Studies on deoxyribonucleoprotein structure. Redistribution of proteins in mixtures of deoxyribonucleoproteins, DNA and RNA

Long molecules of free DNA in the sheared chromatin preparation

Hydrodynamic shearing of chromatin in the presence of Mg(2+) ions produces two discrete types of particles: (1) molecules of completely free DNA which comprise 20-23% of the total DNA and (2) histone-covered DNA molecules which contain all five histone fractions. The average length of free DNA molecules depends on the intensity of shearing and can be as high as 1000 base pairs or more. Shearing of chromatin in the absence of Mg(2+) produces a heterogeneous population of DNP particles; no free DNA is liberated. However, the addition of Mg(2+) to this preparation results in appearance of free DNA molecules and in a complete restoration of the above 'bimodal' distribution.These findings support a previously proposed 'asymmetric hairpin' model of DNA packing in the chromatin [1-3].

Mechanism of chromatin remodeling

Results from biochemical and structural studies of the RSC chromatin-remodeling complex prompt a proposal for the remodeling mechanism: RSC binding to the nucleosome releases the DNA from the histone surface and initiates DNA translocation (through one or a small number of DNA base pairs); ATP binding completes translocation, and ATP hydrolysis resets the system. Binding energy thus plays a central role in the remodeling process. RSC may disrupt histone-DNA contacts by affecting histone octamer conformation and through extensive interaction with the DNA. Bulging of the DNA from the octamer surface is possible, and twisting is unavoidable, but neither is the basis of remodeling.

Pyrimidine dimer formation as a probe of nucleosome core and linker structure in situ

The photoinduced dimerization of adjacent pyrimidines in DNA is influenced in predictable ways by DNA conformation. A method is described for determining patterns of pyrimidine dimer formation under conditions in which the chromatin is minimally perturbed. The relation of such patterns to the conformation of nucleosomal core DNA and linker DNA, as well as the interaction of histone H1 with nucleosomal DNA, is presented. Such data indicate that sharp bends in the path of DNA seen in crystals of isolated nucleosome core particles are also present in intact chromatin. They also indicate that most of the linker has very little curvature except for a small bend at its junction with the nucleosome core. The linker path inferred from such experiments supports models in which the chromatin fiber consists of a zigzag chain of nucleosomes.

In vitro chromatin remodelling by chromatin accessibility complex (CHRAC) at the SV40 origin of DNA replication

DNA replication is initiated by binding of initiation factors to the origin of replication. Nucleosomes are known to inhibit the access of the replication machinery to origin sequences. Recently, nucleosome remodelling factors have been identified that increase the accessibility of nucleosomal DNA to transcription regulators. To test whether the initiation of DNA replication from an origin covered by nucleosomes would also benefit from the action of nucleosome remodelling factors, we reconstituted SV40 DNA into chromatin in Drosophila embryo extracts. In the presence of T-antigen and ATP, a chromatin-associated cofactor allowed efficient replication from a nucleosomal origin in vitro. In search of the energy-dependent cofactor responsible we found that purified 'chromatin accessibility complex' (CHRAC) was able to alter the nucleosomal structure at the origin allowing the binding of T-antigen and efficient initiation of replication. These experiments provide evidence for the involvement of a nucleosome remodelling machine in structural changes at the SV40 origin of DNA replication in vitro.

Influence of histone H1 on the in vitro replication of DNA and chromatin

The influence of histone H1 on DNA replication was studied using the SV40 in vitro replication system with two different templates: histone H1/DNA complexes and SV40 minichromosomes reconstituted with H1. We found that the cytosolic extracts used as a source of enzymes for in vitro replication contained high amounts of RNA which competed with template DNA for the binding of histone H1. Removal of this RNA was necessary to ensure the stability of the templates thus allowing for the first time the study of the replication of histone H1-carrying templates in vitro. In contrast to the inhibitory effect of histone H1 on the initiation of transcription, bound H1, when present at physiological ratios, does not interfere with the in vitro replication of DNA and minichromosomes. Ratios higher than one H1 molecule per nucleosome affected replication of reconstituted SV40 minichromosomes.

Purification of two isoforms of hnRNP-U and characterization of their nucleic acid binding activity

The scaffold attachment factor A (SAF-A; Romig et al., 1992), a human nuclear protein which specifically binds vertebrate SAR (scaffold attached region) DNA, is identical with hnRNP-U (Kiledjian & Dreyfuss, 1992). In this paper, we report on the purification of two forms of this protein that can be chromatographically separated. We show that the purified proteins represent two isoforms, form 1 and form 2 hnRNP-U, which differ in their primary structure. Both isoforms bind to double- and single-stranded DNA and RNA. In addition, they form higher ordered nucleic acid/protein complexes and specifically bind and aggregate the human SAR element MII at physiological ionic strengths. Electron microscopic analysis shows that the isoforms differ from each other, as form 1 hnRNP-U aggregates into long unbranched filamentous protein/DNA complexes whereas form 2 hnRNP-U aggregates as spheres with an average diameter of 35 nm.

Nucleoprotein hybridization: a method for isolating active and inactive genes as chromatin

The developmentally regulated sea urchin early histone gene repeat (SUEHGR) from Strongylocentrotus purpuratus was isolated as chromatin by nucleoprotein hybridization. This technique is a novel method to isolate specific sequences as chromatin. Because the purification scheme is based only on the gene sequence and is independent of other physical properties such as protein composition and transcriptional activity, we were able to isolate the same gene in different functional states. Gene size chromatin fragments were solubilized by restriction endonuclease digestion of cell nuclei. Using T7 gene 6 exonuclease, the 3'termini of the fragments were exposed and then hybridized in solution to a biotinylated oligonucleotide complementary to one end of the SUEHGR fragment. The hybrids were bound to an Avidin D matrix. DTT cleavage of the biotin linker yielded a chromatin fraction greater than 700 fold enriched in SUEHGR. Overall yields were between 2% and 15%. The purity of the isolated material was independently measured to be greater than 80%. The homogeneous native structure of the inactive genes was preserved as shown by electron microscopy and micrococcal nuclease digestion of the purified SUEHGR. Minor heterogeneity was observed for the purified active genes by micrococcal nuclease digestion but the main features of the active chromatin were preserved during isolation. This isolation offers the first opportunity to study the structure of an RNA polymerase II gene at different stages of the cell cycle and development.

Histone H1 represses transcription from minichromosomes assembled in vitro

We have previously shown that transcription from a Xenopus 5S rRNA gene assembled into chromatin in vitro can be repressed in the absence of histone H1 at high nucleosome densities (one nucleosome per 160 base pairs of DNA) (A. Shimamura, D. Tremethick, and A. Worcel, Mol. Cell. Biol. 8:4257-4269, 1988). We report here that transcriptional repression may also be achieved at lower nucleosome densities (one nucleosome per 215 base pairs of DNA) when histone H1 is present. Removal of histone H1 from the minichromosomes with Biorex under conditions in which no nucleosome disruption was observed led to transcriptional activation. Transcriptional repression could be restored by adding histone H1 back to the H1-depleted minichromosomes. The levels of histone H1 that repressed the H1-depleted minichromosomes failed to repress transcription from free DNA templates present in trans. The assembly of transcription complexes onto the H1-depleted minichromosomes protected the 5S RNA gene from inactivation by histone H1.

Histone H1 represses transcription from minichromosomes assembled in vitro

We have previously shown that transcription from a Xenopus 5S rRNA gene assembled into chromatin in vitro can be repressed in the absence of histone H1 at high nucleosome densities (one nucleosome per 160 base pairs of DNA) (A. Shimamura, D. Tremethick, and A. Worcel, Mol. Cell. Biol. 8:4257-4269, 1988). We report here that transcriptional repression may also be achieved at lower nucleosome densities (one nucleosome per 215 base pairs of DNA) when histone H1 is present. Removal of histone H1 from the minichromosomes with Biorex under conditions in which no nucleosome disruption was observed led to transcriptional activation. Transcriptional repression could be restored by adding histone H1 back to the H1-depleted minichromosomes. The levels of histone H1 that repressed the H1-depleted minichromosomes failed to repress transcription from free DNA templates present in trans. The assembly of transcription complexes onto the H1-depleted minichromosomes protected the 5S RNA gene from inactivation by histone H1.

Chromatin association and DNA binding properties of the c-fos proto-oncogene product

As a first step in the analysis of the molecular function of the nuclear c-fos proto-oncogene product we have studied its subnuclear localization in serum-stimulated mouse fibroblasts where it forms a non-covalent, apparently monodisperse complex with another nuclear protein, p39. The c-fos/p39 complex is almost quantitatively released from intact nuclei by DNasel or micrococcus nuclease treatment under conditions where only a minor fraction of DNA and nuclear proteins is released. In gel filtration experiments, c-fos/p39 comigrates with chromatin and seems to be associated with regions of increased DNasel accessibility. c-fos/p39 is bound to chromatin by electrostatic forces of moderate strength since greater than 90% of the complex can be eluted from nuclei at 0.4 M NaCl. In vitro, the c-fos/p39 complex in nuclear extracts binds to double- and single-stranded calf thymus DNA, suggesting that the association of c-fos/p39 with chromatin is at least in part due to its interaction with DNA. In agreement with this conclusion, c-fos/p39 is released from nuclei by incubation with tRNA, presumably due to competition for binding sites. Our observations are compatible with the hypothesis that c-fos may play a role in the regulation of gene expression.

Abundant nuclear ribonucleoprotein form of CAD RNA

Transcripts of the CAD gene in Syrian hamster cells are as abundant in the nucleus as in the cytoplasm. This was shown by in situ hybridization of whole cells and by solution and blot hybridization of subcellular fractions. Similar results were obtained both for wild-type cells and for a mutant containing amplified CAD genes in which the level of CAD RNA is 150-fold greater. CAD nuclear RNA is indistinguishable from mature mRNA by gel electrophoresis and blot hybridization. Discrete higher-molecular-weight precursors are undetectable, although the persistence of a short length of intervening sequence in the otherwise fully processed RNA is not excluded. CAD RNA is released from nuclei by sonication in physiological conditions in a ribonucleoprotein form that sediments as a broad peak at about 200S in a sucrose gradient. CAD sequences extracted from nuclei by treatment with EDTA and RNase are found in the 30S particles previously described.

Histone crosslinking patterns indicate dynamic binding of histone H1 in chromatin

Crosslinking of histone H1 molecules to each other and to the core histones with bifunctional reagents in mouse liver nuclei and chromatin was compared with that under the conditions of random 'contacts' between these molecules. The patterns of crosslinking of the H1 subfractions (H1A, H1B, and H10) to each other in nuclei, chromatin and in solution at different ionic strengths due to random collisions were essentially the same. Moreover, the contacts between the H1 molecules were qualitatively the same in nuclei, chromatin and in solution also at the level of the chymotryptic halves of the H1 molecules. The contacts between the H1 molecules and the core histones in nuclei were similar to those obtained in chromatin at 70 mM NaCl, when H1 molecules readily migrate, and at 0.6 M NaCl, when H1 molecules are dissociated from chromatin. We conclude that spatial arrangement of H1 subfractions and mutual orientation of H1 molecules in isolated nuclei are random-like at least in terms of cross-linking. The static and dynamic models of histone H1 binding to chromatin compatible with the known data are considered. Although unequivocal verification of the models is not possible at present, the dynamic models do correspond better to recent data on the location of the histone H1 in nuclei and chromatin.

Abundant nuclear ribonucleoprotein form of CAD RNA

Transcripts of the CAD gene in Syrian hamster cells are as abundant in the nucleus as in the cytoplasm. This was shown by in situ hybridization of whole cells and by solution and blot hybridization of subcellular fractions. Similar results were obtained both for wild-type cells and for a mutant containing amplified CAD genes in which the level of CAD RNA is 150-fold greater. CAD nuclear RNA is indistinguishable from mature mRNA by gel electrophoresis and blot hybridization. Discrete higher-molecular-weight precursors are undetectable, although the persistence of a short length of intervening sequence in the otherwise fully processed RNA is not excluded. CAD RNA is released from nuclei by sonication in physiological conditions in a ribonucleoprotein form that sediments as a broad peak at about 200S in a sucrose gradient. CAD sequences extracted from nuclei by treatment with EDTA and RNase are found in the 30S particles previously described.

Effect of polycations and polyanions on cell division of cultured mammalian cells

The polycations (H1 histone and polylysine) and polyanions (heparin and various RNA preparations) stimulate cell division of cultured mammalian cells. The mechanisms by which both polycations (H1 histone and polylysine) and polyanions (heparin and RNA) may increase the rate of cell division are discussed.

Nucleosome arrangement in green monkey alpha-satellite chromatin. Superimposition of non-random and apparently random patterns

We have studied the structure of tandemly repetitive alpha-satellite chromatin (alpha-chromatin) in African green monkey cells (CV-1 line), using restriction endonucleases and staphylococcal nuclease as probes. While more than 80% of the 172-base-pair (bp) alpha-DNA repeats have a HindIII site, less than 15% of the alpha-DNA repeats have an EcoRI site, and most of the latter alpha-repeats are highly clustered within the CV-1 genome. EcoRI and HindIII solubilize approximately 8% and 2% of the alpha-chromatin, respectively, under the conditions used. EcoRI is thus approximately 30 times more effective than HindIII in solubilizing alpha-chromatin, with relation to the respective cutting frequencies of HindIII and EcoRI on alpha-DNA. EcoRI and HindIII solubilize largely non-overlapping subsets of alpha-chromatin. The DNA size distributions of both EcoRI- and HindIII-solubilized alpha-chromatin particles peak at alpha-monomers. These DNA size distributions are established early in digestion and remain strikingly constant throughout the digestion with either EcoRI or HindIII. Approximately one in every four of both EcoRI- and HindIII-solubilized alpha-chromatin particles is an alpha-monomer. Two-dimensional (deoxyribonucleoprotein leads to DNA) electrophoretic analysis of the EcoRI-solubilized, sucrose gradient-fractionated alpha-oligonucleosomes shows that they do not contain "hidden" EcoRI cuts. Moreover, although the EcoRI-solubilized alpha-oligonucleosomes contain one EcoRI site in every 172-bp alpha-DNA repeat, they are completely resistant to redigestion with EcoRI. This striking difference between the EcoRI-accessible EcoRI sites flanking an EcoRI-solubilized alpha-oligonucleosome and completely EcoRI-resistant internal EcoRI sites in the same alpha-oligonucleosome indicates either that the flanking EcoRI sites occur within a modified chromatin structure or that an altered nucleosome arrangement in the vicinity of a flanking EcoRI site is responsible for its location in the nuclease-sensitive internucleosomal (linker) region. Analogous redigestions of the EcoRI-solubilized alpha-oligonucleosomes with either HindIII, MboII or HaeIII (both before and after selective removal of histone H1 by an exchange onto tRNA) produce a self-consistent pattern of restriction site accessibilities. Taken together, these data strongly suggest a preferred nucleosome arrangement within the EcoRI-solubilized subset of alpha-oligonucleosomes, with the centers of most of the nucleosomal cores being approximately 20 bp and approximately 50 bp away from the nearest EcoRI and HindIII sites, respectively, within the 172-bp alpha-DNA repeat. However, as noted above, the clearly preferred pattern of nucleosome arrangement within the EcoRI-solubilized alpha-oligonucleosomes is invariably violated at the ends of every such alpha-oligonucleosomal particle, suggesting at least a partially statistical origin of this apparently non-random nucleosome arrangement.(ABSTRACT TRUNCATED AT 400 WORDS)

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

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

Studies on structure and function of chromatin

This article covers research work in this laboratory on the structure and function of chromatin. Early studies have led to discovery of skeletal fibrils (nucleonemas) within the nuclei and showed the specific role of histone H1 in chromatin condensation and in restriction of transcription. More recently with the aid of a novel DNP electrophoresis technique the relation of histone H1 and non-histone proteins to nucleosomes was studied. Three types of mononucleosomes and a number of subnucleosomes were identified in chromatin digests. The complexes of certain HMG proteins with short DNA segments were isolated and found to originate frm transcriptionally active chromatin. Different forms of SV40 minichromosome were characterized. A method for the analysis of nucleosome distribution along the DNA sequence was elaborated and used to show non-random (phased) location of nucleosomes on SV40 DNA. The attachment of DNA to skeletal elements of interphase nuclei and metaphase chromosomes was shown to be a non-random, probably sequence-specific process.

Different chromatin structures in Physarum polycephalum: a special form of transcriptionally active chromatin devoid of nucleosomal particles

Nonnucleolar chromatin from interphase nuclei of Physarum polycephalum plasmodia occurs in two different structural configurations as seen in electron microscopic spread preparations. While the majority of the chromatin is devoid of nascent ribonucleoprotein (RNP) fibrils and compacted into nucleosomal particles, a minor proportion (10-20%) is organized differently and reveals a smooth contour. It is this form of smooth chromatin which is rich in transcription units (mean length: 1.36 +/- 0.21 micrometer). Only occasionally are solitary nascent RNP fibrils observed which are associated with beaded strands of chromatin. In transcribed smooth chromatin nucleosomal particles are not only absent from the transcription units but also from their nontranscribed flanking regions, indicating that this special structural aspect is not merely a direct consequence of the transcriptional process. The existence of ca. 10-20% of Physarum chromatin in the smoothly contoured form is discussed in relation to reports of a preferential digestibility of a similar proportion of Physarum chromatin by DNAse I (Jalouzot et al., 1980) and to the altered configuration of "peak A" chromatin subunits after micrococcal nuclease digestion (Johnson et al., 1978 a, b).

A new method for the isolation of replicative chromatin: selective deposition of histone on both new and old DNA

We have developed a new method for isolating subcellular components after fixation of whole cells with formaldehyde. By a number of criteria we establish that the fixation does not alter or cause rearrangement of nucleosomal structure of either newly replicated or old chromatin. Using this approach we can almost completely resolve newly replicated chromatin from preexisting material on the basis of the difference in density. Newly replicated chromatin (even from cycloheximide-treated cells) appears to contain nucleosomes on both daughter strands. Exploiting the ability to separate newly synthesized chromatin, we have reexamined the question of the deposition of new histone at the replication fork. We find that newly synthesized histones H3 and H4 are deposited onto new DNA and stay in place for a significant time. In contrast new H1 is deposited on old DNA and new H2A-H2B, while they may be transiently bound to new DNA, are largely associated with preexisting chromatin.

Selective removal of histone H1 from nucleosomes at low ionic strength

The method for removal of histone H 1 from chromatin by treatment with ion-exchange resin AG 50 WX 2 in the presence of 100 mM NaCl and 50 mM phosphate buffer (Thoma and Koller, 1977, Cell, 12, 101-107) results in production not only of H1-depleted chromatin but also free DNA. We have not modified this procedure so that the nucleosome is treated with the cation exchange resin in two steps, first in 50 mM sodium phosphate buffer and then in 50 mM sodium phosphate and 50 mM NaCl whereby histone H 1 is selectively removed without a release of free DNA at low resin concentrations.

DNA wrapping in nucleosomes. The linking number problem re-examined

Chromatin was assembled in vitro from relaxed closed circular DNA (SV40) and core histones at histone to DNA ratios of 0.2 to 0.3 (g/g) and incubated with topoisomerase I to relax supercoils in DNA regions not constrained by protein. Addition of histones H1 + H5 to the chromatin at an ionic strength of 0.1 M, in the presence of the solubilizing agent, polyglutamic acid, and topoisomerase I, increased the magnitude of the DNA linking number change, relative to protein-free DNA. No change in the linking number distribution occurred for relaxed protein-free DNA under these conditions. Control experiments indicated that the increase in the absolute value of the DNA linking number change in the chromatin could not be attributed to an increase in the number of nucleosomes per DNA molecule. These data suggest a solution to the linking number problem associated with models of chromatin structure.

Salt induced transitions of chromatin core particles studied by tyrosine fluorescence anisotropy

Chromatin core particles containing 146 base pairs of DNA have been found to undergo a single defined transition below 10 mM ionic strength as studied by both sedimentation velocity and tyrosine fluorescence anisotropy. A method is described for the preparation of such core particles from chicken erythrocytes with greater than 50% yield.

Structure of the chromosomal material in inactive nuclei of chicken red blood cells

Electron microscope sections have been cut of chicken red blood cell nuclei by a novel procedure that produces zones of material below 100 A in thickness. After fixing and staining, electron dense structures are observed that have dimensions closely correlating with those determined for nucleosomes. These structures appear as wedge-shaped or as circular objects with a diameter of approximately 90-100 A. Five to eight of these objects are arranged in a spiral around a central core giving rise to a 250-300 A structure which may represent a superbead or a cross section of a solenoidal fibre.

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

The organization of nucleosomes in higher order chromatin structures has been studied by electron microscopy of chick red blood cell nuclei. Chromatin appears as a thick fiber with an average diameter of approximately 300 A when prepared for electron microscopy in buffers which approximate physiological ionic strength. Progressive steps of disassembly of the thick fiber into individual nucleosomes could be induced either by ionic strength reduction or by tRNA treatment (which removes histone H1 and some non-histone chromosomal proteins). When disassembly was induced by ionic strength reduction in the presence of Mg++ (or Ca++), the lengths of the intermediate disassembly products were found to be multiples of 330 A. The diameter of these structures was estimated to be 275 A. This intermediate in the disassembly process is not observed if thick fiber disassembly is induced by ionic strength reduction in the absence of divalent cations. To investigate whether the higher order structural unit is present in the thick fiber at physiological ionic strengths, tRNA treatment was used to induce thick fiber disassembly under physiological monovalent ionic conditions. In this case, either with or without divalent cations, a supranucleosomal unit was found with dimensions similar to those given above. This data provides evidence for a slightly oblong supranucleosomal structure (330 x 275 A) whick forms a repeating unit in the chromatin thick fiber.

Reversible dissociation of linker histone from chromatin with preservation of internucleosomal repeat

Procedures are described for the dissociation of histones H1 and H5 from chicken reticulocyte chromatin without disruption of the native core histone-DNA complex. The comparative properties of native and depleted chromatin with respect to sedimentation, thermal denaturation, and sensitivity to nuclease digestion have been studied. The changes in these properties resulting from removal of the linker histones are fully reversed when histone H5 is added back to the depleted chromatin.

Chromatin condensation. Possible dehydrating and stabilizing factors

The effect of Na+, Mg2+, spermidine and spermine on the dehydration of chromatin gel and precipitation of soluble chromatin has been compared. Considerable differences have been found in the relative ratios within the studied group (Na+, Mg2+, spermidine and spermine) between the ability to dehydrate (1 : 32 : 53 : 67) and to precipitate (1 : 53 : 800 : 2000) chromatin. On the basis of the dependence of precipitation on initial chromatin concentration it has been suggested that the observed effect as contributed considerably by interparticle aggregation is a relatively good measure of the ability of cation to stabilize higher order structures of chromatin through direct crosslinking or induction of hydrophobic associations at selected sites. In contrary to that the method estimating the direct dehydration measures the overall dehydrating effect of a cation exerted on the whole chromatin. It has been suggested on the basis of the above comparative data that the in vivo regulation of the degree of overall chromatin hydration should occur through changes in concentration of free small inorganic cations. Larger organic polycations like polyamines should be mainly involved in stabilization of the higher order chromatin structures. The stabilizing role of large polyanions like RNA has been ruled out. It has also been found that the unwinding of chromatin DNA results in considerable chromatin hydration.

Native and reconstituted chromosome fiber fragments

The structure of hen erythrocyte chromatin fibers was studied with the electron microscope. Chromatin fiber fragments with a length of about 5,000 A and an average diameter of 320 A are composed of 13 globular subunits (superbeads) which contain different numbers of nucleosomes. Their number average corresponds to 17 nucleosomes. - The interaction of lysine-rich histones with nucleosome chains was investigated by reconstitution experiments and was found to be semi-cooperative.

Rearrangement of chromatin structure induced by increasing ionic strength and temperature

Native rat liver chromatin fragments exposed to 600 mM NaCl at 37 degrees C for 45 min exhibit substantial modification of their original (approximately 200 base pairs) repeating subunit structure: a new repeat of 140 base pairs, superimposed on a high background, is observed after micrococcal nuclease digestion. The same material appears, in the electron microscope, as clusters of tightly packed beads connected by stretches of 'free' DNA. These modifications are not observed when the native chromatin is incubated at 37 degrees C at NaCl concentrations up to 400 mM. When native rat liver chromatin depleted of histone H1 by tRNA extraction is exposed to ionic strengths up to 600 mM NaCl at 4 degrees C, almost no modifications of the original native repeating structure are observed. However, when the incubation is carried out at 37 degrees C in 150, 300 or 400 mM NaCl, rearrangements of the native structure occur as indicated by micrococcal nuclease digestion and electron microscopic studies. Incubation of H1-depleted chromatin at 600 mM NaCl for 45 min at 37 degrees C induces, as for the native chromatin, a complete rearrangement characterized by the appearance of a 140-base-pair repeat superimposed on a high background upon digestion by micrococcal nuclease. It is suggested that these rearrangements are mediated by hydrophobic interactions between the histone cores and are prevented at ionic strengths lower than 500 mM by the presence of histone H1.