Nuclease cleavage of chromatin at 100-nucleotide pair intervals

A new way to visualize DNA's base succession: the Caenorhabditis elegans chromosome landscapes

In the eukaryotic genomes, the genetic diseases are generally associated with the tandem repeats. These repeats seem to appear frequently. In this paper, we are describing a wavelet transform technique which provides a new way to represent the DNA succession bases as a DNA progression images. These images offer DNA landscapes, visualizing and following up periodicities through genomes. We investigated in a structural coding technique the Pnuc. Then, we illustrated, with time-frequency representation, the existence and the superposition of the periodicities in some biological features, their locations and the different ways in which they appear. The representations generated showed that one periodicity can sometimes be alone, but generally, it is incorporated to others. These periodicities associations create, in the Caenorhabditis elegans chromosome, a precise structural image of biological features, such as CeRep, Helitrons, repeats and satellites.

The nucleosome family: dynamic and growing

Ever since the discovery of the nucleosome in 1974, scientists have stumbled upon discrete particles in which DNA is wrapped around histone complexes of different stoichiometries: octasomes, hexasomes, tetrasomes, "split" half-nucleosomes, and, recently, bona fide hemisomes. Do all these particles exist in vivo? Under what conditions? What is their physiological significance in the complex DNA transactions in the eukaryotic nucleus? What are their dynamics? This review summarizes research spanning more than three decades and provides a new meaning to the term "nucleosome." The nucleosome can no longer be viewed as a single static entity: rather, it is a family of particles differing in their structural and dynamic properties, leading to different functionalities.

The controversial 30 nm chromatin fibre

DNA is packed as chromatin on several levels in the eukaryotic nucleus. Dissection of chromatin with nucleases produces three stable substructures: the nucleosome core particle, the chromatosome and the 30 nm fibre. Whilst the first two allow transcription, the 30 nm fibre is taken to be the first level of transcriptionally dormant chromatin and it has an important functional role in cell differentiation and epigenetic regulation. Its structure has been a subject of continuing discussion since native fibres cannot readily be crystallized. This problem has recently been addressed by reconstitution of fibres on repeats of DNA sequences having nucleosome-positioning properties and two different structures were reported. The reconstitution results and their interpretations are compared in this review with experimental data from native chromatin and it is shown that the results of Robinson et al. conform well with the known structural features of native fibres and are a good first step towards understanding the structure of the fibre.

DNase I digestion reveals alternating asymmetrical protection of the nucleosome by the higher order chromatin structure

DNase I was used to probe the higher order chromatin structure in whole nuclei. The digestion profiles obtained were the result of single-stranded cuts and were independent of pH, type of divalent ion and chromatin repeat length. Furthermore, the protection from digestion of the DNA at the entry/exit points on the nucleosome was found to be caused not by the H1/H5 histone tails, but by the compact structure that these proteins support. In order to resolve symmetry ambiguities, DNase I digestion fragments over several nucleosome repeat lengths were analysed quantitatively and compared with computer simulations using combinations of the experimentally obtained rate constants (some of which were converted to 0 to simulate steric protection from DNase I digestion). A clear picture of precisely defined, alternating, asymmetrically protected nucleosomes emerged. The linker DNA is inside the fibre, while the nucleosomes are positioned above and below a helical path and/or with alternating orientation towards the dyad axis. The dinucleosomal modulation of the digestion patterns comes from alternate protection of cutting sites inside the nucleosome and not from alternating exposure to the enzyme of the linker DNA.

Quantitative analysis of DNase I digestion patterns of oligo- and polynucleosomes

DNase I digestion of unlabelled chromatin has been used to determine the orientation of nucleosomes in the higher-order structure of chromatin. DNA digestion patterns were analysed quantitatively and compared with simulation curves that were generated with the experimentally obtained rate constants for cutting inside nucleosomes and the half-height widths of the bands. The rate constants for cutting at the linker DNA were varied to fit the experimental curves. By comparing the digestion profiles of polynucleosomes, oligonucleosomes and H1/H5-depleted oligonucleosomes we have been able to distinguish between protection caused by H1/H5 histones only and protection caused by the higher-order structure. By the nature of this method the area protected by H1/H5 histones appears symmetrical around the centre of the nucleosomal DNA on the dyad axis (position S[0]), but it can also be interpreted as a superposition of two separate protected areas that are symmetrical around position S[0]. Protection by the higher-order structure shows that the nucleosomes are oriented with their S[0] positions inside the 30 nm fibre and that there is a minimum number of nucleosomes required for this structure to be formed. We have also found that the linker DNA is cut in a continuous (non-periodical) way and that there are considerable amounts of nucleosomes at discrete distances of multiples of ten nucleotides (10a nt) as well as stretches of nucleosomes positioned either at random or at distances of (10a + 5)nt.

Condensation of rat telomere-specific nucleosomal arrays containing unusually short DNA repeats and histone H1

Vertebrate telomeres contain arrays of nucleosomes with unusually short and regular repeat lengths (Makarov, V. L., Lejnine, S., Bedoyan, J., and Langmore, J. P.(1993) Cell 73, 775-787; Lejnine, S., Makarov, V., and Langmore, J. P. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 2393-2397). In order to better define the specific structural features of telomere chromatin, we examined the condensation and H1 content of telomere nucleoproteins from rat liver. Velocity sedimentation analysis shows that telomeric nucleosome arrays condense with increasing ionic strength and molecular weight in a manner comparable with that of bulk chromatin despite the very short repeat length. However, these condensed structures do not exhibit the approximately 100-base pair deoxyribonuclease II repeat characteristic of condensed bulk chromatin. Frictional coefficient calculations suggest that telomere-specific higher order structure is more compact than bulk chromatin. Nucleoprotein gel electrophoresis shows that telomeric dinucleosomes from soluble chromatin contain H1. Finally, direct isolation and analysis of telomere nucleoproteins from formaldehyde-cross-linked nuclei indicate the presence of core histone proteins and H1. These results are consistent with the view that a major fraction of the long telomeres of rat are organized as specialized nucleosome arrays with features similar but not identical to those of bulk chromatin.

A novel magnesium-dependent structural transition of chicken erythrocyte chromatin in situ

Lowering magnesium concentration below the value of 1 mM leads to a structural transition of chicken erythrocyte chromatin in situ, which results in a change in its fragmentation by pancreatic DNAase (DNAase I) from double-nucleosome to 100-basepairs mode. At 0.75 mM MgCl2, the pattern of chromatin fragmentation by DNAase I is similar to that generated by DNAase II, and it is further changed at lower concentrations of magnesium. This transition is, at least partly, reversible, and is, presumably, related to packing of the 25-30 nm chromatin fiber into higher-order structures.

Nuclease digestion patterns as a criterion for nucleosome orientation in the higher order structure of chromatin

Nuclease digestion patterns have been used to discriminate between possible orientations of nucleosomes in the higher order structure of chromatin. Computer simulations were done assuming 3 basically different orientations of nucleosomes which include all proposed models for the '30 nm fibre'. It is found that only alternating exposure of consecutive nucleosomes can explain the DNase I and DNase II digestion patterns.

Higher order chromatin structure determines double-nucleosome periodicity of DNA fragmentation

Double-nucleosome periodicity of DNA fragmentation with DNAse I in the nuclei of cells differing in size of the linker DNA length and lysine-rich histone composition was analyzed by means of nondenaturing agarose gel electrophoresis. DNAse I revealed this type of periodicity in rat thymus and CHO cell nuclei as well as in erythrocyte nuclei. It has been deduced that the so-called nucleodisome structure is also typical of cells possessing a usual DNA repeat length (200 bp or less) and lysine-rich histone H1. Two probably related events are important for establishing a clear double-nucleosome periodicity of DNA fragmentation: the replacement of H1 histone by a specific arginine-rich histone fraction (H5 histone in the case of erythrocyte) and the increase of the linker DNA length. The results are interpreted in terms of supranucleosomal organization of chromatin which may determine the dinucleosome periodicity of DNA fragmentation due to a specific packing of nucleosomes.

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.

DNA-histone interactions in nucleosomes

We have utilized micrococcal nuclease digestion and thermal denaturation studies to investigate the binding of DNA to the histone core of the nucleosome. We conclude that a total of approximately 168 base pairs (bp) of DNA can interact with the histone core under appropriate solution conditions, even in the absence of lysine-rich histones. The interactions in this total length of DNA can be divided into three classes: (a) approximately 22 bp at the ends is bound only at moderate ionic strength. It is easily displaced, and its removal yields the 146 bp core particle. (b) approximately 46 bp near the ends of the core DNA are quite weakly bound to the core, and are displaced at quite moderate temperatures. (c) The remaining central 100 bp are strongly bound, and interact with all of the sites on the histones which strongly protect DNA against DNAse I digestion. A theoretical analysis of the cleavage of nucleosomal DNA by DNAse I has been used to develop evidence that the pattern of protection offered by the histone core is very similar in nuclei to that in isolated core particles.

Deoxyribonuclease I generates single-stranded gaps in chromatin deoxyribonucleic acid

Production of 10-base multiple DNA ladder fragments during DNase I digestion of chromatin is explained by a model which does not involve site-specific nicking by the DNase I. This model was tested because it explains why 10-base (actually 10.4 base) multiple-related fragments are paradoxically generated by both endonucleolytic (DNase I) and exonucleolytic (exonuclease III) mechanisms. This new model also explains the phenomenon of substantial single-stranded DNA production during DNase I digestion of chromatin. The latter phenomenon has been widely observed but is not explained by previous models. The single-stranded gap model to be presented makes testable predictions. Primarily, these are that DNase I produces single-stranded gaps in chromatin DNA and that the termini of 10-base multiple ladder fragments are separated by single-stranded gaps. Single-stranded gap production by DNase I was confirmed by a number of methods. Sensitivity of ladder band components (from DNase I but not staphylococcal nuclease digests) to S1 nuclease suggested that the ladder fragments themselves may compose a significant portion of these gaps. Separation of ladder fragment termini by single-stranded gaps was verified by demonstrating both resistance to the nick-specific NAD+-dependent ligase and sensitivity to T4 ligase which can ligate across gaps. Many single-stranded gaps, occurring both individually and clusters, were observed by electron microscopy using either cytochrome c labeling (where the gaps) are thinner than duplex) or gene 32 protein labeling (gaps thicker than duplex). Gap sizes were estimated by protecting them with gene 32 protein and digesting away unprotected duplexes. By this method, gap sizes fall into a ladder distribution (from 10 or 20 bases up to 120 bases), which, at least in the region of the shorter sizes, clearly indicates the sizes of single-stranded gaps formed in chromatin by DNase I.

High-resolution fractionation of nucleosomes: minor particles, "whiskers," and separation of mononucleosomes containing and lacking A24 semihistone

Staphyloccal nuclease digests of HeLa chromatin fractionated on low ionic strength nucleoprotein gels have been further analyzed by second-dimension DNA and protein gel electrophoresis. In vivo radioactive labeling of chromatin components and use of longer gels allowed a higher sensitivity and resolution than has been previously reported for this approach. A number of nonhistone protein spots and about 20 DNA spots can be detected in the mononucleosomal region of the second-dimension gel. In particular, there are three DNA spots identical in DNA size that correspond to three discrete kinds of core mononucleosomes resolved on the first-dimension nucleoprotein gel. Analysis of protein composition shows that the most rapidly migrating particle contains all four core histones but no A24 semihistone (A24 is a covalent conjugate of histone H2A and a specific nonhistone protein, ubiquitin), whereas the other two core mononucleosomes contain A24 semihistone. Thus, one can now quantitatively separate the A24-lacking core mononucleosomes from those containing A24, making it possible to directly address the question of whether A24 is associated with nucleosomes containing a specific subset of DNA sequences. Additional features of two-dimensional nucleoprotein-DNA patterns are "whiskers," which run slower than core mononucleosomes in the nucleoprotein dimension and both faster and slower than core-length DNA in the DNA dimension. In more extensive digests, "secondary whiskers" are observed, which run faster than core mononucleosomes in both dimensions and appear to coincide with previously described subnucleosomal particles SN7 and SN8 [Bakayev, V., Bakayeva, T. & Varshavsky, A. (1977) Cell 11, 619-629]. Possible mechanisms of whisker formation are discussed.

Evidence for the formation of nucleosome-like histone complexes on single-stranded DNA

Using histones reconstituted with RNA and DNA celluloses, we have shown elsewhere that histones elute identically with salt from single- and double-stranded DNA, but differently from RNA (Palter and Alberts, 1979). In this paper we characterize further the suspected specific binding interactions between histones and single-stranded DNA. Nuclease digestion of complexes of histone reconstituted with single-stranded DNA generates only a small yield of discrete (approximately 9S) particles. We can, however, efficiently obtain such 9S "nucleosome-like" complexes when nuclease treatment is avoided and histones are reconstituted directly with short single-stranded DNA pieces. Strikingly, these 9S subunits contain an equimolar composition of the four nucleosomal histones. When these subunits are visualized in the electron microscope, they appear as globular particles which are morphologically indistinguishable from normal mononucleosomes. Based on their sedimentation properties, histone-to-DNA ratio, histone composition and particle diameter, we conclude that they represent an octamer of the four histones (containing two molecules of each histone) associated with single-stranded DNA. These data, viewed in the context of other information concerning chromatin, suggest that nucleosome cores may become transiently bound to single strands of DNA as DNA and RNA polymerases pass.

Binding of antibodies against histone H1 to unfolded and folded nucleofilaments

Rabbit antibodies to calf thymus histone H1 were purified by affinity chromatography on histone-H1--Sepharose and used as a probe for detecting histone H1 in the nucleofilaments prepared from rat liver nuclei. Binding of the antibodies to the unfolded form of nucleofilaments in 5 mM NaC1 and to the folded form in 80 mM NaC1 Was compared. Sucrose density gradient analyses clearly show that the antibodies can preferentially bind to nucleofilaments in 5 mM NaC1 but not in 80 mM NaC1. The antibodies, however, can bind to mononucleosomes in 80 mM NaC1. These results suggest that antigenic determinants of histone H1 in unfolded nucleofilaments and in mononucleosomes are accessible to the antibodies, while those in folded nucleofilaments are not. This is consistent with the view that histone H1 is used for folding and packing of a nucleosomal chain.

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.

Chromatin structure through the cell cycle. Studies with regeneration rat liver

Liver nuclei were prepared through the first cell cycle in partially hepatectomized young rats showing 30% parenchymal cell synchrony. To determine if nucleosome structure altered during this period, liver nuclei from sham-operated rats were compared with nuclei isolated at various times after partial hepatectomy. These nuclei were exposed to deoxyribonuclease I (EC 3.1.4.5), deoxyribonuclease II (EC 3.1.4.6) or micrococcal nuclease (EC 3.1.4.7) and the nucleosome-associated DNA length was ascertained. In no case was a difference in the DNA lengths associated with nucleosome structure observed. Differences were observed with regard to the histones and their relative association with nuclear material. When nuclei from normal rat livers were incubated in hypo-osmolar medium 9% of histone 1 and 4% of the other histones were released. These released histones, unlike those remaining bound to the nuclei, showed high [3H]adenosine and [3H]acetate uptakes in vivo. [32P]P1 uptake was also much greater into released than bound histones 1 and 3, but was not different for histone2A. At 3.5-4.5 h after partial hepatectomy, the release of histone 1 was trebled and that of histone 4 doubled. By 13.5 h, when phosphorylation of the bound forms of histones 2A and especially 1 was increased, no further changes in histone release in hypo-osmolar medium were found. The released histones from partially hepatectomized livers had indistinguishable [3H]adenosine uptakes from controls. The roles are discussed of phosphorylation and ADP-ribosylation in labilizing histone binding.

Estrogen receptor in hen oviduct chromatin, digested by micrococcal nuclease

Nuclei from laying hen oviduct were prepared according to Hewish and Burgoyne i.e. in the presence of spermine and spermidine and in the absence of divalent cations and were then moderately digested by micrococcal nuclease. When the resulting chromatin was analysed by ultracentrifugation on a sucrose gradient, a peak of specific estradiol-binding sites was observed, sedimenting slightly faster (13-14 S) than the mononucleosomes (12 S). When the chromatin was centrifuged on a gradient containing heparin (5 microngram/ml) the sedimentation coefficient of the estradiol receptor peak shifted to 7-8 S; it returned to the 13-14 S position in the absence of heparin, when target organ chromatin was also present in the gradient. The preparation of the chromatin is described and the validity of the method to explore receptor localisation is discussed, as is the specificity of the receptor-DNA interaction.

Nucleosomal DNA is digested to repeats of 10 bases by exonuclease III

Nucleosomes were treated with increasing concentrations of exonuclease III (Exo III) from E. coli. At low levels of Exo III, the heterogeneous distribution of monomers (with associated DNA fragments ranging in size between 140 and 170 bp) is "trimmed" down to a discrete core of 140 bp. The "trimming" of monomers to 140 bp results from a 3' exonucleolytic digestion accompanied by a 5' clipping activity which is specific for the conformation of internucleosomal DNA. At higher concentrations of Exo III, the enzyme digests the 140 bp "trimmed" nucleosome core from both 3' ends without associated 5' nuclease activity. Most striking is the observation that the fragments produced during such a digestion display discrete single-stranded lengths that are integer multiples of 10 bases. For some dimer nucleosomes, Exo III can digest as many as 200 bases from at least one 3' end and produce a 10 base interval ladder from about 400 bases down to 180 bases. This suggests that the enzyme can traverse the length of an entire nucleosome without destroying whatever structural features are necessary to produce a 10 base DNA ladder.

Closely spaced nucleosome cores in reconstituted histone.DNA complexes and histone-H1-depleted chromatin

It has been demonstrated by digestion studies with micrococcal nuclease that reconstitution of complexes from DNA and a mixture of the four small calf thymus histones H2A, H2B, H3, and H4 leads to subunits closely spaced in a 137 +/- 7-nucleotide-pair register. Subunits isolated from the reconstituted complex contain nearly equimolar amounts of the four histones and sediment at 11.6S. On DNase I digestion both the reconstituted complex and the separated subunits gave rise to series of single-stranded DNA fragments with a 10-nucleotide periodicity. This indicates that the reconstitution leads to subunits very similar to nucleosome cores. Nucleosome cores closely spaced in a 140-nucleotide-pair register were also obtained upon removal of histone H1 from chromatin by dissociation with 0.63 M NaCl and subsequent ultracentrifugation. In reconstitution experiments with all five histones (including histone H1) our procedure did not lead to tandemly arranged nucleosomes containing about 200 nucleotide pairs of DNA. In the presence of EDTA, DNase II cleaved calf thymus nuclei and chromatin at about 200-nucleotide-pair intervals whereas in the presence of Mg2+ cleavage at intervals of approximately half this size was observed. The change in the nature of the cleavage pattern, however, was no longer found after removal of histone H1 from chromatin. This indicates that H1 influences the accessibility of DNase II cleavage sites in chromatin. This finding is discussed with respect to the influence of histone H1 on chromatin superstructure.

Chromatin

The approximate shape of the chromatin subunit called the nucleosome is now known, but its internal architecture is not well understood. Recent studies reveal details of the organisation of DNA within the nucleosome, and show that the arginine-rich histones are essential to DNA folding. Nucleosomes or structures related to them seem to be present at points of DNA replication and transcription; interactions within and between nucleosomes are likely to play a critical part in these processes.

Subunit associations among chromatin particles

The self-association of oligonucleosomal chromatin particles in solution has been studied by light scattering and sedimentation. In the absence of magnesium ions no association is observed. In the presence of 70mM sodium or 2mM magnesium ions mono, di, tri and tetranucleosomes self-associate only if they contain bound histone 1. This association leads to the formation of compact aggregates and is continuous and non-cooperative. The relevance to higher order arrangements of nucleosomes is discussed.