30-nm Fiber Research Articles

Nuclear scaffolds and scaffold-attachment regions in higher plants.

DNA in the nuclei of eukaryotic organisms undergoes a hierarchy of folding to be packaged into interphase and metaphase chromosomes. The first level of packaging is the 11-nm nucleosome fiber, which is further coiled into a 30-nm fiber. Evidence from fungal and animal systems reveals the existence of higher order packaging consisting of loops of the 30-nm fibers attached to a proteinaceous nuclear scaffold by an interaction between the scaffold and specific DNA sequences called scaffold-attachment regions (SARs). Support for the ubiquitous nature of such higher order packaging of DNA is presented here by our work with plants. We have isolated scaffolds from tobacco nuclei using buffers containing lithium diiodosalicylate to remove histones and then using restriction enzymes to remove the DNA not closely associated with the scaffold. We have used Southern hybridization to show that the DNA remaining bound to the scaffolds after nuclease digestion includes SARs flanking three root-specific tobacco genes. This assay for SARs is termed the endogenous assay because it identifies genomic sequences as SARs by their endogenous association with the scaffold. Another assay, the exogenous assay, depends upon the ability of scaffolds to specifically bind exogenously added DNA fragments containing SARs. The tobacco scaffolds specifically bind a well-characterized yeast SAR, and cloned DNA fragments derived from the 3'-flanking regions of the root-specific genes are confirmed to contain SARs by this exogenous assay.

Inoculation Study of Alzheimer Buffy Coat into Hamster Brain

Buffy coats from 4 members of a family with Alzheimer''s disease and 2 genetically unrelated healthy subjects were inoculated into the hamster brain. Eighteen months after the inoculation, the brains were studied by immunostaining with antibodies against neurofilaments, tau, ubiquitin, and paired-helical filaments (PHF) as well as by electron microscopy. Vacuolar or spongioform degeneration was minimum. Intense positive staining by antibodies against neurofilament 200K protein was demonstrated in neuronal perikarya of the lower brain stem nucleus in the hamster inoculated with the buffy coats from the 2 patients with Alzheimer''s disease and 2 children of the patient, which was not observed in the hamster brain inoculated with the buffy coat from the control subjects. Electron microscopy revealed intracytoplasmic accumulation of 10-nm neurofilament-like fibers. The accumulated neurofilaments were positively stained by antitau and antiubiquitin, but not by anti-PHF. The neurons containing massive intracytoplasmic neurofilament accumulation resembled ballooned neurons in some degenerative diseases including Alzheimer''s disease. The results indicate that the buffy coat obtained from the patients and members of a family with Alzheimer''s disease contains a factor which produces intracytoplasmic accumulation of neurofilament-like fibers in neurons of the lower brain stem nuclei.

Changes in chromatin chain flexibility during condensation induced by sodium chloride, as evidenced by electric dichroism

The electric linear dichroism of chicken erythrocyte chromatin has been measured as a function of NaCl concentration in the 1–28 mM ionic strength range, using a specially designed Kerr cell with reduced pathlength, and thus, smaller electrode surface. This allowed the determination of the dichroism of compact chromatin in conditions where artifacts due to possible contribution from turbidity are avoided, which was not the case for previous studies in the presence of di- or multivalent cations. The linear dichroism of compact chromatin was found to be positive, as expected from models of the 30-nm fibre in which the linker DNA runs perpendicular to the fibre axis. The dependence of the relaxation times on ionic strength reveals that the process of compaction is first accompanied by an increase in flexibility of the chain followed by a decrease, in the range of 5–10 mM NaCl, and a further decrease above 10 mM NaCl, corresponding to the compaction of the 30 nm fibre.

Studies on Scaffold Attachment Sites and Their Relation to Genome Function

This chapter focuses on the evidence for loops in the genome and on the potential function of this higher-order folding. The loop hypothesis for the organization of DNA arose largely from observation—by electron microscope—of loops emanating from histone-depleted chromosomes and nuclei. The proteinaceous structures that remained after membrane and histone extraction are variously called “scaffolds,” “nuclear matrices,” “cages,” “nucleo- or karyoskeletons,” or the “nuclear matrix-pore complex-lamina fraction (NMPCL).” Electron microscopy of histone-depleted scaffolds and scaffold-attached regions (SAR)-mapping studies favors a model in which the 30-nm solenoid fiber is constrained in looped domains. The nuclear matrices and scaffolds are considered useful tools for subfractionation and purification of various nuclear components. The specificity of the DNA–scaffold interaction and the conservation of these binding sites between higher eukaryotes and yeast are encouraging. The characterization of the SAR-binding scaffolding proteins is necessary to evaluate the role this level of nuclear architecture plays in promoting and coordinating various nuclear activities during the cell cycle.

Kinetochore structure: electron spectroscopic imaging of the kinetochore.

The structure of the kinetochore in thin section has been studied in the Indian muntjac by an electron spectroscopic imaging technique. This procedures allows the analysis of the distribution of phosphorus within the layers of the kinetochore. The results indicate that this element is a major component of both the inner and outer plates whereas it is largely absent in the middle plate and fibrous corona. The majority of the phosphorus is localized to a 30-nm fiber(s) that is woven through the layers of the kinetochore. The presence of phosphorus within this fiber, along with its morphological and biochemical features, indicates that it contains DNA. The fiber(s) occupies a major portion of the inner and outer plate where it forms a series of rows. It is rarely observed in the middle layer except where it passes between the inner and outer layers. The absence of structure in the middle plate suggests that it may represent a space rather than a plate that in turn may be related to the function of this region. The distribution of phosphorus within the kinetochore is neither altered by treatment with colcemid nor by the presence of microtubules at the kinetochore. Analysis of conventional micrographs of the kinetochore together with structural information obtained by electron spectroscopic imaging suggests that most microtubules insert and terminate between the rows of kinetochore fibers in the outer plate. However, some microtubules continue through the middle layer and terminate at the lower plate. The insertion of microtubules at different levels of the kinetochore may reflect the existence of functionally distinct microtubule classes. Electron spectroscopic imaging indicates that the microtubules associated with the kinetochore are phosphorylated.

The globular region of histone H5 is equally accessible to antibodies in relaxed and condensed chromatin.

The accessibility of histone H5 in chromatin was examined with monoclonal antibodies recognizing several epitopes of the globular region (GH5) of the histone (Rózalski, M., Lafleur, L., and Ruiz-Carrillo, A. (1985) J. Biol. Chem. 260, 14379-14385). The stoichiometry of the chromatin-antibody complexes indicated that while 0-86% of the H5 molecules were able to react, depending on the particular epitope, the extent of antibody binding to relaxed chromatin (in 5 mM KCl) and condensed chromatin (in 100 mM KCl or 0.35 mM MgCl2) was virtually identical. This indicates that the topography of H5 does not change during the conformational transition of chromatin. The data suggest that H5 is not completely internalized in the 30-nm fiber or that the fiber is flexible enough to allow full exposure of the GH5 epitopes. Several control experiments, including monoclonal antibody binding, sedimentation analysis, DNase II digestion, and glutaraldehyde cross-linking, showed that epitope accessibility is not due to H5 exchange or to perturbation of the chromatin fiber. The accessibility of GH5 suggests ways in which inactive chromatin may be unfolded in vivo.

UV-induced pyrimidine dimers and trimethylpsoralen cross-links do not alter chromatin folding in vitro.

We have examined the ability of intact and histone H1 depleted chromatin fibers to fold into higher ordered structures in vitro following DNA damage by two different agents: UV irradiation at 254 nm and trimethylpsoralen plus near-UV light. Both agents damage DNA specifically, yet cause different degrees of unwinding (and possibly bending) of the DNA helix. In addition, trimethylpsoralen forms interstrand DNA cross-links. The structural transitions of intact and histone H1 depleted chromatin fibers, induced by NaCl, were monitored by analytical ultracentrifugation, light scattering, and circular dichroism. Our results indicate that when chromatin fibers contain even large, nonphysiological amounts of DNA photodamage by either agent, the salt-induced folding of these fibers into higher ordered structures is unaffected. The compact 30-nm fiber must therefore be able to accommodate a large amount of DNA photodamage (greater than one UV-induced photoproduct or trimethylpsoralen interstrand cross-link per nucleosome) with little or no change in the overall size or compaction of this structure.

Chromatin and nuclear envelope of freeze-fractured, neuronal interphase nuclei, resolved by scanning electron microscopy.

High-resolution scanning electron microscopy (SEM) has previously been used to study intracellular detail, including chromatin. It has, however, been commonly carried out either on cellular subfractions or following extraction methods to visualize detail. In the work presented here, intracellular detail of neurons of the dorsal root was visualized in situ by viewing freeze-fracture faces obtained after hypotonic expansion. This procedure permits the detailed resolution, by SEM, of juxtanuclear and intranuclear detail to a degree impossible without hypotonic dispersal. In agreement with work previously reported, nuclear chromatin of these interphase cells presents largely as 30-nm fibers, with a next higher hierarchical structure imparted by swelling in magnesium chloride. Detailed analyses showed that particles as small as 10-nm nucleosomes comprising the 30-nm chromatin fiber could be resolved, with "end-on" views of such fibers showing 5 nucleosomes per helical turn of the fiber. Chromatin fibers positioned subjacent to nuclear pores, or associated with "nuclear spaces" communicating with nuclear pores, were frequently found to be resolved as clusters, in an apparently more decondensed conformation, rather than tightly coiled into the 30-nm fiber. In addition, details of the nuclear envelope, including nuclear pores and perinuclear filaments as well as membranes of the endoplasmic reticulum, decorated with ribosomes, were clearly resolved.

Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy.

Neutron scattering in solution and scanning transmission electron microscopy were simultaneously done on chicken erythrocyte chromatin at various salt and magnesium concentrations. We show that chromatin is organized into a higher-order structure even at low ionic strength and that the mass per unit length increases continuously as a function of salt concentration, reaching a limiting value of between six and seven nucleosomes per 11 nm. There is no evidence of a transition from a 10-nm to a 30-nm fiber. Fiber diameter is correlated with mass per unit length, showing that both increase during condensation. We also find that there is no essential difference between the mass per unit length measured by scanning transmission electron microscopy and neutron scattering in solution, showing that the ordered regions seen in micrographs are representative of chromatin in solution.

Chromatin structure. Evidence that the 30-nm fiber is a helical coil with 12 nucleosomes/turn.

Sedimentation analysis has been used to compare the structure of 30-nm chromatin fibers, isolated and digested under conditions that maintain the native structure, with relaxed-refolded chromatin. The native chromatin fibers show sharp, ionic strength-dependent changes in sedimentation coefficient that are not apparent in relaxed-refolded fibers. The first transition at approximately 20 mM ionic strength reflects the organization of the 10-nm polynucleosome chain into a loose helically coiled 30-nm fiber. Between 20 and 60 mM ionic strength there is considerable interaction between nucleosomes within the coils to generate a stable helical array with 12 nucleosomes/turn. Above 60 mM ionic strength the helical coil continues to condense until it precipitates at ionic strengths slightly greater than those considered physiological, indicating that there is no end point in fiber formation. The data is incompatible with a solenoid model with 6 nucleosomes/turn and also rules out the existence of a beaded subunit structure.

Chromatin structure. Further evidence against the existence of a beaded subunit for the 30-nm fiber.

The size distribution of chromatin fragments released by micrococcal nuclease digestion of liver chromatin at various ionic strengths was examined. Below 20 mM ionic strength, gradient profiles with a peak centered at 6 nucleosomes are generated, whereas between 20 and 50 mM the peak is always centered on 12 nucleosomes, and above 50 mM ionic strength the 30-nm fiber becomes less accessible to the nuclease and there is a corresponding increase in the size distribution of fragments in the gradients. However, extensive digestions always give profiles with a peak of 12 nucleosomes as nuclease-resistant dodecamers accumulate. All of these observations are consistent with the winding of the 10-nm polynucleosome chain into a helical coil commencing at about 20 mM ionic strength. The helical turns are stabilized by histone H1 interactions between 20 and 50 mM ionic strength producing stable dodecamers. Above 50 mM ionic strength the coil condenses longitudinally and the profiles are consistent with a random attack of this fiber by the nuclease. Consequently it is not necessary to invoke the existence of a subunit bead to explain the profiles. We further define the conditions at which specific structural transitions take place and provide methodology for the preparation of chromatin at various levels of condensation.

The higher order structure of the centromere

The architecture of the centromere region of mouse chromosomes has been studied in cells grown in the presence of 5-azacytidine. This drug interferes with normal condensation producing elongated centromere regions. It has been found that this effect is reversible in the presence of the drug, allowing the observation of the repackaging of the extended centromere into a structure exhibiting native centromere morphology. Light microscopy as well as transmission and scanning electron microscopy of this condensation process suggests that the native centromere is formed by the helical folding of a subfiber with an approximate diameter of 100 nm. This fiber is in turn composed of loops of the 30-nm fiber class. The boundary between successive gyres of the subfiber are obscured at the completion of condensation resulting in the formation of a homogenous 250- to 300-nm fiber that is the native centromere. These observations provide evidence for an additional level of chromatin organization within the metaphase chromosome.

Modulation of the sensitivity of chromatin to exogenous nucleases: implications for the apparent increased sensitivity of transcriptionally active genes.

We have examined the effects of changing the ionic composition of the buffers in which nuclei are isolated on the sensitivity of chromatin to micrococcal nuclease and deoxyribonuclease I. Unless nuclei are isolated in buffers containing physiological levels of monovalent (150 mM KCl) and divalent (2-5 mM MgCl2) cations, there is a substantial loss of higher order structure. The ionic composition of the buffer in which the digestion is carried out also affects the amount of material digested both by modulating higher order structure and by determining the solubility of the released material. Magnesium ion concentrations greater than 2 mM and calcium ions at virtually any concentration precipitate substantial amounts of the released chromatin fragments. These observations can be interpreted in light of the known effects of the ions on 10- and 30-nm fiber structure and used as a basis for improvements in techniques for isolating chromatin and for studying its structure and function using exogenous nuclease probes. The apparent nuclease sensitivity of transcriptionally active chromatin was reexamined and shown to be more likely a reflection of differential solubility rather than an overall increase in nuclease sensitivity.

Chromatin structure. Nuclease digestion profiles reflect intermediate stages in the folding of the 30-nm fiber rather than the existence of subunit beads.

Conditions have been found for the isolation of rat liver nuclei which maintain chromatin in its native state and suppresses endogenous nuclease activity. Chromatin prepared in this way can be dispersed into buffers containing various concentrations of monovalent or divalent cations so that the 30-nm fiber is either totally or partially decondensed. When probed with micrococcal nuclease, the digestion profiles show that although the 30-nm fiber can be cleaved periodically to generate superbead-like particles this only occurs under certain ionic conditions when the fiber is partially decondensed. It is likely that this cleavage pattern reflects the transient exposure of specific nuclease sensitive sites as the 30-nm fiber condenses, rather than the existence of a specific subunit of a beaded 30-nm fiber. The periodicity of these nuclease-sensitive sites appear to be related to the asymmetric distribution of histone H1 molecules along the length of the fiber.

Influence of DNA-binding drugs on chromatin condensation

We have used transient electric dichroism to study the ability of DNA-binding drugs to affect the folding of chromatin from the 10- to the 30-nm fiber, either by themselves or in conjunction with multivalent cations. Variables considered include the cationic charge of the drug, the comparative influence of intercalation and groove binding as modes of interaction, and the effect of bis-intercalation compared to mono-intercalation. In parallel with our findings with other cations, we observe that a drug must have a charge of 3+ or greater in order to condense chromatin at concentrations substantially lower than the concentration of chromatin, measured in base pairs. Drugs of low charge, whether groove binders or mono-or bis-intercalators, are unable to condense chromatin on their own. Bis-intercalators of high charge, however, are extremely efficient condensers, being able to cross-link chromatin with greater efficiency than polyamines of corresponding charge. When Mg2+ is used in combination with bis-intercalators of high charge, the order of addition of the two determines whether compaction or cross-linking is favored. Finally, the antibiotics actinomycin D, daunomycin, and distamycin, despite varied modes of binding to DNA, all inhibit the compaction of chromatin beyond a critical point in a remarkably similar manner.

Condensation of chromatin: role of multivalent cations.

We have used electric dichroism to investigate the influence of multivalent cations upon the compaction of chicken erythrocyte chromatin from the unfolded, 10-nm fiber to the 30-nm solenoid and subsequent aggregation. The pattern of condensation, which consists of compaction plus aggregation, is found to be strikingly similar for a variety of cations of differing charge, including the physiologically important polyamines spermine and spermidine. With a few exceptions such as Cu2+ and Gd3+, an optimally compacted fiber with reproducible hydrodynamic properties is produced prior to the onset of aggregation. We report the concentrations of di-, tri-, and tetravalent cations required for optimal condensation; in addition, for tri- and tetravalent cations, we were able to estimate the extent of charge neutralization produced by their binding to the optimally compacted fiber. The results show that the multivalent ion concentration required for optimal compaction decreases as cationic charge increases. In addition, the effect of a mixture of dilute mono- and multivalent cations on chromatin condensation is synergistic, rather than competitive as has been found for the multivalent cation induced condensation of DNA or the B----Z conformational transition. A simple calculation indicates that the entropy of ion uptake in chromatin condensation is surprisingly constant for a range of ionic conditions; this factor may be a dominant one in determining the folding equilibrium.

Orientation of nucleosomes and linker DNA in calf thymus chromatin determined by photochemical dichroism.

The dichroism for photochemical attachment of a psoralen derivative to Mg2+-stabilized chromatin fibres is used to deduce the orientation of nucleosomal disks and linker DNA in the 30-nm fibre. The new technique of photochemical electric dichroism should have general applicability to problems of nucleic acid organization in cellular subunits and viruses.

Electron microscopy of surface spread polytene chromosomes of Drosophila and Stylonychia

The ultrastructure of polytene chromosomes of Drosophila and Stylonychia were compared in whole-mount spread preparations. In Drosophila the chromomeres appear as dense, unresolvable structures interconnected by 10-nm interband fibers. In contrast, chromomeres of Stylonychia polytene chromosomes are formed by aggregates of 30-nm loops laterally attached to 10-nm interband fibers. It is suggested that the polytene chromosomes in these two species are analogous rather than homologous structures.

Differences in evolutionary stability among mammalian H1 subtypes. Implications for the roles of H1 subtypes in chromatin.

The metabolic and developmental properties that differentiate five H1 subtypes of the mouse, H1a-H1e, are shown to have been conserved in the course of mammalian evolution. The structures of the subtypes, however, as judged by their mobilities in two-dimensional gel electrophoresis, have been conserved to varying extents. H1a and H1c have undergone the most structural variation, each having a different electrophoretic mobility in every species examined. H1b is much less varied, while H1d and H1e are invariant by these electrophoretic criteria. These results suggest that H1a and -c differ fundamentally from H1b, -d, and -e in their interactions with other chromatin components. It is suggested that this difference is in the ability to promote the coiling of 10-nm chromatin fibers into higher order chromatin structures.

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.