Electron microscopy of defined lengths of chromatin

Potential capacity of interferon-α to eliminate covalently closed circular DNA (cccDNA) in hepatocytes infected with hepatitis B virus

Interferon-alpha (IFN-α) and nucleot(s)ide analogs (NAs) are first-line drugs for the treatment of chronic hepatitis B virus (HBV) infections. Generally, NAs target the reverse transcription of HBV pregenomic RNA, but they cannot eliminate covalently-closed-circular DNA (cccDNA). Although effective treatment with NAs can dramatically decrease HBV proteins and DNA loads, and even promote serological conversion, cccDNA persists in the nucleus of hepatocytes due to the lack of effective anti-cccDNA drugs. Of the medications currently available, only IFN-α can potentially target cccDNA. However, the clinical effects of eradicating cccDNA using IFN-α in the hepatocytes of patients with HBV are not proficient as well as expected and are not well understood. Herein, we review the anti-HBV mechanisms of IFN-α involving cccDNA modification as the most promising approaches to cure HBV infection. We expect to find indications of promising areas of research that require further study to eliminate cccDNA of HBV in patients.

Biophysics of Chromatin Dynamics

Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.

Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo

Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin-nucleosomes-are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an "open" configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome-nucleosome associations.

DNA methylation effects on tetra-nucleosome compaction and aggregation

DNA CpG methylation has been associated with chromatin compaction and gene silencing. Whether DNA methylation directly contributes to chromatin compaction remains an open question. In this study, we used fluorescence fluctuation spectroscopy (FFS) to evaluate the compaction and aggregation of tetra-nucleosomes containing specific CpG patterns and methylation levels. The compactness of both unmethylated and methylated tetra-nucleosomes is dependent on DNA sequences. Specifically, methylation of the CpG sites located in the central dyad and the major grooves of DNA seem to have opposite effects on modulating the compactness of tetra-nucleosomes. The interactions among tetra-nucleosomes, however, seem to be enhanced because of DNA methylation independent of sequence contexts. Our finding can shed light on understanding the role of DNA methylation in determining nucleosome positioning pattern and chromatin compactness.

Analysis of chromatin organisation

Terms to be familiar with before you start to solve the test: chromatin, nucleases, sucrose density gradient centrifugation, melting point, gel electrophoresis, ethidium bromide, autoradiography, Southern blotting, Northern blotting, Sanger sequencing, restriction endonucleases, exonucleases, linker DNA, chloroform extraction, nucleosomes, nucleosomal histones, histone H1, nonhistone proteins, laminin, lamin, solenoid, DNA methylation, CpG islands, histone acetylation, centromere, histone octamers, "beads-on-a-string", euchromatin, heterochromatin.

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

We propose definitions and procedures for comparing nucleosome maps and discuss current agreement and disagreement on the effect of histone sequence preferences on nucleosome organization in vivo.

Plant SET domain-containing proteins: structure, function and regulation

Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein-protein interactions through both intra- and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense-antisense RNA.

Molecular mechanisms of HIV-1 proviral latency

While great strides have been made in the treatment of HIV infection with highly active antiretroviral therapy, an actual cure remains out of grasp. One confounding factor is the persistence of a small population of infected cells containing transcriptionally silent but reactivatable HIV proviruses. Following cessation of highly active antiretroviral therapy, these latently-infected cells serve as an inoculum for re-establishing an active infection. Recent progress in our understanding of the molecular mechanisms underlying HIV proviral latency will be reviewed. Recent advances in the study of transcriptional regulation and the completion of the Human Genome Project underscore the role of chromatin and the site of viral integration on HIV transcription. Finally, experimental therapies designed to eliminate the latent population will be highlighted.

Autoantibodies in SLE but not in scleroderma react with protein-stripped nucleosomes

Autoantibodies against nucleosomes (ANuA) are known to be sensitive markers for systemic lupus erythematosus (SLE), but their clinical relevance seemed to be limited because sera from patients with progressive systemic sclerosis (PSS) also showed positive reactions with conventional ANuA ELISA test systems (anti-Nu1 ELISA). It was generally assumed thatANuA were associated with both diseases. Using discontinuous sucrose gradient centrifugation to generate pure nucleosomes, we discovered by chance that at the 30-50% sucrose interface an antigen (Nu2) banded which was demonstrably free of non-histone components and histone H1. The two different nucleosome preparations, Nu1 and Nu2, were used in parallel as antigenic substrates in standardised ELISA tests to analyse sera from SLE (295 patients), PSS (119) and patients with other rheumatic diseases (101). With Nu1, 62% of the SLE and 52% of the PSS sera showed positive reactions. Two sera from patients suffering from Sjögren's syndrome (SS) and one from polymyositis were also positive. Using the Nu2 preparation, 58% of the SLE but none of the PSS sera showed a positive reaction. One serum from a patient with SS was also positive. It could be shown that it was the PSS-specific autoantigen Scl-70 in the nucleosome preparation (Nu1) which contributed to the positive reactions of the PSS sera in conventional ANuA test systems, whereas in the Nu2 preparation no remaining Scl-70 was detectable. The present study definitely proved that ANuA are highly and specifically associated with SLE but not with PSS.

HU: promoting or counteracting DNA compaction?

The role of HU in Escherichia coli as both a protein involved in DNA compaction and as a protein with regulatory function seems to be firmly established. However, a critical look at the available data reveals that this is not true for each of the proposed roles of this protein. The role of HU as a regulatory or accessory protein in a number of systems has been thoroughly investigated and in many cases has been largely elucidated. However, almost 30 years after its discovery, convincing evidence for the proposed role of HU in DNA compaction is still lacking. Here we present an extensive literature survey of the available data which, in combination with novel microscopic insights, suggests that the role of HU could be the opposite as well. The protein is likely to play an architectural role, but instead of being responsible for DNA compaction it could be involved in antagonising compaction by other proteins such as H-NS.

Structural organization of the hepatitis B virus minichromosome

The replicative intermediate of hepatitis B virus (HBV), the covalently closed, circular DNA, is organized into minichromosomes in the nucleus of the infected cell by histone and non-histone proteins. In this study we investigated the architecture of the HBV minichromosome in more detail. In contrast to cellular chromatin the nucleosomal spacing of the HBV minichromosome has been shown to be unusually reduced by approximately 10 %. A potential candidate responsible for an alteration in the chromatin structure of the HBV minichromosome is the HBV core protein. The HBV core protein has been implicated in the nuclear targeting process of the viral genome. The association of the HBV core protein with nuclear HBV replicative intermediates could strengthen this role. Our findings, confirmed by in vivo and in vitro experiments indicate that HBV core protein is a component of the HBV minichromosome, binds preferentially to HBV double-stranded DNA, and its binding results in a reduction of the nucleosomal spacing of the HBV nucleoprotein complexes by 10 %. From this model of the HBV minichromosome we propose that the HBV core protein may have an impact on the nuclear targeting of the HBV genome and be involved in viral transcription by regulating the nucleosomal arrangement of the HBV regulatory elements, probably in a positive manner.

Two types of telomeric chromatin in Tetrahymena thermophila

The telomeric d(GGGGTT).d(AACCCC) repeat tracts (G4T2 repeats) in Tetrahymena thermophila macronuclei were shown previously to be packaged in a non-nucleosomal DNA-protein complex. Here, we demonstrate that these telomeric repeats, together with a short region of the immediately adjacent non-telomeric sequence, exist in two distinct types of chromatin. The non-nucleosomal complex (type I complex) comprises approximately 90 to 97% of telomeric DNA, has no apparent underlying periodic nucleosomal substructure, and includes the whole telomeric tract as well as the immediately adjacent sequence. Type II chromatin, comprising the remaining approximately 3 to 10% of the total telomeric DNA, consists of tightly packed nucleosomes clustered at the inner border of the telomeric tracts, with a periodicity of 154(+/-3) bp. This packing is similar to that of telomeric nucleosomes in vertebrates. However, in contrast to the unstability of vertebrate telomeric mononucleosomes, the T. thermophila mononucleosomes were stable to micrococcal nuclease digestion. During the natural lengthening of the T. thermophila telomeric DNA tracts that occurs in vegetatively dividing cells, the overall ratio of type I and type II chromatin did not change. However, type I complex expanded with the length of the telomeric DNA repeat tract, and the number of telomeric nucleosomes increased from an average of one, up to three to four, per telomeric tract. This finding of telomeric nucleosomes in T. thermophila suggests that the difference between vertebrates and lower eukaryotes in telomeric chromatin structure is quantitative rather than qualitative. We propose that deposition of nucleosomes competes with non-nucleosomal complex formation on telomeric DNA, resulting in a sub-population of chimeric telomeres containing inner nucleosomes abutting a distal, variable length of type I complex.

Visualization and analysis of chromatin by scanning force microscopy

The use of the scanning force microscope (SFM) to visualize and analyze chromatin fiber structures is presented. Protocols to prepare chromatin fibers for SFM imaging of fibers in air and in buffer are first discussed. Next, the conditions for acquiring high-quality SFM images such as optimal instrumental parameters, appropriate deposition substrates, and adequate procedures of sample deposition are described. It is shown that analysis and quantitation of the SFM images support an irregular, three-dimensional arrangement of nucleosomes in the native chromatin fiber. This structure is lost in linker histone-depleted fibers, which show, instead, a beads-on-a-string structure. Molecular modeling of the chromatin fiber structures and computer simulation of the SFM imaging process indicate that the natural variability of the linker length may be the major determinant of the structural irregularity of the native chromatin fiber. Removal of linker histones (H1/H5) may change the amount of DNA wrapped around the histone octamer, which in turn may induce the transition from a three-dimensional irregular helix to an extended beads-on-a-string structure. Studies of trinucleosomes indicate that both the average successive nucleosome center-to-center distance and the average angle between two successive linkers increase upon the removal of linker histone.

Direct detection of linker DNA bending in defined-length oligomers of chromatin

Linker DNA, which connects between nucleosomes in chromatin, is short and, therefore, may be essentially straight and inflexible. We have carried out hydrodynamic and electron microscopic studies of dinucleosomes--fragments of chromatin containing just two nucleosomes--to test the ability of linker DNA to bend. We find that ionic conditions that stabilize the folding of long chromatin cause linker DNA in dinucleosomes to bend, bringing the two nucleosomes into contact. The results uphold a key prediction of the solenoid model of chromosome folding and suggest a mechanism by which proteins that are separated along the DNA can interact by direct contact.

c-Ha-rasVal 12 oncogene-transformed NIH-3T3 fibroblasts display more decondensed nucleosomal organization than normal fibroblasts

We have compared the nucleosomal organization of c-Ha-rasVal 12 oncogene-transformed NIH-3T3 fibroblasts with that of normal fibroblasts by using micrococcal nuclease (MNase) as a probe for the chromatin structure. The bulk chromatin from asynchronously and exponentially growing ras-transformed cells was much more sensitive to MNase digestion than chromatin from the normal cells. Southern hybridization analyses of the MNase digests with probes specific for the ornithine decarboxylase (odc) and c-myc genes showed that the coding and/or 3' end regions of these growth-inducible genes carry a nucleosomal organization both in ras-transformed and normal cells. Studies with cells synchronized by serum starvation showed that in both cell lines the nucleosomal organization of chromatin is relatively condensed at the quiescent state, becomes highly decondensed during the late G1 phase of the cell cycle, and starts again to condense during the S phase. However, in ras-transformed cells the decondensation state stayed much longer than in normal cells. Moreover, irrespective of the phase of the cell cycle the bulk chromatin as well as that of the odc and c-myc genes was more sensitive to MNase digestion in the ras-transformed cell than in the normal fibroblast. Decondensation of the chromatin was also observed in the normal c-Ha-ras protooncogene-transfected cells, but to a lesser extent than in the mutant ras-transformed cells. Whether the increased degree of chromatin decondensation plays a regulatory role in the increased expression of many growth-related genes in the ras-transformed cells remains an interesting object of further study.

The effect of histone H1 on the compaction of oligonucleosomes. A quasielastic light scattering study

The structural properties of H1-depleted oligonucleosomes are investigated by the use of quasielastic laser light scattering, thermal denaturation and circular dichroism and compared to those of H1-containing oligomers. To obtain information on the role of histone H1 in compaction of nucleosomes, translational diffusion coefficients (D) are determined for mono-to octanucleosomes over a range of ionic strength. The linear dependences of D on the number of nucleosomes show that the conformation of stripped oligomers is very extended and does not change drastically with increasing the ionic strength while the rigidness of the chain decreases due to the folding of linker DNA. The results prove that the salt-induced condensation is much smaller for H1-depleted than for H1-containing oligomers and that histone H1 is necessary for the formation of a supercoiled structure of oligonucleosomes, already present at low ionic strength.

Chromatin structure at the 44D larval cuticle gene locus in Drosophila: the effect of a transposable element insertion

The chromatin structure of the larval cuticle gene cluster at 44D was characterized in embryos from wild-type (Oregon R) and a variant line (2/3) of Drosophila melanogaster. A major DNase I hypersensitive (DH) site was found between genes II and III in the chromatin, in a position 5' to the transcriptional start of the genes in the cluster. The introduction of a 7.3 kilobase transposable element into the cluster in the 2/3 variant enhanced the sensitivity of the major site in 2/3 chromatin but had no other effect upon the pattern of DH sites associated with the wild-type sequences. The wild-type sequences were packaged into an ordered nucleosome-like array in embryos, as revealed by digestion with the chemical cleavage reagent (methidiumpropyl-EDTA) iron (II) [MPE . Fe(II)]. Nucleolytic cleavage within the transposable element chromatin shows it to be organized in an ordered array punctuated by several DH sites. While the patterns of DNase I hypersensitivity are similar in the vicinity of the direct terminal repeats, the patterns revealed by micrococcal nuclease and MPE . Fe(II) are not, indicating a different chromatin organization of these two identical sequences.

Structural properties of barley nucleosomes

The structural properties of barley oligonucleosomes are investigated and compared to those of rat liver oligomers. Extraction of barley chromatin was performed using mild nuclease digestion of isolated nuclei leading to a low ionic strength soluble fraction. Oligonucleosomes were fractionated on sucrose gradients and characterized for DNA and histone content. Physico-chemical studies (sedimentation, circular dichroism and electric birefringence) showed that barley oligonucleosomes exhibit properties very close to those of the H1-depleted rat liver counterparts. Moreover, in situ, barley linker DNA was more sensitive to micrococcal nuclease digestion than that of rat liver. These results suggest that barley oligonucleosomes show a less compact structure than their rat liver counterparts and appear to be in contradiction with the very condensed organization of barley chromatin previously suggested.

Chromatin superstructure: synchrotron radiation X-ray scattering study on solutions and gels

X-ray small angle scattering patterns of solutions and gels of native chicken erythrocyte chromatin and chromatin depleted of H5 histones have been measured under several ionic conditions using synchrotron radiation. Features of the patterns are interpreted as resulting from a superstructure with an outer diameter of about 300A which is already present in uncondensed nucleofilaments. This superstructure which is shown to be maintained by the H5 histones also explains the rapid condensation of the nucleofilaments in higher ionic strengths.

Interaction of oestrogen and progesterone receptors with specific subfractions of laying-hen oviduct chromatin

Salt (NaCl)-extracted nuclear oestrogen receptor from hen oviduct was incubated with salt-depleted oviduct chromatin and dialysed to low salt. The oestrogen receptor (re)associated with chromatin to form a 13-14S-sedimenting fraction, as found in 'native' chromatin, and saturation of this interaction was obtained for very low receptor concentrations (approx. 0.04 nM). Similarly, purified progesterone receptor from chick oviduct cytosol associated with depleted chromatin to form an 11-12S-sedimenting fraction, as in 'native' chromatin; this interaction tended towards saturation for much higher concentrations of progesterone receptor (approx. 8 nM) than that observed for oestrogen receptor. When the two receptors were incubated with depleted chromatin from hen kidney or erythrocytes, their s values were as for oviduct chromatin. However, no saturation of these interactions was seen, even for high concentrations of receptor. Steroid-hormone receptors can therefore bind in vitro to particular subfractions of non-target-tissue chromatin, but with a much lower affinity than to target-tissue chromatin.

Chromatin structure in barley nuclei

In order to study the chromatin structure of a higher plant we used a high-yield method, which allows one to obtain up to 10(9) nuclei/kg fresh barley leaves. Significant amounts of low-ionic-strength-soluble chromatin can be extracted from these nuclei. Physicochemical properties were examined and discussed. Electric birefringence allowed us to observe the same transition in electro-optical properties as has been observed for animal chromatin, and suggested the existence of a symetrical structure occurring for approximately six nucleosomes. Circular dichroism showed that barley oligonucleosomes exhibit a higher molar ellipticity at 282 nm than total soluble chromatin and than their animal counterparts.

The protein responsible for the repeating structure of cytoplasmic poly(A)-ribonucleoprotein

A 75,000-dalton protein has been purified approximately 1,000-fold from rat liver, based on its capacity to organize poly(A) in a 27-residue repeating structure. This protein may be identified with the major polypeptide component of cytoplasmic poly(A)-ribonucleoprotein (RNP) previously described. The poly(A)-organizing activity of the protein is detected only in cytoplasmic fractions. Upon nuclease digestion of the 75,000-dalton protein-poly(A) complex, monomers, and higher multimers of RNP subunits can be resolved in a sucrose gradient. The sedimentation rate of the monomer is compatible with a composition of one 75,000-dalton protein molecule and one 27-residue segment of poly(A).

Simian virus 40 encapsidation: characterization of early intermediates

Simian virus 40 chromosomes were separated into various species by a two-step purification consisting of low-ionic-strength glycerol gradient sedimentation followed by low-ionic-strength agarose gel electrophoresis. For each species of simian virus 40 chromosome purified, the comigrating DNA and proteins were identified by agarose or polyacrylamide gel electrophoresis, respectively. Two species of chromosomes were identified which contained form I and form II DNA and large amounts of viral protein; they migrated more slowly than most of the free simian virus 40 chromosomes, which contained very little viral protein. The nuclease susceptibility of these chromosomes suggests to us that they are intermediates in encapsidation, and we describe an encapsidation model.

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.

The role of histone H1 in compaction of nucleosomes. Sedimentation behaviour of oligonucleosomes in solution

The dependence of sedimentation coefficients of oligonucleosomes on the number of nucleosomes in the chain in solutions of different ionic strength has been studied for oligonucleosomes both containing and lacking histone H1. The analysis of these dependencies has shown that oligonucleosomes with H1 at low concentration (I = 0.01 mol/l) may be described by the model of a short cylinder with an average length of the chain per nucleosome l0 = 11 nm where the neighbouring nucleosomes are in close contact. Oligonucleosomes without H1 at I = 0.01 mol/l can be described by the model of a worm-like chain with l0 = 27 nm. This suggests that when H1 is removed the linker DNA unfolds completely. In 0.15 M NaCl the oligonucleosome chain without H1 folds up to a compact configuration typical of oligonucleosomes with H1 at I = 0.01 mol/l. Thus, the linker DNA, with charges being screened, may fold due to interactions with core histones. Oligonucleosomes with H1 in 0.15 M NaCl form a supercoiled structure, whose stable conformation is accounted for by cooperative interactions of no less than five nucleosomes.

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.

Repeating structure of cytoplasmic poly(A)-ribonucleoprotein

A repeating structure of cytoplasmic poly(A)-ribonucleoprotein is revealed by digestion with T2 RNase. A pattern of fragments that are multiples of about 27 residues is obtained. The repeating structure is readily reconstituted from purified poly(A) and cytoplasmic factors. Reconstitution is specific for poly(A), as shown by the lack of competition by poly(G), poly(C), poly(dA), and tRNA. The repeating structure is absent from the nucleus, and so appears to be formed upon transport to the cytoplasm.

The basis of chromatin fiber assembly within chromosomes studied by histone-DNA crosslinking followed by trypsin digestion

To determine the structural basis of chromatin assembly that leads to chromosome formation in mitosis, crosslinks were introduced by formaldehyde between contiguous components within chromosomes. Crosslinked stable products were then observed by electronmicroscopy after non-crosslinked portions were briefly digested by trypsin to unfold chromosomes.--When the DNA-histone crosslink was the primary product, trypsin readily unfolded the whole chromosome structure while preserving the 250 A unit chromatin fiber intact; only a single unit fiber was tracked within the centromere region connecting the arms of each chromatid. When a histone polymer was formed by a prolonged formaldehyde crosslinking, trypsin digestion gave rise to chromatin fibers interacting with others at certain distances, and the typical chromosome structure remained unchanged. Regardless of the degree of crosslinking, there were neither thick supercoiled unit fibers nor proteinaceous cores.--These results suggest that the fiber connection may represent, to some extent, the interacting sites of folded chromatin fibers in situ within chromosomes, and also that the 250 A unit fibers are the sole, highest structural basis in chromosomes. Since virtually no appreciable histone digestion took place in the crosslinked chromosomes, the observation that even after DNA-histone crosslinking the fiber interacting sites were accessible to trypsin preferentially over other portions, may be consistent with our recent results that the exposed, lysine-rich tails of histones represent such interacting sites.

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.

Disappearance of a structural chromatin protein A24 in mitosis: implications for molecular basis of chromatin condensation

A chromatin protein, A24, a conjugate of histone H2A and evolutionally conserved ubiquitin, was virtually the only structural polypeptide that was present in interphase but missing in mitosis of a Chinese hamster cell line (DON). Because a 10% increase in the H2A/DNA ratio observed in interphase-mitosis transition explained the stoichiometric conversion of A24 to H2A, it appears that ubiquitin bound to H2A of nucleosomal surfaces in interphase is released at mitosis whereas the total H2A remains as a structural component of nucleosomes. Regardless of protein synthesis, ubiquitin was again bound to H2A when cells entered the G1 phase. Based on the electrostatic nature of the COOH-terminal region of H2A, where ubiquitin binds, and the mitosis-specific rise of covalently linked phosphates in histones H1 and H3, we propose that an ionic interaction between the positively charged H2A COOH-terminal regions on fibers and negatively charged phosphates linked to serine or threonine of H1 and H3 molecules on adjacent fibers could generate an assembly of chromatin fibers in mitosis.

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.

Structural changes in simian virus 40 chromatin as probed by restriction endonucleases

The structure of simian virus 40 (SV40) chromatin was probed by treatment with single- and multiple-site bacterial restriction endonucleases. Approximately the same fraction of the chromatin DNA was cleaved by each of three different single-site endonucleases, indicating that the nucleosomes do not have unique positions with regard to specific nucleotide sequences within the population of chromatin molecules. However, the extent of digestion was found to be strongly influenced by salt concentration. At 100 mM NaCl-5 mM MgCl2, only about 20% of the simian virus 40 (SV40) DNA I in chromatin was converted to linear SV40 DNA III. In contrast, at lower concentrations of NaCl (0.05 or 0.01 M), an additional 20 to 30% of the DNA was cleaved. These results suggest that at 100 mM NaCl only the DNA between nucleosomes was accessible to the restriction enzymes, whereas at the lower salt concentrations, DNA within the nucleosome regions became available for cleavage. Surprisingly, when SV40 chromatin was digested with multiple-site restriction enzymes, less than 2% of the DNA was digested to limit digest fragment, whereas only a small fraction (9 to 15%) received two or more cuts. Instead, the principal digest fragment was full-length linear SV40 DNA III. The failure to generate limit digest fragments was not a consequence of reduced enzyme activity in the reaction mixtures or of histone exchange. When the position of the principal cleavage site was mapped after HpaI digestion, it was found that this site was not unique. Nevertheless, all sites wree not cleaved with equal probability. An additional finding was that SV40 chromatin containing nicked-circular DNA II produced by random nicking of DNA I was also resistant to digestion by restriction enzymes. These results suggest that the initial cut which causes relaxation of topological constraint in SV40 chromatin DNA imparts resistance to further digestion by restriction enzymes. We propose that this may be accomplished by either "winding" of the internucleosomal DNA into the body of the nucleosome, or as suggested by others, by successive right-hand rotation of nucleosomes.

The effect of clupein on anisotropy and basophilia of polytene chromosomes

When polytene chromosomes are subjected to a clupein treatment, their properties of basophilia and anisotropy are affected. The basophilia is deeply reduced, except in the nucleolar zones, puffs and sites of RNA accumulation. On the other hand, the chromosome birefringence increases. The phenomenon of anomalous dispersion of birefringence usually observed on polytene chromosomes stained with toluidine blue solutions turns into a normal negative dispersion of birefringence, when staining is preceded by clupein treatment. It is concluded that the clupein molecules attach orderly and preferentially to sequential DNA phosphates unbound to chromosome proteins, accentuating DNA anisotropic characteristics. The clupein molecules appear not attaching to RNA phosphates.

Characteristics of transcriptionally active and inactive neuronal and nonastrocytic glial rat brain chromatin fractions

Rapid and reliable fractionation of neuronal and nonastrocytic glial (NAG) cerebral rat brain chromatin in transcribable and repressed portions was achieved employing the DNAase II/Mg++-solubility method of Gottesfeld et al. (1974). Compositional and transcriptional properties of these fractions have been investigated. Compared to transcriptionally repressed fractions, template-active neuronal and NAG chromatin fractions are associated with an increased content of nonhistone chromosomal (NHC-) proteins. Both of the transcribable as well as both of the repressed fractions are strikingly different in their composition as assessed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. Comparative acid urea gel electrophoretic patterns of histones revealed that histone fraction H 1 is almost completely absent in actively transcribed neuronal chromatin and reduced in the corresponding NAG fraction while in template-inactive neuronal and NAG chromatin all five main histone fractions are present in equal amounts. The total number of RNA initiation sites available for exogenously added homologous RNA polymerase on template-active and -inactive neuronal and NAG chromatin was quantitatively measured under assay conditions completely eliminating reinitiation. Unlike the template-active neuronal and NAG fractions which are differently enriched in RNA initiation sites, transcriptionally more repressed neuronal and NAG fractions demonstrated a minimal ability to initiate RNA synthesis. Under assay conditions allowing repeated initiation of RNA chains at the same initiation site, rat brain RNA polymerase molecules were found to utilize neuronal initiation sites more frequently than NAG ones.

Simple isolation of DNA hydrophobically complexed with presumed gene regulatory proteins (M3)

Chromatin from chicken reticulocytes and mouse Ehrlich ascites tumor cells has been extracted with 2 M NaCl, leaving a portion of the DNA still complexed with a fraction of nonhistones (designated M3, since it can be dissociated from DNA in solutions of 3 M NaCl containing 5 M urea). The DNA complexed with M3, separated from the bulk DNA by centrifugation, was found to contain sequences poorly represented in bulk DNA. Specifically we found that DNA--M3 complexes isolated from chicken reticulocyte chromatin were enriched in globin gene sequences by 20-fold relative to unfractionated DNA and by over 1000-fold relative to DNA rendered free of protein following the extraction of chromatin with 2 M NaCl. We have therefore isolated DNA fractions complexed with M3 which are enriched in specific sequences as may be determined by M3.

A histone programme during the life cycle of the sea urchin

The histone complement of chromatin from early gastrula, late gastrula and from fully differentiated gut cells of the sea urchin Parechinus angulosus has been fractionated by molecular sieve and ion-exchange chromatography. Several of the subfractions thus isolated have been characterized by amino acid composition and partial amino acid sequences as a series of variants of the histones H1, H2A and H2B. Specific histone variants are present in chromatin at specific stages of differentiation.

Modification of DNA in chromatin with methyltransferase from Haemophilus influenzae Rd

The accessibility of DNA in nucleosome dimers (as a model of the chromosomal chain of nucleosomes) was determined by means of modification methylases from Haemophilus influenzae Rd. Using these enzymes, the rate of modification of nucleosome dimers is about one fifth the rate observed with protein-free DNA from chromatin subunit dimers. Methylated DNA sites in nucleosome dimers are readily accessible to micrococcal nuclease. The analysis of the fragment pattern of nucleosomes after methylation and mild nuclease treatment reveals that the methylated sites are predominantly located in the internucleosomal linker DNA. Polylysine binding experiments further support this interpretation. This compound preferentially interacts with the nucleosomal core DNA and protects it against internal cleavage. It neither affects the degradation of methylated sites drastically nor does it inhibit the methylation of nucleosome dimers. Thus, a combination of protection, cleavage and modification is proposed as a useful tool for the analysis of the structure of chromatin.

Nucleosomes from normal and regenerating rat liver

Micrococcal-nuclease digestion of rat liver nuclei selectively released mononucleosomes associated with ADP-ribosylated [Caplan, Ord & Stocken (1978) Biochem. J.174, 475-483] histone H1. Two classes of mononucleosome were detected, those that leaked out during digestion and those that were subsequently released by 5mm-sodium phosphate buffer (pH6.8)/0.2mm-NaEDTA. The former, from which histone H1 had been dissociated, contained 140-base-pair-length DNA and core histones;the latter contained core particles and mononucleosomes with histone H1 and 200-base-pair-length DNA. When normal liver nuclei were phosphorylated with [gamma-(32)P]ATP, dissociated histone H1, which could be separated from core particles with Sephadex G-200, showed (32)P uptake. (32)P uptake into histones H2A and poly(ADP-ribosyl)ated H3 was appreciable in core particles, but was less evident in nucleosomes still containing histone H1. When [(3)H]-thymidine was given to partially hepatectomized rats in S-phase, 5-10min pulses in animals of over 300g body wt. showed the presence of high-specific-radioactivity DNA in released core particles and mononucleosomes compared with DNA retained in the nuclear pellets. Mononucleosomes from rat livers in S-phase with new, [(3)H]lysine-containing histones, had higher (32)P incorporation in histones H1 and their core histones, than for di- or tri-nucleosomes. Thermal-denaturation properties of control and phosphorylated mononucleosomes and core particles were very similar; removal of histone H1 and non-histone chromosomal proteins in 0.5m-NaCl markedly increased the proportion of DNA ;melting' below 70 degrees C.

Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones

In this paper we describe a detailed investigation of the reconstitution of nucleosome cores from poly (dA-dT) and the octamer of histones. We also attempted the reconstitution from the copolymers poly dA.poly dT, poly dG.poly dC and poly (dG-dC). The repeat of the reconstituted chromatin fibre is discussed. The micrococcal nuclease released poly (dA-dT) core particle is found to contain a considerably narrower DNA size distribution that of the native random DNA nucleosome core (12). In addition we have succeeded in obtaining small crystals of the poly (dA-dT) nucleosome core. The DNAase I digestion pattern of the poly (dA-dT) containing nucleosome core is presented. The periodicity of DNAase I cutting sites is found to be about 10.5 bases and is similar to that of the native nucleosome core (12, 13).

Nucleosome packing in chromatin as revealed by nuclease digestion

Chromatin DNA of rat thymus nuclei was cleaved by Serratia marcescens endonculease. The fragments have been examined by polyacrylamide gel electrophoresis under denaturing conditions. The results obtained are interpreted to mean that the internucleosomal DNA is cleaved by the endonuclease into fragments which are multiples of 10 nucleotides. The 10 nucleotide periodicity in fragmentation of internucleosomal DNA is independent of the presence of histone H1 and is likely to be determined by the interaction of this DNA stretch with the histone core of nucleosomes. Such interaction implies a close association between the nucleosomes in the chromatin thread. Quasi-limit chromatin digest (50--55% of DNA hydrolysis) contains undegraded DNA fragments with length of up to 1000 nucleotides or more. A part of this resistant DNA consists of single-stranded fragments or contains single stranded regions. These data may be accounted for by a very compact nucleosome packing in the resistant chromatin in which one of the DNA stands is more accessible to the endonuclease action.

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.

Digestion of chromosomal proteins in formaldehyde treated chromatin

Treatment of chromatin subunits (nucleosome monomers) with formaldehyde results in the formation of cross-links between DNA and histones and between histones and histones. Digestion of chromosomal proteins with proteinase K does not lower the protein/DNA weight ratio below 0.08 to 0.1 as determined by cesium chloride gradient centrifugation of the digestion product from formaldehyde-treated nucleosomes. In addition to proteinase K, formaldehyde-treated nucleosomes were tested for accessibility to trypsin and pronase. The CsCl gradient patterns show, that pronase digestion and proteinase K treatment yield similar results. Trypsin treatment of control and formaldehyde-treated nucleosomes shows, that the sites which are accessible for trypsin in native nucleosomes, are blocked after formaldehyde treatment. Analysis of the CsCl gradient peak fractions in polyacrylamide gels shows, that the reliability of DNA fragment size determinations depends on the completeness of deproteinization.