Nuclease digestion in between and within nucleosomes

Dynamics of modeled oligonucleosomes and the role of histone variant proteins in nucleosome organization

Elucidation of the structural dynamics of a nucleosome is of primary importance for understanding the molecular mechanisms that control the nucleosomal positioning. The presence of variant histone proteins in the nucleosome core raises the functional diversity of the nucleosomes in gene regulation and has the profound epigenetic consequences of great importance for understanding the fundamental issues like the assembly of variant nucleosomes, chromatin remodeling, histone posttranslational modifications, etc. Here, we report our observation of the dominant mechanisms of relaxation motions of the oligonucleosomes such as dimer, trimer, and tetramer (in the beads on a string model) with conventional core histones and role of variant histone H2A.Z in the chromatin dynamics using normal mode analysis. Analysis of the directionality of the global dynamics of the oligonucleosome reveals (i) the in-planar stretching as well as out-of-planar bending motions as the relaxation mechanisms of the oligonucleosome and (ii) the freedom of the individual nucleosome in expressing the combination of the above-mentioned motions as the global mode of dynamics. The highly dynamic N-termini of H3 and (H2A.Z-H2B) dimer evidence their participation in the transcriptionally active state. The key role of variant H2A.Z histone as a major source of vibrant motions via weaker intra- and intermolecular correlations is emphasized in this chapter.

Herpes simplex virus 1 DNA is in unstable nucleosomes throughout the lytic infection cycle, and the instability of the nucleosomes is independent of DNA replication

Herpes simplex virus 1 (HSV-1) DNA is chromatinized during latency and consequently regularly digested by micrococcal nuclease (MCN) to nucleosome-size fragments. In contrast, MCN digests HSV-1 DNA in lytically infected cells to mostly heterogeneous sizes. Yet HSV-1 DNA coimmunoprecipitates with histones during lytic infections. We have shown that at 5 h postinfection, most nuclear HSV-1 DNA is in particularly unstable nucleoprotein complexes and consequently is more accessible to MCN than DNA in cellular chromatin. HSV-1 DNA was quantitatively recovered at this time in complexes with the biophysical properties of mono- to polynucleosomes following a modified MCN digestion developed to detect potential unstable intermediates. We proposed that most HSV-1 DNA is in unstable nucleosome-like complexes during lytic infections. Physiologically, nucleosome assembly typically associates with DNA replication, although DNA replication transiently disrupts nucleosomes. It therefore remained unclear whether the instability of the HSV-1 nucleoprotein complexes was related to the ongoing viral DNA replication. Here we tested whether HSV-1 DNA is in unstable nucleosome-like complexes before, during, or after the peak of viral DNA replication or when HSV-1 DNA replication is inhibited. HSV-1 DNA was quantitatively recovered in complexes fractionating as mono- to polynucleosomes from nuclei harvested at 2, 5, 7, or 9 h after infection, even if viral DNA replication was inhibited. Therefore, most HSV-1 DNA is in unstable nucleosome-like complexes throughout the lytic replication cycle, and the instability of these complexes is surprisingly independent of HSV-1 DNA replication. The specific accessibility of nuclear HSV-1 DNA, however, varied at different times after infection.

Native chromatin immunoprecipitation

Native chromatin immunoprecipitation refers to a method that allows for identification and quantification of DNA that is associated with specific chromatin proteins without altering the structure of these proteins. The method has been used with great success in the past and has some advantages over the more widely used cross-linking chromatin immunoprecipitation. We describe here a protocol that was specifically optimized for low cell numbers.

During lytic infections, herpes simplex virus type 1 DNA is in complexes with the properties of unstable nucleosomes

The genomes of herpes simplex virus type 1 (HSV-1) are regularly chromatinized during latency such that their digestion with micrococcal nuclease (MCN) releases nucleosome-sized DNA fragments. In lytically infected cells, in contrast, MCN releases HSV-1 DNA in primarily heterogeneously sized fragments. Consistently, only a small percentage of this HSV-1 DNA coimmunoprecipitates with histones. Most current models propose that histones associate with HSV-1 DNA during lytic infections at low occupancy. However, histone modification or occupation is also proposed to regulate HSV-1 transcription. It remains unclear how the histones associated with a small percentage of HSV-1 DNA may regulate transcription globally. Moreover, the physical properties of the complexes containing histones and HSV-1 DNA are unknown. We evaluated the HSV-1 DNA-containing complexes at 5 h after (lytic) infection by biochemical fractionations. Nuclear HSV-1 DNA did not fractionate as protein-free HSV-1 DNA but as DNA in cellular nucleosomes. Moreover, MCN released HSV-1 DNA in complexes that fractionate as cellular mono- and dinucleosomes by centrifugation followed by sucrose gradients and size-exclusion chromatography. The HSV-1 DNA in such complexes was protected to heterogeneous sizes and was more accessible to MCN than DNA in most cellular chromatin. Using a modified MCN digestion to trap unstable digestion intermediates, HSV-1 DNA was quantitatively recovered in discrete mono- to polynucleosome sizes in complexes fractionating as cellular mono- to polynucleosomes. The HSV-1 DNAs in complexes fractionating as mono- to dinucleosomes were stabilized by cross-linking. Therefore, most HSV-1 DNA forms particularly unstable nucleosome-like complexes at 5 h of lytic infection.

Role of chromatin states in transcriptional memory

Establishment of cellular memory and its faithful propagation is critical for successful development of multicellular organisms. As pluripotent cells differentiate, choices in cell fate are inherited and maintained by their progeny throughout the lifetime of the organism. A major factor in this process is the epigenetic inheritance of specific transcriptional states or transcriptional memory. In this review, we discuss chromatin transitions and mechanisms by which they are inherited by subsequent generations. We also discuss illuminating cases of cellular memory in budding yeast and evaluate whether transcriptional memory in yeast is nuclear or cytoplasmically inherited.

Structural organization of satellite I chromatin of calf liver

The organization of liver calf satellite DNA I chromatin has been studied. Precisely seven nucleosomes per DNA satellite repeat (1.4 kb) are shown to be present. Several strict positionings of the nucleosomes along the satellite DNA repeat have been described. One of these positionings, the major phase, was shown to be preferentially organized in clustered repeats. Most of the non-methylated CpG restriction sites were shown to be located in the linker DNAs of the satellite I nucleosomes, whilst, accordingly, methylated HpaII sites were found in the core satellite I DNA. The significance of these results is discussed.

Temperature-dependent cleavage of chromatin by micrococcal nuclease near the nucleosome center

Digestion of nuclei at 4 degrees C with micrococcal nuclease results in significant intranucleosomal cleavage compared to digestion conducted at 37 degrees C. Employing nucleoprotein gel electrophoresis in one dimension followed by DNA electrophoresis in a second dimension, we demonstrate that such temperature-sensitive, internal cleavage predominantly occurs about 20 bp from the nucleosome center. We suggest that lower temperatures reduce the stability of hydrophobic interactions within the histone octamer and lead to a conformational alteration in nucleosomes that is detected by micrococcal nuclease.

Positioning of nucleosomes in satellite I-containing chromatin of rat liver

The location of nucleosomes on rat satellite I DNA has been investigated using a new approach. Nucleosome cores were prepared from rat liver nuclei with micrococcal nuclease, exonuclease III and nucleases S1. From the total population of core DNA fragments the satellite-containing fragments were isolated by molecular cloning and the complete sequence of 50 clones was determined. The location of nucleosomes along the satellite sequence was found to be non-random. Our results show that nucleosomes occupy a number of positions on satellite I DNA. About 35 to 50% of all nucleosomes are positioned in two corresponding major sites, the remainder in about 16 less preferred sites. The major nucleosome positions are apparently strictly defined with the precision of a single base-pair. These results were confirmed by other approaches, including restriction nuclease digestion experiments. There are good indications of a defined long-range organization of the satellite chromatin fiber in two or more oligonucleosomal arrays with distinct nucleosome configurations.

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.

Deoxyribonuclease II as a probe to sequence-specific chromatin organization: preferential cleavage in the 72 bp modulator sequence of SV40 minichromosome

T prove sequence-specific chromatin structure of SV40 minichromosome, we further modified previously described hybridization mapping. Actually (i) the digestion patterns by two nucleases (micrococcal and DNAase II) were compared and (ii) the kinetics of nuclease digestion was analyzed from early time points when only a fraction of minichromosomes was cleaved once to longer digestions when oligo- and mononucleosomal bands appeared. DNAase II is shown to possess certain sequence specificity different from that of micrococcal nuclease. The major finding is that DNAase II preferentially cleaves the SV40 minichromosome at a distinct region of the genome known as 72 bp modulator element. Other hypersensitive sites are located near the replication origin and T-ag binding site II and also near BamHI site where termination of replication and "late" transcription occurs. Micrococcal nuclease splits the BglI-Hpaii region in a different manner.

Partitioning of zinc and copper within subnuclear nucleoprotein particles

Nuclei from frozen calf thymus suspended in buffer were analyzed for metal content prior to and after repeated washing. After three such extractions about 0.1 micrograms Zn/mg DNA and 0.025 micrograms Cu/mg DNA remained tightly associated with chromatin. This level of metal was essentially unchanged with subsequent washings. Digestion of extracted nuclei with micrococcal nuclease yielded soluble nucleoprotein containing zinc and copper. Metal enriched regions of chromatin appeared to be preferentially solubilized by digestion, and the solubilized metal was only partially dializable either with or without EDTA. Metal profiles generated from gel (A-5m) chromatography analysis of chelated and non-chelated solubilized chromatin were distinctive in that copper was undetectable (by flame AA) while zinc was associated only with low molecular weight products when EDTA was used. In contrast, both metals were detected with higher molecular weight oligonucleosomes in the absence of chelating agents. Additionally, the two metals localized within nucleoprotein peaks and these metal-containing regions were only resolved by gel chromatography when EDTA was omitted throughout the procedure. A discrete Cu-rich species in a region of the profile suggests a subset of Cu-rich nucleoprotein complexes.

Different repeat lengths in rat satellite I DNA containing chromatin and bulk chromatin

The nucleosome repeat structure of a rat liver chromatin component containing the satellite I DNA (repeat length 370 bp) was investigated. Digestion experiments with micrococcal nuclease, DNAase II, and the Ca2+/Mg2+-dependent endogenous nuclease of rat liver nuclei revealed a repeat unit of 185 nucleotide pairs which is shorter by approximately 10 bp than the repeat unit of the bulk chromatin of this cell type. The difference seems not to be related to the histone composition which was found to be similar in the two types of chromatin.

Nucleosomes structure and its dynamic transitions

The discovery of nucleosomes as a basic repeating unit of the chromatin structure organizing the major part of eukaryotic DNA greatly catalyzes the expansion of our knowledge on chromatin. Several lines of experimental evidence have led to the formulation of the nucleosome conception: the observation of chains of globular particles in electron micrographs of chromatin (Olins & Olins, 1974); the demonstration that DNA is released as a set of discrete sizes upon digestion of chromatin with endogenous nucleases (Hewish & Burgoyne, 1973); the isolation of discrete nucleoprotein particles upon digestion of chromatin with micrococcal nuclease (Rill & Van Holde, 1973).

The non-histone proteins of the rat liver nucleus and their distribution amongst chromatin fractions as produced by nuclease digestion

The search for proteins involved in maintaining higher order chromatin structures has led to a systematic examination of the non-histone proteins (NHP) of rat liver nuclei in the context of nuclease digestion studies. 40-45% of the 3H-tryptophan labelled NHP originally present could be removed by extensive washing in a "physiological" buffer, incubation at 37 degrees C with or without nuclease and a further wash step. Nuclei at this stage had a remarkably constant NHP content (ca. 0.73 micrograms/micrograms DNA), independent of the degree of digestion with micrococcal nuclease or HaeIII. The solubilized chromatin produced by limited digestion with either nuclease contained 0.3-0.5 microgram NHP/microgram DNA, this value falling to ca. 0.16 after more extensive cleavage. Insoluble chromatin fractions were between 2-fold (very limited digestion) and 16-fold (extensive digestion) richer in NHP than the corresponding soluble fractions. Gel electrophoresis revealed about 12 NHP bands in soluble fractions, the most prominent of M.Wt. 41.400, while the insoluble material had at least 50 components. These properties were independent of whether lysis of nuclei occurred in 0.2 or 50 mM ionic strength. The large disparity in NHP content between complementary soluble and insoluble chromatin fractions is considered in terms of chromatin organization in vivo and the possible role of NHP migration.

Cations and the accessibility of chromatin to nucleases

When rat liver nuclei prepared with polyamines as stabilising cations are digested with DNAase II, release of both inactive chromatin and Mg-soluble, active chromatin is greatly reduced, in comparison to digestion of liver nuclei prepared with Mg2+ as stabilising cation. Chromatin release from polyamine stabilised nuclei is also inhibited relative to Mg-stabilised nuclei following digestion with micrococcal nuclease under two very different cation conditions. Nuclei prepared with polyamines and monovalent ions as stabilising cations exhibit properties intermediate between these two extremes with both nucleases. These effects are due to residual binding of polyamines to chromatin, which is thus maintained in a condensed state, inaccessible to nucleases. Since polyamine binding is not easily reversed, concentrations of polyamines and other cations must be rigidly controlled in experiments on chromatin structure if artefacts are to be avoided. The significance of these findings to the nature and properties of active chromatin within the intact nucleus is considered.

Characterization of restriction nuclease prepared chromatin by electron microscopy

Chromatin was solubilized from rat liver nuclei by digestion with the restriction nuclease EcoRI or HaeIII in the presence or absence of EDTA and sodium chloride. The samples were investigated by electron microscopy after positive and negative staining with uranyl acetate under a number of conditions. Depending on the salt concentration during solubilization the chromatin appeared as beads on the string or in more compact form. Solenoid- and superbead-like structures were seen as had been reported for chromatin solubilized with micrococcal nuclease.

Subunit structure of Eutherian sperm chromatin

The beta-mercaptoethanol induced decondensation of spermatozoon cell nuclei from several Eutherian species has been followed from the intact spermatazoon cell to the solubilized linear unit sperm chromosomal fiber using fluorescence and electron microscopy. Data from nuclease digestion studies in conjunction with electron microscopic evidence indicate that the gross structure of the unit Eutherian sperm chromosomal fiber consists of DNA folded around sperm specific histone multimers spaced regularly along the fiber generating a linear array of sperm nucleosomes connected by short stretches of uncomplexed DNA. The sperm nucleosomes, 80 A in diameter are separated by 20 A filaments of DNA. This structure is remarkably similar to the structure of somatic chromatin although the protein components of the two chromosomes are markedly different. It seems likely that chromosomal fibers, similar to those described herein, may be present in the male pronucleus following fertilization.

Nucleosome mono, di, tri-, and tetramers from chicken embryo chromatin

The fractionation of gram quantities of nuclease digested chromatin from chicken embryos into nucleosome mono-, di-, tri-, and tetramers is described in detail. Each of these nucleosomal species contains a fraction soluble in 0-1 M KC1 that decreases with increasing repeat number. Less histone H1 is associated with the nucleosome fractions soluble as compared to the respective fractions precipitated in 0.1 M KC1. Thermal denaturation profiles of the four nucleosomal species are monophasic. The same Tm of 78 degrees C has been determined for the KC1-soluble nucleosomes and for the KC1-insoluble monomer. The Tm of the KC1-insoluble oligomers is 79.8 degrees C. Multiphasic melting curves were recorded for nucleosomal material that was concentrated by lyophilisation or stored at 4 degrees C in 0.25 mM EDTA. Total nucleosome mono-, di-, tri-, and tetramers (consisting of both the fraction soluble and insoluble in 0.1 M KC1) have been analyzed concerning their sedimentation, diffusion, partial specific volume, and molecular weight and compared with the sedimentation and molecular weight data of KC1-soluble nucleosome mono- and tetramers.

Compact form of SV40 viral minichromosome is resistant to nuclease: possible implications for chromatin structure

We report two new findings bearing on the "supranucleo-somal" level of the structure of the Simian Virus 40 minichromosome. I) Isolated SV40 minichromosome which contains all five histones including HI/I/ exists in solution under approximately physiological ionic conditions as a compact roughly spherical particle approximately 300 A in diameter which is capable of fitting within the virus capsid. In spite of such a compact conformation of the minichromosome individual nucleosomes can be readily visualized within the particle. Compact state of SV40 minichromosome depends on both the presence of histone HI and maintenance of approximately physiological ionic strength of solution (micron approximately 0.15). Removal of HI results in a conversion of the compact minichromosomes into an extended (circular beaded) structure. 2) The compact form of the SV40 minichromosome in contract to its circular beaded form is virtually completely resistant to staphylococcal nuclease, strongly suggesting that in particular nuclease-sensitive parts of the internucleosomal DNA regions are not exposed on the outside of the compact SV40 minichromosome. On the other hand, DNase I which is known to attack both inter-and intranucleosomal DNA in the chronatin /2,3/ readily digests the compact form of the SV40 minichromosome. Possible models of the compact minichromosome and implications for higher order structures of the cellular chromatin are discussed.

Prepartation of soluble chromatin and specific chromatin fractions with restriction nucleases

By digestion of rat liver nuclei with EndoR HaeIII, EndoR EcoRI, and EndoR Bam and subsequent lysis of the nuclei approx. 90%, 40%, and 45%, respectively, of the chromatin were solubilized. The plateau values of solubilization are in agreement with a model in which the chromatin strands are crosslinked and/or attached to a supporting structure. The distribution of DNA lengths in the soluble and insoluble chromatin fractions were determined. According to digestion experiments with restriction nucleases rat liver DNA contains highly repetitive sequences, some of which are arranged in tandem repeats of 95 and 380 nucleotide pairs, respectively. With EndoR EcoRI chromatin containing the repetitive RNA was preferentially solubilized and, by subsequent sucrose gradient centrifugation, purified to about 90%. The useful properties of chromatin prepared by the specific action of restriction nucleases are discussed.

Nuclease cleavage of chromatin at 100-nucleotide pair intervals

Digestion of mouse liver nuclei with DNase II leads to a novel cleavage pattern with a 100-nucleotide pair periodicity. From chromatin, this pattern or the standard 200-nucleotide pair repeat can be produced depending on the ionic conditions. The results are interpreted by assuming different conformational states of the nuclear material, including condensed and extended forms.