A repeating unit of higher order chromatin structure in chick red blood cell nuclei

Nucleosome-level 3D organization of the genome

Nucleosomes are the unitary structures of chromosome folding, and their arrangements are intimately coupled to the regulation of genome activities. Conventionally, structural analyses using electron microscopy and X-ray crystallography have been used to study such spatial nucleosome arrangements. In contrast, recent improvements in the resolution of sequencing-based methods allowed investigation of nucleosome arrangements separately at each genomic locus, enabling exploration of gene-dependent regulation mechanisms. Here, we review recent studies on nucleosome folding in chromosomes from these two methodological perspectives: conventional structural analyses and DNA sequencing, and discuss their implications for future research.

Chromatin organization in detergent-lysed chicken erythrocyte nuclei

A method for electron microscopic demonstration of supranucleosomal (20-30 nm chromatin) fiber loops was developed. Chicken erythrocytes were treated with varying concentrations of detergents, such as Joy, sodium N-lauroyl sarcosinate, and sodium laurylsulfate, and then fixed with a formalin solution. The fixed cells were centrifuged onto an electron microscope grid, followed by staining and metal shadowing. Thin-sectioned specimens of the fixed cells were prepared routinely. Although supranucleosomal fiber loops could be observed when any one of these detergents was used, Joy gave the best result. Electron micrographs of rotary-shadowed specimens of erythrocyte ghosts formed by treatment with a low concentration (0.07-0.11 w/w%) of Joy showed a halolike, radial arrangement of supranucleosomal fiber loops around the ghost cells. The width of the halo was about 3 micron. By increasing the detergent concentration (approximately 8% Joy), nucleosome fibers and naked DNA appeared and increased in number, indicating that the supranucleosomal fibers were disassembled by the action of the detergent. Thin-sectioned specimens of cells treated with 0.09% Joy showed granulofibrillar chromatin radially dispersed from the nuclear cage. The fibers were thought to be identical with the supranucleosomal fibers observed in the rotary-shadowed specimens.

Structural organization of the sperm chromatin in a fern (Scolopendrium vulgare) studied by spreading methods

To investigate chromatin organization, we applied the spreading techniques to nuclei isolated from Scolopendrium spermatozoids. Well-dispersed chromatin shows three types of fibers: beaded fibers corresponding to a nucleosomal filament with adjacent nucleosomes in close contact, smooth fibers (14 nm in diameter) associated in a complex network, and knobby fibers constituted by local supercoiling of a very thin (4 nm) smooth filament. Along the knobby fibers, beads of variable size are irregularly spaced. The knobby fibers lie parallel and coalesce in thick bundles. The sperms basic proteins identified by electrophoretic analysis probably promote the supercoiling and the side-to-side attachment of the knobby fibers, which are all the more abundant in spread preparations. These results indicate that knobby fibers are probably located in the outer part of the sperm nucleus in which the chromatin is densely packed. As for the nucleosomal and smooth filaments, they may be situated in the inner part.

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

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

A lysine-rich protein functions as an H1 histone in Dictyostelium discoideum chromatin

Mononucleosomes released from Dictyostelium discoideum chromatin by micrococcal nuclease contained two distinctive DNA sizes (166-180 and 146 bp). Two dimensional gel electrophoresis suggested a lysine-rich protein protected the larger mononucleosomes from nuclease digestion. This was confirmed by stripping the protein from chromatin with Dowex resin. Subsequently, only the 146 bp mononucleosome was produced by nuclease digestion. Reconstitution of the stripped chromatin with the purified lysine-rich protein resulted in the reappearance of the larger mononucleosomes. Two-dimensional gel electrophoresis showed the protein was associated with mononucleosomes. Hence, the protein functions as an H1 histone in bringing the two DNA strands together at their exit point from the nucleosome. Trypsin digestion of the lysine-rich protein in nuclei resulted in a limiting peptide of approx. 10 kilodaltons. Trypsin concentrations which degraded the protein to peptides of 12-14 kilodaltons and partially degraded the core histones did not change the DNA digestion patterns obtained with micrococcal nuclease. Thus, the trypsin-resistant domain of the lysine-rich protein is able to maintain chromatosome structure.

The higher-order structure of chromatin: evidence for a helical ribbon arrangement

Both intact and nuclease-isolated chromatin fibers have been examined at different degrees of salt-induced compaction, using a variety of preparation techniques. The results suggest that the initial folding step in nucleosome packing involves the formation of a zig-zag ribbon as has been proposed by others (Thoma F., T. Koller, and A. Klug, 1979, J. Cell Biol., 83:403-427; Worcel A., S. Strogartz, and D. Riley, 1981, Proc. Natl. Acad. Sci. USA, 78:1461-1465), and that subsequent compaction occurs by coiling of the ribbon to form a double helical structure. This type of folding generates a fiber in which the nucleosome-nucleosome contacts established in the zig-zag ribbon are maintained and in which the histone H1 molecules occupy equivalent sites. The diameter of the fiber is not dependent upon the nucleosome repeat length. Direct mass values for individual isolated fibers obtained from electron scattering measurements showed that the mass per length was dependent on ionic strength, and ranged from 6.0 X 10(4) daltons/nm at 10 mM NaCl to 27 X 10(4) daltons/nm at 150 mM salt. These values are equivalent to 2.5 nucleosomes/11 nm at 10 mM NaCl and to 11.6 nucleosomes/11 nm at 150 mM salt and are consistent with the range of packing ratios for the proposed helical ribbon.

Differences of supranucleosomal organization in different kinds of chromatin: cell type-specific globular subunits containing different numbers of nucleosomes

Fractions of homogeneously-sized supranucleosomal particles can be obtained in high yield and purity from various types of cells by brief micrococcal nuclease digestion (10 or 20 s) of condensed chromatin in 100 mM NaCl followed by sucrose gradient centrifugation and agarose gel electrophoresis. These chromatin particles, which contain only DNA and histones, differed according to cell type. Sea urchin spermatozoa (Paracentrotus lividus) gave rise to heavy particles (ca. 260 S) with a mean diameter (48 nm). These resembled the unit chromatin fibrils fixed in situ, which contain an average of 48 nucleosomes, as determined both by electron microscopy after unraveling in low salt buffer and gel electrophoresis. In contrast, higher order particles from chicken erythrocyte chromatin were smaller (105 S; 36-nm diam) and contained approximately 20 nucleosomes. The smallest type of supranucleosomal particle was obtained from chicken and rat liver (39 S; 32-nm diam; eight nucleosomes). Oligomeric chains of such granular particles could be recognized in regions of higher sucrose density, indicating that distinct supranucleosomal particles of globular shape are not an artifact of exposure to low salt concentrations but can be obtained at near-physiological ionic strength. The demonstration of different particle sizes in chromatin from different types of nuclei is contrary to the view that such granular particles are produced by artificial breakdown into "detached turns" from a uniform and general solenoid structure of approximately six nucleosomes per turn. Our observations indicate that the higher order packing of the nucleosomal chain can differ greatly in different types of nuclei and the supranucleosomal organization of chromatin differs between cell types and is related to the specific state of cell differentiation.

Neutron diffraction of chromatin in interphase nuclei and metaphase chromosomes

We have used neutron diffraction to study chromatin structure in interphase nuclei and metaphase chromosomes as a function of decreasing ion concentration. Aliquots of a suspension of rat liver nuclei prepared in a polyamine-free buffer were washed in buffers of 1/3, 1/6 and 1/12 if the original concentration of monovalent and divalent cations (40 mM KCl; 20 mM NaCl; 1.2 mM MgCl2). After the first dilution step (1/1 to 1/3), only small changes occurred in the diffraction pattern. They can be interpreted by a loosening of the original structure, i.e. by the formation of isolated buffer-filled spaces with an overall size of the order of 35-45 nm. Drastic changes in the diffraction pattern were observed, however, when the nuclei were washed in the more diluted buffers (1/6 and 1/12). The profiles of the distances distribution functions indicate the formation of supranucleosomal particles with an overall diameter of 40-50 nm. The compact chromatin structure disassembled directly into these fundamental structural units. Structural transformations in the Chinese hamster ovary metaphase chromosomes were induced by diminishing the Ca2+ ion concentration of the buffer from originally 3.0 mM to 0.3 mM and/or by increasing the pH value of the buffer from originally 7.0 up to 8.0. The neutron diffraction patterns remained essentially unchanged during these treatments, i.e. the decondensation of the chromosomes as observed in the light microscope is not accompanied by disassembly at the ultrastructural level between 2 nm and 150 nm.

Comparisons of liver chromatin proteins and template activities in parental and heterotic rats during postweaned development

Electrophoretic profiles of acid-extractable proteins from Holtzman rat liver chromatin display four minor and five major histone bands through certain stages of postweaned development but are qualitatively different from the chromatin protein profiles previously reported during postweaned development for the Fisher 344 rat strain and the F344 X Holtzman heterotic progeny [Tallman, G., et al. (1979). Biochem, Genet. 17:185]. The protein profiles from the heterotic progeny do not reflect and are not combinations of the profiles from the parental strains. Levels of in vitro transcription with Escherichia coli RNA polymerase of total chromatin and of acid-extracted chromatin from Holtzman rat liver tissue fluctuate in an age-specific manner during postweaned development and are higher than previously published levels determined for the Fisher and F344 X H strains during the same developmental period [Tallman, G., et al. (1978). J. Hered. 69:282]. The degrees of stimulation in the transcription assays resulting from the acid treatment vary with the age of the animal but are similar for the maternal Holtzman and hybrid strains. These studies suggest that regulation of heterotic growth may involve dominant, or maternal genetic influences.

Mg2+-dependent compactness of heterochromatic chromosome segments

The stability of heterochromatic blocks in pachytene chromosomes of Tenebrio molitor (Insecta, Coleoptera) was analysed at the chromosomal level using a modified Miller spreading technique. Incubation of nuclei in solutions of different ionic strength and composition revealed that the characteristic compactness of heterochromatic segments was preserved in the presence of at least 0.6 mM MgCl2. The compactness of these segments was lost in solutions of different ionic strength and composition revealed that the characteristic compactness of heterochromatic segments was preserved in the presence of at least 0.6 mM MgCl2. The compactness of these segments was lost in solutions containing NaCl (0.1-100 mM), but no MgCl2. They then resembled the euchromatic segments. The decondensed heterochromatic segments could be recompacted by adding MgCl2 to a final concentration of 1.0 mM. The characteristic compactness of heterochromatin of pachytene chromosomes therefore depends on the presence of Mg2+, but is independent of Na+.

Supranucleosomal organization of chromatin. Electron microscopic visualization of long polynucleosomal chains

A systematic study of the effect of different ionic conditions on the morphology of the 25-30 nm chromatin fiber from chicken erythrocytes has revealed that, as the ionic strength is increased, knobby fibers with a clear superbead structure are formed in the presence of either Mg++ or Na+, or both. A further increase in ionic strength results in smooth chromatin fibers due to a tight packing of superbeads. Cross-linking such fibers with formaldehyde and reversal of the ionic conditions, demonstrates the superbead structures underlying the smooth fibers observed at high ionic concentrations. The average size of the superbeads is 34 nm along the length of the fibers, in agreement with the value found in embedded sea cucumber chromatin. A second class of superbeads has an average length of 25 nm and probably corresponds to partially disrupted structures.

Chicken erythrocyte nucleus contains two classes of chromatin that differ in micrococcal nuclease susceptibility and solubility at physiological ionic strength

Inactive chromatin of the chicken erythrocyte nucleus is shown to consist of two distinct classes (I and S). I chromatin (approximately 60% of the total genome) is insoluble at greater than 0.1 M ionic strength whereas S chromatin (approximately 40% of the total genome) is soluble at all ionic strengths studied (0.01--0.3 M). These chromatins are released from nuclei upon digestion with micrococcal nuclease by two separate parallel processes that do not have a precursor--product relationship to each other. Isolated I-chromatin fragments show a progressive reduction in size from 250 to approximately 50 nucleosome equivalents with increasing digestion times at 0-2 degrees C. Prolonged digestion of nuclei at 37 degrees C results in conversion of I chromatin to mononucleosomes that are insoluble at greater than 30 mM NaCl. Isolated S-chromatin fragments show a constant size distribution, independent of digestion time, that peaks at approximately 35 nucleosome equivalents. Prolonged digestion of nuclei at 37 degrees C results in the conversion of S chromatin to mononucleosomes that are soluble at physiological ionic strength. Both I and S chromatins contain a full complement of histones with no nonhistone proteins.

The subunit structure of chromatin fibres

Optimal conditions for studying the ultrastructure of chromatin fibers of histone-containing spermatozoa in thin sections have been determined. Better results for preservation in sperm of the sea cucumber Holothuria tubulosa, have been found than in different frog species studied. The fine structure of chromatin fibers after different treatments was studied by computer materials. A clear superbead structure was found under all conditions which preserve the chromatin fibres. These have a diameter of 30 nm, with superbeads about 33 nm long. In the best preserved cases an additional periodicity of 11 nm along the fibres was found. There is no clear relationship of this periodicity with an eventual solenoidal structure of the chromatin fibers.