Chromatin assembly in isolated mammalian nuclei.

Cellular DNA replication was stimulated in confluent monolayers of CV-1 monkey kidney cells following infection with SV40. Nuclei were isolated from CV-1 cells labeled with [3H]thymidine and then incubated in the presence of [alpha-32P]deoxyribonucleoside triphosphates under conditions that support DNA replication. To determine whether or not the cellular DNA synthesized in vitro was assembled into nucleosomes the DNA was digested in situ with either micrococcal nuclease or pancreatic DNase I, and the products were examined by electrophoretic and sedimentation analysis. The distribution of DNA fragment lengths on agarose gels following micrococcal nuclease digestion was more heterogeneous for newly replicated than for the bulk of the DNA. Nonetheless, the state of cellular DNA synthesized in vitro (32P-labeled) was found to be identical with that of the DNA in the bulk of the chromatin (3H-labeled) by the following criteria: (i) The extent of protection against digestion by micrococcal nuclease of DNase I. (ii) The size of the nucleosomes (180 base pairs) and core particles (145 base pairs). (iii) The number and sizes of DNA fragments produced by micrococcal nuclease in a limit digest. (iv) The sedimentation behavior on neutral sucrose gradients of nucleoprotein particles released by micrococcal nuclease. (v) The number and sizes of DNA fragments produced by DNase I digestion. These results demonstrate that cellular DNA replicated in isolated nuclei is organized into typical nucleosomes. Consequently, subcellular systems can be used to study the relationship between DNA replication and the assembly of chromatin under physiological conditions.     

ADP-ribosylation in isolated nuclei of Physarum polycephalum.

ADP-ribosylation of histones and non-histone nuclear proteins was studied in isolated nuclei during the naturally synchronous cell cycle of Physarum polycephalum. Aside from ADP-ribosyltransferase (ADPRT) itself, histones and high mobility group-like proteins are the main acceptors for ADP-ribose. The majority of these ADP-ribose residues is NH2OH-labile. ADP-ribosylation of the nuclear proteins is periodic during the cell cycle with maximum incorporation in early to mid G2-phase. In activity gels two enzyme forms with Mr of 115,000 and 75,000 can be identified. Both enzyme forms are present at a constant ratio of 3:1 during the cell cycle. The higher molecular mass form cannot be converted in vitro to the low molecular mass form, excluding an artificial degradation during isolation of nuclei. The ADPRT forms were purified and separated by h.p.l.c. The low molecular mass form is inhibited by different ADPRT inhibitors to a stronger extent and is the main acceptor for auto-ADP-ribosylation. The high molecular mass form is only moderately auto-ADP-ribosylated.     

RNA transport in isolated myeloma nuclei. Transport from membrane- denuded nuclei

Nuclei prepared from MOPC-21 cells were treated with the nonionic detergents Triton X-100 or Nonidet P-40. Chemical analysis revealed that nearly 90% of the nuclear phospholipid was removed by detergent treatment. The membrane-denuded nuclei remained intact with preservation of nuclear pore complexes as demonstrated by electron microscopy. Ribonucleic acid transport from detergent-treated nuclei proceeded at the same rate and to the same extent as in control nuclei. Normal nuclear restriction of nucleic acids was unaltered by removal of the nuclear membranes. The effect of temperature on transport of RNA from freshly isolated myeloma nuclei with intact nuclear envelopes was studied. No temperature transition was associated with the transport process. These data indicate that the transport of macromolecules from isolated myeloma nuclei is independent of the nuclear membrane.     

ADP-ribosyltransferase in isolated nuclei from sea-urchin embryos.

The activity of ADP-ribosyltransferase in nuclei isolated from sea-urchin embryos was estimated by the incorporation of [adenosine-14C]NAD+ into the acid-insoluble fraction. Hydrolysis of this acid-insoluble product by snake venom phosphodiesterase yielded radioactive 5'-AMP and phosphoribosyl-AMP. The incorporation of [14C]-NAD+ was inhibited by 3-aminobenzamide and nicotinamide, potent inhibitors of ADP-ribosyltransferase. [14C]NAD+ incorporation into the acid-insoluble fraction results from the reaction of ADP-ribosyltransferase. The optimum pH for the enzyme in isolated nuclei was 7.5. The enzyme, in 50 mM-Tris/HCl buffer, pH 7.5, containing 0.5 mM-NAD+ and 0.5 mM-dithiothreitol, exhibited the highest activity at 18 degrees C in the presence of 14 mM-MgCl2. The apparent Km value for NAD+ was 25 microM. The activity of the enzyme was measured in nuclei isolated from the embryos at several stages during early development. The activity was maximum at the 16-32-cell stage and then decreased to a minimum at the mesenchyme blastula stage. Thereafter its activity slightly increased at the onset of gastrulation and decreased again at the prism stage.     

DAPI fluorescence in nuclei isolated from tumors.

In DNA histograms of some human solid tumors stained with nuclear isolation medium--4,6-diamidino-2-phenylindole dihydrochloride (NIM-DAPI), the coefficient of variation (CV) of the G0/G1 peak was broad, and in nuclear volume vs DNA scattergrams, a prominent slope was seen. To determine the cause for this, nuclei from frozen breast tumors were stained with NIM-DAPI and analyzed after dilution or resuspension in PBS. In two-color (blue vs red) analysis, most of the slope and broad CV was due to red fluorescence of nuclei stained with NIM-DAPI, which was reduced on dilution or resuspension in PBS, resulting in elimination of the slope and tightening of the CV.     

RNA synthesis in isolated HeLa cell nuclei.

RNA synthesis has been studied in isolated nuclei of HeLa cells. The incubation medium has been optimized for RNA synthesis and the requirements for the presence of specific components previously used by other investigators has been examined. Nuclei isolated by centrifugation through 2 M sucrose synthesize RNA linearly for at least 1 h only at low temperature (25 degrees C). Low molecular weight RNA is found in the supernatant fraction after incubation; this RNA accounts for about 10% of the RNA synthesized. The RNA which remains within nuclei is of high molecular weight and processing of this RNA into molecules of the size of cytoplasmic mRNA does not seem to occur in isolated nuclei. We have studied the effect of an inhibitor of protein-nucleic acid interaction - aurintricarboxylic acid - on RNA synthesis by isolated nuclei. At concentrations below 0.1 mM, this drug does not inhibit RNA synthesis effectively, whereas at concentrations above 0.1 mM it inhibits RNA synthesis by about 80%. In view of the proposed mechanism of action of aurintricarboxylic acid, we suggest that completion of nucleotide chains initiated before nuclei isolation accounts for 20% of the RNA synthesized in our system by isolated nuclei, whereas nucleotide chains initiated during the in vitro incubation account for 80% of the RNA synthesized.     

Acetylation of histones in isolated avian erythroid nuclei.

1. Suspensions of avian erythroid nuclei, of high purity, were prepared. Acetylation of histones was observed when nuclei were incubated in the presence of [1-14C]acetyl CoA, but not in the presence of sodium [3H]acetate. 2.The acetylation reaction was very heat labile and reproduced the in vivo reaction with high fidelity. The reaction was strongly inhibited by divalent cations and cysteine. 3. Studies, in which intact cells were pre-incubated with cycloheximide prior to the isolation of nuclei, suggested that histone acetylation in isolated erythroid nuclei was largely independent of histone synthesis. 4. The pH profile suggested the presence of at least two histone acetyltransferases, with pH optima at 8.0 and 8.6. Acetylation of histone H4 appeared to be favoured at pH 8.0. 5. Studies on histone acetylation in isolated nuclei should be very useful in correlating observations on histone acetylation in vivo, with experiments using purified histone acetyltransferases.     

Proflavine sensitivity of RNA processing in isolated nuclei.

The intercalating agent proflavine inhibits the processing and subsequent release of preformed messenger RNA and ribosomal RNA from isolated liver nuclei to surrogate cytoplasm. The direct effect of proflavine on these processes, as monitored in a reconstituted cell-free system, supports the theory that base-paired segments (i.e. hairpin loops) in the precursor RNA's are involved as recognition sites in nuclear RNA processing.     

Some enzymes of isolated nuclei

THE COMPOSITION OF ISOLATED NUCLEI AND CELL PREPARATIONS FROM TISSUES OF CALF, BEEF, HORSE, AND FOWL WAS STUDIED WITH RESPECT TO THE FOLLOWING COMPONENTS: 1. Liver and kidney arginase, catalase, and uricase; pancreatic lipase and amylase; cardiac muscle myoglobin; erythrocyte hemoglobin; intestinal alkaline phospharase. These are referred to as "special" components in view of their characteristically restricted distribution reflecting the differentiated nature of the tissues in question. 2. Esterase, beta-glucuronidase, alkaline and nucleotide phosphatases, adenosine deaminase, guanase, and nucleoside phosphorylase. These are enzymes of general distribution. The differences in nuclear composition noted with respect to the "special" components, together with the broad variability in nuclear activity found for enzymes of general distribution, led to the conclusion that nuclei are differentiated structures. The following distribution was observed: 1. "Special" components: Hemoglobin was found to be present in fowl and goose erythrocyte nuclei, but myoglobin was entirely absent from heart muscle nuclei; of the special enzymes listed, only catalase and arginase appeared to be concentrated in some of the nuclei. There was no significant nuclear concentration of lipase, amylase, uricase, or alkaline phosphatase. No simple relationship was found between the concentration of a special enzyme in a tissue and its activity in the corresponding nuclei. For example, arginase activity, which is high in mammalian liver and in fowl kidney, was found in liver, not kidney, nuclei. Similarly, catalase activity was demonstrated only in mammalian liver nuclei, although, in mammals, both liver and kidney are rich sources of this enzyme. 2. Enzymes of general distribution fell into three classes: (a) Those present in low concentrations, if at all, in the nuclei-alkaline phosphatase, the nucleotide phosphatases) and beta-glucuronidase. (b) Those present in nuclei in varying concentrations-esterase. (c) Those present in high proportions in most nuclei-adenosine deaminase, nucleoside phosphorylase, and guanase. The exceptionally low nuclear activity of intestinal mucosa with respect to these enzymes was discussed in relation to physiological considerations. The response of nuclei to changes in physiological state was demonstrated by experiments on starvation. The outstanding aspect of this response was a change in nuclear enzymatic activity opposing that observed in the cytoplasm. A comparison of fetal and adult mucosa cells led to the following tentative interpretation of the observed intracellular enzyme distribution: In cells tending to moribundity, as in those subjected to starvation, relative nuclear enzymatic activity falls. The occurrence of special enzymes in nuclei was considered in terms of differentiation, and the high nuclear concentration of the nucleoside-specific enzymes was interpreted in terms of general nuclear metabolic activity.     

Nodule-specific kinases phosphorylating nuclear factors in isolated nuclei.

In vitro phosphorylation of total nuclear proteins from soybean (Glycine max L) nodules formed by Bradyrhizobium japonicum 61A76 showed several differences in comparison with those from uninfected roots or embryonic-axes nuclei. Three types of protein phosphorylations were observed in nodule nuclei: Ca(2+)- and calmodulin-independent, Ca(2+)- and calmodulin-dependent, and Ca(2+)-dependent but calmodulin-independent. In addition, Ca(2+)-dependent dephosphorylation of some nuclear proteins was observed in nodule nuclei. The first and second types of phosphorylations were also present in root nuclei, but the trifluoperazine-insensitive and Ca(2+)-dependent phosphorylation (indicating calmodulin independence) occurs only in nodules. The latter appears to phosphorylate a nodule-specific protein of 65 kilodaltons and this protein was purified from other nuclear phosphorylated proteins. In addition, some nuclear proteins from uninfected tissue were found to be phosphorylated or dephosphorylated by kinases or phosphatases that originated from the nodule nuclei. These data suggest that some activities of nuclear factors in nodules may be regulated by specific phosphorylation or dephosphorylation during symbiotic interactions with rhizobia.