcription units. Further analysis of the morphology of nascent fibers may elucidate the contributions of proteins and successive RNA sequences to RNP structure.