Assembly of new nucleosomal histones and new DNA into chromatin.

The assembly of chromatin from newly synthesized nucleosomal histones (labeled with [3H]arginine) and new DNA (density-labeled with [125I]iododeoxyuridine)was studied in growing cultured mouse cells. The nucleosomal histones were specifically examined by dissociating histone H1 and nonhistone proteins from unsheared chromatin either by incubation in 0.6 M NaCl or by digestion with micrococcal nuclease to release nucleosomes. In both cases, the four nucleosomal histones (H2A, H2B, H3, and H4) are essentially the only proteins that remain bound to DNA and that are labeled by [3H]arginine. After formaldehyde fixation, H1-depleted chromatin containing dense DNA can be completely resolved in CsCl buoyant density gradients from that containing unreplicated DNA; separation of nucleosomes is satisfactory although less complete. New DNA and new histones are already assembled into chromatin possessing characteristic nucleosomal structure after 3 min of synthesis (the shortest time studied), as shown by the kinetics of digestion of new DNA by micrococcal nuclease, by the distribution of new DNA and new histones in nucleosomes. However, after 3-30 min of synthesis most new nucleosomal histones are associated with unreplicated DNA rather than with new DNA. It is concluded that new nucleosomes are assembled on DNA at some distance from DNA replication sites, with concomitant migration of preexisting nucleosomes onto new DNA.     

Limited action of micrococcal nuclease on trout testis nuclei generates two mononucleosome subsets enriched in transcribed DNA sequences.

Hybridization experiments show that DNA extracted from two distinct subsets of mononucleosomes (MNI and MN2) generated by a limited action of micrococcal nuclease on trout testis nuclei is enriched approximately 7-fold in sequences that are transcribed into cytoplasmic polyadenylated RNA in trout testis cells. Both subsets of mononucleosomes contain eight core histones, but MNI also possesses one or two molecules of a small, basic, high-mobility-group (HMG) protein H6 [Levy W., B., Connor, W. & Dixon, G. H. (1979) J. Biol. Chem. 254, 609-620], bound to a DNA fragment of 140 base pairs. In contrast, MN2 contains 1 molecule of H1 but no H6, and its DNA length is somewhat longer at 140-190 base pairs. The preferential release of these two subsets of mononucleosomes is correlated with the presence of a second larger HMG protein, HMG-T, in the linker regions flanking both types of mononucleosomes. The HMG-T-containing linker regions appear to be considerably more susceptible to attack by micrococcal nuclease than H1-containing linkers. Cross-reassociation reactions between the DNA from MN1 and MN2 subsets indicate that they share a significant extent of sequence overlap but also that each subset contains specific sequences that are absent in the other subset.     

3,5,3'-triiodothyronine receptor-containing chromatin fragments: production by nuclease digestion

Nuclear thyroid hormone (T3) receptors are nonhistone proteins which are tightly bound to rat liver chromatin. The solubilization of the T3 receptors by micrococcal nuclease was studied using an assay which allows the delection of in vitro hormone binding and which is independent of the state of solubility of the chromatin. Nuclease digestion produces a receptor containing moiety which sediments at a rate of 5--6S. This form of the receptor is different than that released from chromatin at high ionic strength (3.8S) and potentially represents the stable association of the receptor which other elements of chromatin. Partial release of chromatin compaction by the use of dilute buffer solutions increases the rate of nuclease digestion, facilitates the release of the (5--6S) T3-receptor complex, and allows the isolation of sucrose gradient fractions which are enriched with receptor.     

Reconstitution of hyperacetylated, DNase I-sensitive chromatin characterized by high conformational flexibility of nucleosomal DNA

Increased acetylation at specific N-terminal lysines of core histones is a hallmark of active chromatin in vivo, yet the structural consequences of acetylation leading to increased gene activity are only poorly defined. We employed a new approach to characterize the effects of histone acetylation: A Drosophila embryo-derived cell-free system for chromatin reconstitution under physiological conditions was programmed with exogenous histones to assemble hyperacetylated or matching control chromatin of high complexity. Hyperacetylated chromatin resembled unmodified chromatin at similar nucleosome density with respect to its sensitivity toward microccal nuclease, its nucleosomal repeat length, and the incorporation of the linker histone H1. In contrast, DNA in acetylated chromatin showed an increased sensitivity toward DNase I and a surprisingly high degree of conformational flexibility upon temperature shift pointing to profound alterations of DNA/histone interactions. This successful reconstitution of accessible and flexible chromatin outside of a nucleus paves the way for a thorough analysis of the causal relationship between histone acetylation and gene function.     

Preferential and asymmetric interaction of linker histones with 5S DNA in the nucleosome.

We establish that linker histones H1 and H5 bind preferentially to a Xenopus borealis somatic 5S RNA gene associated with an octamer of core histones rather than to naked 5S DNA. This preferential binding requires free linker DNA to either side of the nucleosome core. Incorporation of a single linker histone molecule into the nucleosome protects an additional 20 bp of linker DNA from micrococcal nuclease digestion. This additional DNA is asymmetrically distributed with respect to the nucleosome core. Incorporation of linker histones causes no change to the cleavage of DNA in the nucleosome by hydroxyl radical or DNase I.     

Regulation of activity of chromatin receptors for thyroid hormone: possible involvement of histone-like proteins.

Thyroid hormone receptors lose their capability for high-affinity binding of the biologically active triiodothyronine after solubilization and separation from other chromatin proteins. The high-affinity triiodothyronine-binding capacity can be reconstituted by addition of a histone-containing extract of chromatin of purified core histones (H2A, H2B, H3, and H4); a number of other acidic or basic proteins tested were ineffective. The data support a model of the receptor in which a "core" receptor subunit that contains a thyroid hormone-binding site interacts with a regulatory subunit, which is possibly a histone or histone-like species. This interaction with the "core" subunit enables the resulting "holo" receptor to bind biologically active hormones. These data also suggest that histones or related proteins can modulate the activity of nonhistone chromosomal proteins that are involved in regulating the expression of specific genes.     

DNA strand breaks alter histone ADP-ribosylation.

Histone ADP-ribosylation was studied using two-dimensional gel electrophoresis after cleavage of the nuclear DNA with nucleases. Modified histones carrying different numbers of ADP-ribose groups form a ladder of bands above each variant histone. Cellular lysates containing unfragmented DNA mainly synthesize mono(ADP-ribosylated) histones. Cleavage of the DNA with either DNase I or micrococcal nuclease to fragments of an average size of 10-20 kilobases (kb) dramatically induces the formation of poly(ADP-ribosylated) species of histones in nuclei. As the number of DNA strand breaks produced by either DNase I or micrococcal nuclease increases and a great number of DNA cuts is introduced (fragments of 0.4-0.2 kb), the size of the poly(ADP-ribose) chains on the histones decreases. Finally, in the presence of 10 mM cAMP as an inhibitor of poly(ADP-ribose) glycohydrolase, human lymphoid nuclei synthesize hyper(ADP-ribosylated) histone H2B with at least 40 ADP-ribose groups attached to it. Lateral ladders emanating at precise points of the linear ladder on hypermodified H2B can arise from branching of poly(ADP-ribose) or from multiple monomodifications of glutamic (or aspartic) acid residues. Branching or de novo monomodifications occur after a precise number of ADP-ribose groups have been added to a histone molecule. Poly(ADP-ribosylated) histones thus appear to be intermediates in nuclear processes involving DNA strand breaks.     

Acetylated histone H4 is preferentially associated with template-active chromatin.

Chromatin from trout testis at an early stage of development was digested with DNase II (deoxyribonucleate 3'-oligonucleotidohydrolase; EC 3.1.4.6), and the solubilized products were fractionated into Mg2+-soluble and -insoluble components. An examination of the histones from these fractions by one- and two-dimensional polyacrylamide gels showed that the highly acetylated species of histone H4 (di-, tri-, and tetra-acetylated) were associated mainly with the Mg2+-soluble material. Digestion of this chromatin fraction with pancreatic ribonuclease converted more than half of it to an insoluble state, and the acetylated H4 remained associated with the precipitated fraction. No changes in the other histones were noted, but two other basic proteins were also found to be associated with the Mg2+-soluble fraction. Since this fraction is enriched in transcribing gene sequences, it is concluded that the histone H4 of active genes is present in a highly acetylated state.     

Presence of protein A24 in rat liver nucleosomes.

Two-dimensional gel profiles of the 0.2 M H2SO4-soluble proteins of monomer nucleosomal fractions were found to contain protein A24. Protein A24 is of interest because it is composed of histone 2A and "ubiquitin", apparently joined by an isopeptide linkage [Goldknopf, I.L. & Busch, H. (1977) Proc. Natl. Acad. Sci. USA 74, 864-868; Hunt, L.T. & Dayhoff, M.O. (1977) Biochem. Biophys. Res. Commun. 74, 650-655]. Monomer nucleosomal fractions were obtained by sucrose density gradient centrifugation of micrococcal nuclease digests of rat liver nuclei. As shown by their DNA size, the monomer fractions were highly purified. Proteins A24 and Bu, another protein of unknown characteristics, were found along with histones 1, 2A, 2B, 3, and 4 in the monomer fractions in relative amounts similar to those found in extracts from whole nuclei and chromatin. Other acid-soluble proteins found in the nuclear and chromatin extracts were essentially absent from the monomer fraction. Inasmuch as protein A24 and Bu were found in lesser amounts than the histones, it is suggested that they are associated with specialized subsets of nucleosomes.     

Nucleosomes associated with newly replicated DNA have an altered conformation

In vitro DNA synthesis was studied in HeLa cell nuclei, with emphasis on the question of whether newly replicated DNA is associated with nucleosomes. The newly replicated DNA was twice as sensitive to digestion by micrococcal nuclease as mature chromatin DNA, reaching a limit digest at 20-25% acid-insoluble product. Examination of the intermediates of digestion by micrococcal nuclease showed the nuclease-resistant, new DNA to be complexed in nucleosomes. However, structural differences were evident at both the polynucleosomal and the core particle level. The nucleosomes on newly replicated DNA were arranged with a repeat size of 165-170 base pairs-i.e., smaller than the 185-base-pair repeat of mature chromatin. The heterogeneity of polynucleosomal multimers, evident in digests of whole chromatin, was reduced in newly replicated chromatin such that the multimers resolved as sharply defined bands. Nucleosomal core particles associated with newly replicated DNA had a different conformation from particles in mature chromatin based on the following lines of evidence: (i) during micrococcal nuclease digestion, the monomer nucleosomes did not accumulate but were rapidly degraded under certain conditions; (ii) micrococcal nuclease limit digest patterns and DNase I digestion patterns, both of which reflect internal nucleosomal protein DNA associations, differed significantly from control patterns. These findings bear directly on models postulated for nucleosome-DNA interactions during chromation replication. A possible mechanism to account for the conformational change and its role in replication are discussed.     

Subunit structure of chromatin and the organization of eukaryotic highly repetitive DNA: Nucleosomal proteins associated with a highly repetitive mammalian DNA

Component alpha DNA is a homogeneous, highly repetitive fraction that comprises nearly a quarter of the African green monkey (Cercopithecus aethiops) genome. By restriction enzyme analysis, it has a repeat periodicity of 176 +/- 4 nucleotide base pairs, corresponding closely with the length of DNA contained within a nucleosome. The sequence is organized into large blocks of constitutive heterochromatin. A method is described here for the isolation of intact polynucleosomal arrays containing only component alpha sequences. Isolated monkey nuclei are treated with EcoRI, which releases only component alpha nucleosomal arrays; the arrays are then fractionated and purified by sedimentation in sucrose gradients. The method permits a compositional analysis of the proteins associated with a constitutively repressed, heterochromatic sequence.The major differences in the proteins associated with component alpha nucleosomes that distinguish them from the bulk DNA nucleosomes are a decrease in the content of the H1 histones in the component alpha nucleosomes and a concomitant increase in the amount of certain nonhistone proteins. The specific observations are: (i) In the component alpha nucleosomes, 65-70% of the proteins were nonhistone proteins; this contrasts with the value, 40%, for nonhistone proteins associated with nucleosomes containing bulk DNA. (ii) The amount of H1 histone in chromatin containing predominantly bulk DNA was about 13.7%. However, the H1 histone was depleted and possibly absent in component alpha oligonucleosomes. (iii) Coincident with the decrease in the H1 histones and in the same molecular weight range (24,000-43,000), there appeared five minor nonhistone proteins. The minor, low-molecular-weight, nonhistone proteins were not detected in chromatin containing bulk DNA but they represented nearly 12% of the protein in component alpha nucleosomes. The resistance to salt extraction (0.6-2.0 M NaCl) indicates that the low-molecular-weight nonhistone proteins are tenaciously bound to the component alpha nucleosomes. In addition, a class of high-molecular-weight (>100,000) nonhistone proteins was enriched 5- or 6-fold in component alpha oligonucleosomes. The relative amounts of the nucleosome core histones were not changed.     

Age-related changes of the H1 and H1(0) histone variants in murine tissues

The relative proportion of the histone H1(0) which is present in chromatin of nondividing and terminally differentiated cells is shown to increase with age. CNBr nonenzymatic cleavage and SDS-polyacrylamide gel electrophoresis of H1(0) extracted from liver chromatin of young and old mice and from age-related hepatocarcinomas showed that H1(0) consists of two variants, one contains methionine the other is methionine-free. The ratio between these two H1(0) variants also changes with age. The relative amounts of specific minor H1 and H1(0) histone fractions which are more loosely bound in chromatin and are extractable with 0.35 M NaCl, together with the HMG nonhistone proteins decrease in ageing mouse tissues. The age-related alteration of the ratio between H1(0) variants probably represents the chromatin repair process, whereas the age-related replacement of H1A and H1B subfractions by H1(0) histones may reflect the continuing process of differentiation.     

Isolation of a protein scaffold from mitotic HeLa cell chromosomes

We have recently shown that, after the histones and most of the nonhistone proteins are gently removed from HeLa metaphase chromosomes, the chromosomal DNA is still highly organized and relatively compact. The structure of these histone-depleted chromosomes is due to the presence of a number of nonhistone proteins that form a central scaffold that retains the approximate size and shape of intact chromosomes and to which the DNA is attached, predominantly forming loops. We now demonstrate that the protein scaffold may be isolated independently of the DNA by treating HeLa chromosomes with micrococcal nuclease before removing the histones.The chromosomal scaffolds may be isolated by sucrose density gradient centrifugation as a well-defined peak that is stable in 2 M sodium chloride, but is dissociated by treatment with proteases, 4 M urea, or 0.1% sodium dodecyl sulfate. Polyacrylamide gel electrophoresis reveals that the protein content of scaffold preparations is identical to that of histone-depleted chromosomes. Fluorescence microscopy of purified scaffolds in isolation buffer shows that the particles still possess the familiar chromosome morphology. When the scaffolds are examined in the electron microscope, a fibrous structure with the approximate size and shape of intact, paired chromatids is seen. Less than 0.1% of the chromosomal DNA and virtually no histones are associated with the purified scaffold structures.     

Age-dependent structural changes in human neuronal chromatin.

After partial digestion with micrococcal nuclease, DNA was extracted from nuclei of cerebral cortex neurons from young (23--36 y.) and old (78--85 y.) humans. The DNA fragments were subjected to gel electrophoresis, and their base-pair content determined. The nucleosomal DNA repeat length was found to increase from 170 (+/- 18) base-pairs in the young group to 199 (+/- 8) base-pairs in the old group. This increase of 29 base-pairs appears to be confined to the linker region of the nucleosomal DNA, since the core-DNA was always found to contain approx. 140 base-pairs. In addition, the amount of nuclear DNA digested by the micrococcal nuclease was observed to vary with age: after 30 min. of incubation at 37 degrees C hydrolysis of up to 80% of the nuclear DNA in the young but only up to 60% in the old neuronal nuclei was achieved. The age-dependent increase in chromosomal DNA repeat length is a direct proof of alterations in the basic chromatin structure with aging. It cannot be decided, however, whether the change in DNA digestibility is dependent on alterations of the chromatin basic structure, its superstructure, or both.