Preparation of metaphase chromatin of Physarumpolycephalum without the loss of repressed RNA synthesis

A novel method for the preparation of intact chromatin from the slime mold $\text{Physarum}\text{polycephalum>}$ which retains the $\text{in}\text{vivo}$ property of RNA synthesis is described. Preparations from G₂-cells were highly active, while those from metaphase-cells were inactive. The plasmodial cells were disrupted by gentle homogenization on a polyethylene sieve in a neutral isotonic sucrose medium containing Mg⁺⁺, deoxycholate and EGTA, a Ca⁺⁺-chelating agent. The nuclei were lysed in a hypotonic buffer without use of EDTA and chromatin was precipitated by centrifugation after addition of Mg⁺⁺.     

ISOPYCNIC CENTRIFUGATION OF CHROMATIN IN RENOGRAFIN SOLUTIONS

Solutions of Renografin (30–60%) can be centrifuged to form density gradients in the range from 1.0 g/cm³ to 1.4 g/cm³ or, alternatively, preformed gradients can be made which under appropriate conditions of centrifugation have an indefinite stability. Such solutions have a low viscosity and a relatively low ionic strength. The density of DNA in such solutions is surprisingly low (~1.14 g/cm³). Crude chromatin can be sedimented to an equilibrium position in such gradients, corresponding to a density of 1.2₄ g/cm³, or slightly lower, depending on the method of preparation. The complex is shown to contain DNA, RNA, protein, and possibly some lipoprotein. Most of the RNA can be removed with RNase without any significant effect on the density of the chromatin.     

Isolation of a rat ventral prostate chromatin fraction exhibiting a singular melting profile

Rat ventral prostate chromatin, prepared by a gentle procedure in which marked shearing forces were avoided, was separated by sucrose gradient centrifugation into a quantitatively minor less dense (L) fraction, and 2 heavier components, (H₁) and (H₂). The (L) fraction, comprising 5–15 percent of the totäl chromatin DNA, had a unique melting profile, with a Tm_app. of 59°, compared to 82.5°, 85° and 80.5° for total, (H₁) and (H₂) chromatin. (L) chromatin has a number of other properties expected of “euchromatin”. This approach to the preparation of chromatin has been used successfully with other tissues such as liver.     

Circular dichrotic probes for aspects of chromatin structure: aromatic polycationic ionen probes

Two ionens (II and X) formed complexes with DNA and chromatin with extrinsic CD bands and reduced intrinsic bands. The salt and urea sensitive, AT-specific probe (II) gave Δε > 100 L-(residue II)^?1-cm^?1 with DNA and Δε=0–14 with chromatin; II reduced the intrinsic bands from Δε≈0.7 to Δε≈0.5. Ionen X gave Δε₃₄₅=30 with DNA, and Δε₃₄₅=15–20 with chromatin. X reduced the intrinsic band to ?1.6. X show less base specificity. Extrinsic Δε_λ of X increased linearly to r (residue/phosphate) = 0.5 for DNA and only 0.3 in chromatin. DNA in chromatin may have ～10% of the II and 50–60% of the X binding sites and those in an altered conformation.     

Studies on the mode of action of calciferol: Subcellular localization of 1,25-dihydroxyvitamin D3 in chicken parathyroid glands

As a further means of evaluating 1,25-dihydroxyvitamin D₃-parathyroid gland interaction and its relation to calcium homeostasis, a comparative study of the subcellular localization of 1,25-dihydroxyvitamin D₃ [1,25(OH)₂D₃]in the parathyroid glands, intestinal mucosa, kidney, and liver of rachitic chickens has been carried out. Only in the chromatin fraction from parathyroids and intestinal mucosa could there be demonstrated selective and specific localization of the 1,25(OH)₂D₃. The chromatin-bound picomoles of 1,25(OH)₂D₃ (per gram of tissue) was in the ratio (mucosa:parathyroids:kidney:liver) of 1.0:0.23:0.11:0.17 2 h after an intracardial injection of 290 pmol of [³H]1,25(OH)₂D₃. This same ratio after a 30-min (23 °C) homogenate incubation with 1 × 10^?8m [³H]1,25(OH)₂D₃ was 1.0:1.0:0.10:0.03. Analogous results were obtained when reconstituted chromatin and cytosol fractions from the different tissues were compared for chromatin localization efficiency. This chromatin localization of 1,25(OH)₂D₃ in the parathyroid glands was temperature dependent. In addition, parathyroid glands were found to contain 3.0–3.5 S cytoplasmic and KCl-extractable chromatin receptors specific for 1,25(OH)₂D₃.     

Purification and properties of tyrosinases from Vibrio tyrosinaticus

Rat liver chromatin which has been briefly sonicated is fractionated by treatment with low concentrations of magnesium ion. At 1.5 mm Mg²⁺, where approximately 20–25% of the chromatin remains soluble after low-speed centrifugation, chemical and physical analysis of the Mg-soluble and Mg-insoluble chromatin fractions show that the fractions possess markedly different properties. The Mg-soluble chromatin has more protein and RNA than the Mg-insoluble chromatin. The histone composition of the two fractions as shown by electrophoretic analysis is similar, but many of the acidic proteins are qualitatively and quantitatively different. The molecular weight of the Mg-soluble chromatin is less than that of the insoluble chromatin based on sedimentation behavior and gel filtration experiments. The soluble chromatin has nearly twice the template activity for RNA synthesis in vitro with added RNA polymerase as the Mg-insoluble chromatin and contains approximately 80% of the in vivo rapidly labeled RNA found in the total chromatin preparation. In addition the Mg-soluble chromatin has a significantly greater amount of “accessible” DNA (62%) as measured by polylysine binding than Mg-insoluble chromatin (48%). The data suggest that (a) fractionation of chromatin preparations can be achieved by titration with Mg²⁺, and (b) chromatin soluble in low concentrations of Mg²⁺ may be enriched in actively transcribed portions of the genome.     

Binding of [3H]triamcinolone acetonide-receptor complexes to chromatin from the B-cell leukemia line,BCL1

The binding characteristics of partially purified glucocorticoid receptor complexes from hormone sensitive, non-differentiating BCL₁ cells to sequentially deproteinized BCL₁ chromatin-cellulose was investigated. [³H]Triamcinolone acetonide (TA)-receptor complexes were purified (approx. 30-fold) from DEAF-cellulose columns by salt elution which allowed receptor activation only in the absence of molybdate. Addition of 10 mM molybdate completely blocked salt activation. The binding pattern of the activated [³H]TA-receptor complexes to chromatin-cellulose extracted with 0–8 M guanidine hydrochloride revealed three regions of increased binding activity (acceptor sites), at 2, 5 and 7 M guanidine hydrochloride. Acceptor site binding was markedly reduced for chromatin extracted with 3, 6 and 8 M guanidine hydrochloride. Non-activated receptor complexes demonstrated very low binding to deproteinized chromatin. It was also shown that chromatin binding required glucocortical receptors and that free ligand or ligand bound to other proteins did not bind significantly to chromatin. In addition, binding of [³H]TA-receptor complexes to partially deproteinized chromatin was competable by unlabeled TA-receptor complexes. Scatchard analysis demonstrated that chromatin from non-differentiating BCL₁ cells possesses multiple, high-affinity binding sites which differ in their affinity for the glucocorticoid receptor. Partially deproteinized chromatin from lipopolysaccharide-stimulated BCL₁ cells demonstrated a different pattern of receptor binding, i.e., receptor binding was significantly greater to chromatin previously extracted with 6–8 M guanidine hydrochloride. These results suggest that differentiation alters the state of chromatin and the interaction of non-histone protein/DNA acceptor sites with glucocorticoid receptors. These alterations may play a role in the acquisition of hormone resistance.     

Comparative Study of the Condensation of Chicken Erythrocyte and Calf Thymus Chromatins by Di- and Multivalent Cations

Abstract

The condensation of chicken erythrocyte (CE) and calf thymus (CT) chromatins upon addition of di- and multivalent cations has been studied using turbidityJulprecipitation and electric dichroism measurements. For all the cations investigated (Mg²⁺, Tb³⁺, Co(NH₃)₆ ³⁺, spermidine Spd²⁺ and spermine Sp⁴⁺) condensation of CE chromatin occurred before the onset of aggregation, while aggregation of CT chromatin started before condensation with all cations except Mg²⁺ and Tb³⁺. Precipitation of CE chromatin required lower di- and multivalent cations concentrations than CT chromatin. The electric dichroism data for both chromatins, at low ionic strength in the absence of di- or multivalent cations, indicated that the nucleoprotein molecules were not totally decondensed but that a “precondensed” state was already present. A positive electric dichroism was observed for the most condensed chromatin fibers, in agreement with the “cross-linker” models. Tb³⁺ led to less compact condensed particles as judged from the electric dichroism observations, but electron microscopy revealed that “30 nm fibers” were formed. Very little aggregation was produced by Tb³⁺. On the contrary, spermine produced very large networks of condensed molecules, but large spheroidal particles were also observed. The condensation of CE chromatin happened without changes of solution conductivity upon cation salt addition, regardless of the condensing cation, indicating a cooperative uptake of the ions during this process.     

An analysis of the binding of the chick oviduct progesterone-receptor to chromatin

The binding of progesterone-receptor complexes to chromatin from target and nontarget tissues was studied in vitro. Chromatin from both target and non-target tissues responds in a similar manner to saly and cofactors and has the same K_D (approx. 3·10⁻⁹ M) for the progesterone-receptor complex. The only observed difference in the binding of the progesterone-receptor complex to target and nontarget chromatins is the difference in total number of acceptor sites. Oviduct chromatin has approx. 1300 sites/pg DNA, spleen chromatin has approx. 840 sites/pg DNA, and erythrocyte chromatin has about 330 sites/pg DNA. The K_D and number of acceptor sites for progesterone-receptor complex binding to oviduct chromatin remains the same even after extensive purification of the progesterone-receptor complex. Activation of cytosol labeled with [³H]progesterone by preincubation at 25°C, analogous to that required for maximal nuclear binding, occurs if the binding studies to chromatin are performed in 0.025 M salt. The absence of an observable temperature effect when the studies are performed at 0.15 M salt is due to the activation of the receptor by salt. The dissociation of the progesterone-receptor complex from chromatin exhibits a single dissociation rate and the initial event is the appearance of free progesterone rather than a progesterone-receptor complex. Lastly, the treatment of chromatin with an antibody prepared against either single-stranded DNA or double-stranded DNA does not alter the extent of binding of the progesterone-receptor complex. Similarly, pretreatment of chromatin with a single-stranded nuclease does not inhibit the capacity of chromatin to bind the hormone-receptor complex.     

Characterization of the octamer of histones free in solution

The nucleosome “core protein” isolated from chromatin in high-salt solutions (2 m-NaCl) has been characterized in detail. The preparation described yields material which is stable for prolonged periods at either 4 °C or 37 °C. It has an apparent partial specific volume of 0.767 ml/g and a sedimentation coefficient (S_20,w⁰) of 4.77 (±0.04) S. The molecular weight, determined by sedimentation equilibrium, is 107,500 (±7700), which is compatible with an octameric structure of the form (H2A)₂(H2B)₂(H3)₂(H4)₂, as previously proposed.The sedimentation coefficient and molecular weight are very similar to those of cross-linked core protein, which is known to be octameric.     

Changes in the phosphorylation of non-histone chromatin proteins during the cell cycle of HeLa S 3 cells

The phosphorylation of non-histone chromatin proteins in synchronized HeLa S₃ cells was studied in 5 phases of the cell cycle: mitosis, G₁, early and late S, and G₂. The rate of non-histone chromatin protein phosphorylation was found to be maximal during G₁ and G₂, somewhat decreased during S phase, and almost 90% depressed during mitosis. Analysis of the phosphorylated non-histone chromatin proteins by SDS-acrylamide gel electrophoresis showed a heterogeneous pattern of phosphorylation as measured by labeling with ³²P. Significant variations in the labeling pattern were seen during different stages of the cell cycle, and particular unique species appeared to be phosphorylated selectively during certain stages of the cycle.     

Identification of the cell surface and nuclear receptors for NGF in a breast carcinoma cell line

¹²⁵I-nerve growth factor (NGF) was found to be internalized and translocated to the nucleus of SKBr5 breast carcinoma cells. The cytoplasm and chromatin isolated from nonmitotic cells accumulated two-and five-fold, respectively, more of ¹²⁵I-NGF than the cells undergoing mitosis. MAb 20.4 developed against the NGF cell surface receptor immunoprecipitated the 80,000 M_r receptor from plasma membrane and two protein species from the chromatin; 90,000 M_r (major band) and 200,000 M_r (minor band). In SKBr5 cells, binding of NGF to the chromatin did not affect synthesis of rRNA. Proliferation of SKBr5 cells was slightly stimulated by NGF. In control melanoma A875 cells, which express the 230,000 M_r chromatin receptor, NGF inhibited both rRNA synthesis and cell proliferation. We suggest that the 90,000 M_r chromatin receptor expressed by SKBr5 cells represents a “nonactive”, ligand-binding subunit of the high molecular weight receptor for NGF. The critical role of the chromatin receptor for NGF in rRNA-dependent cell proliferation is discussed. © 1993 Wiley-Liss, Inc.     

Histone acetyltransferase in chromatin. Extraction of transferase activity from chromatin

Previous work has attempted to localize nuclear histone acetyltransferase activity in the cromatin. Evidence was presented indicating that the transfer of ¹⁴C-acetate from ¹⁴C-acetyl CoA to histones in chromatin was an enzymatic process. We now report on the extraction of part of the histone acetyltransferase activity from rat liver chromatin, employing a procedure originally described for extraction of DNA-dependent RNA polymerase. The K_m of the extracted transferase activity for the substrate acetyl CoA was 5 × 10⁻⁷, the Q₁₀: 1.8 and the optimal pH: 7.1. Serum albumine, protamine and polylysine were poor substrates as compared to histones. Activity of extracted or heated chromatin was not restored upon incubation in the presence of extract. Also the selectivity exhibited by the transferase activity in unextracted chromatin towards arginine-rich histones, was much less pronounced in the extracts prepared from it. It is possible that the influence of steric factors contributing to this specificity in native chromatin is lost upon isolation of the enzyme from it. Alternatively, a less specific isoenzyme may have been extracted.     

Interphase chromosomal deoxyribonucleoprotein isolated as a discrete structure from cultured cells

A new procedure is described for the preparation of interphase chromatin from cultured mouse cells (line P815). The primary objective of this procedure was to eliminate exchanges of histones between deoxynucleoprotein molecules; this objective is shown experimentally to have been attained. The chromatin is released from cells by the non-ionic detergent Nonidet P40 in medium of low ionic strength (0.1 mM-KNa₂PO₄), and may then be sedimented as a structure which conserves the general form and ultrastructural characteristics of chromatin within the cell. The nuclear envelope cannot be detected in these structures by electron microscopy, and their content of choline-containing phospholipids is less than 10% of that of nuclei. The maintenance of form in this structure must thus depend on properties of the chromatin itself, and possibly on the more compact peripheral chromatin.Soluble DNP² prepared by shearing these structures has the same relative contents of DNA, histones, non-histone proteins and RNA as DNP prepared by standard methods. Analyses by electrophoresis on polyacrylamide gels of the non-histone proteins reveals certain differences from the pattern of these proteins in DNP prepared by a salt precipitation method. The template activity for RNA synthesis, in the presence of Escherichia coli RNA polymerase of sheared, soluble DNP prepared by this procedure, is comparable to that of DNP prepared by other methods. However, in the absence of exogenous RNA polymerase the rate of RNA synthesis by structured (unsheared) chromatin is about ten times higher than the rate using sheared DNP.The rapid removal of the nuclear envelope in this lysis procedure allowed experimental examination of the origin of the histones and non-histone proteins of DNP. When DNP was prepared from a mixture of two populations of cells, one containing DNA distinguishable by a density label and the other containing radioactively labelled proteins, radioactive proteins were found exclusively in DNP of normal density, and not in dense DNP and vice versa. It is concluded that the proteins of DNP prepared in this way are not acquired during the preparation procedure but were already associated with DNA in vivo, and that other proteins are not bound non-specifically to DNA during the preparation of DNP. When a mixture of DNP molecules prepared, in this way is precipitated in 150 mm-NaCl and redissolved, some radioactively labelled histones migrate onto dense DNA molecules.This procedure is suitable for routine, quantitative isolation of chromosomal DNP from small numbers of cells; it is also applicable to cells of other cultured lines.     

Detection of Histone Modifications in Plant Leaves

Chromatin structure is important for the regulation of gene expression in eukaryotes. In this process, chromatin remodeling, DNA methylation, and covalent modifications on the amino-terminal tails of histones H3 and H4 play essential roles^1-2. H3 and H4 histone modifications include methylation of lysine and arginine, acetylation of lysine, and phosphorylation of serine residues^1-2. These modifications are associated either with gene activation, repression, or a primed state of gene that supports more rapid and robust activation of expression after perception of appropriate signals (microbe-associated molecular patterns, light, hormones, etc.)^3-7. Here, we present a method for the reliable and sensitive detection of specific chromatin modifications on selected plant genes. The technique is based on the crosslinking of (modified) histones and DNA with formaldehyde^8,9, extraction and sonication of chromatin, chromatin immunoprecipitation (ChIP) with modification-specific antibodies^9,10, de-crosslinking of histone-DNA complexes, and gene-specific real-time quantitative PCR. The approach has proven useful for detecting specific histone modifications associated with C₄ photosynthesis in maize^5,11 and systemic immunity in Arabidopsis³.