Enzymatic fractionation of nuclei: polynucleosomes and RNA polymerase II as endogenous transcriptional complexes

Relations between clusters of oxidatively damaged nucleotides and active or open nucleosomes in the rat Nth 1 gene

The distribution of oxidative damage to bases such as 8-hydroxyguanine (8-OH-Gua), was determined at the nucleotide level of resolution using the ligation-mediated PCR technique. Administration of a renal carcinogen, ferric nitrilotriacetate (Fe-NTA), is known to induce oxidative stress and subsequent formation of 8-OH-Gua in the kidney. Whole genomic DNA was isolated from the rat kidney with or without Fe-NTA treatment and then digested with formamidopyrimidine-DNA glycosylase (Fpg). As a target, we focused on the gene of a DNA repair enzyme for thymine glycol, Nth 1. Cleaved signals were found in exon 1 and exon 3, but not exon 5. Nucleosomes in these regions, enriched in damaged nucleotides, were highly accessible to micrococcal nuclease, especially in the kidney. Taking into account the function of the protein segment encoded by these regions, we discussed the molecular mechanism of the restricted formation of the damaged nucleotides.

Distribution of globin genes and histone variants in micrococcal nuclease-generated subfractions of chromatin from Friend erythroleukemia cells at different malignant states

The distribution of the alpha and beta-globin genes and histone variants was examined in micrococcal nuclease-generated chromatin fractions of three Friend murine erythroleukemia cell types differing in malignant potential and inducibility to erythroid differentiation. A preferential concentration of globin gene sequences, as compared to satellite DNA, was noted in a physiological salt-soluble, histone H1-depleted, mononucleosomal chromatin fraction (Sup 120) in all Friend cell types, even those in which the globin gene was not capable of transcriptional activation by chemical induction. The level of globin gene enrichment in the Sup 120 fraction was highest in the most malignant and inducible cell type. The chemical induction of erythroid differentiation in this cell line did not change the distribution of globin genes in the chromatin fractions. The Sup 120 chromatin fraction prepared from mouse brain nuclei was not enriched in globin genes. Besides the previously reported low H2A. 1/H2A.2 ratio [Blankstein and Levy: Nature 260:638-640, 1976], chromatin from the most tumorigenic cell type showed the lowest H2B.2 to H2B.1 ratio, highest levels of histone H4 acetylation, and the most pronounced change in relative amounts of two major electrophoretic bands of histone H1 variants as compared to the less malignant cell types. The histone variant content of the micrococcal nuclease-generated chromatin fractions from the three Friend cell types reflected the core histone variant differences for the respective intact nuclei. However, the electrophoretic separation of mononucleosomes by size revealed several classes with different H2A variant ratios. The results demonstrate the existence of structural differences in globin gene and histone variants in erythroleukemia cell chromatin associated with distinguishable phenotypes during malignant cell progression.

Characterization, purification and cDNA cloning of a rat perchloric-acid-soluble 23-kDa protein present only in liver and kidney

A novel protein was extracted with 5% perchloric acid from rat liver and kidney. It is absent from other rat organs. Its apparent molecular mass is 23 kDa as determined by HPLC gel filtration. A single band, corresponding to 10 kDa, was observed after SDS/PAGE, suggesting that the protein consists of two subunits with similar molecular masses. This protein can neither be phosphorylated by ATP, nor acetylated. The sequence of the cDNA encoding this protein was determined. Southern-blot analysis showed that the corresponding gene spanned at least 10 kb and contained at least five introns. Zoo-blot analysis at medium stringency strongly suggests that the gene has been conserved during evolution. The amino-acid sequence of this protein with a highly conserved region is similar to that of a heat-shock protein.

Solid-phase enzyme immunoassay for the detection of HMG nonhistone proteins in their native structure

The use of purified specific antibodies against HMG1 and HMG17 (high mobility group nonhistone chromosomal proteins), together with a very sensitive solid phase enzyme immunoassay, allows the detection of nanograms of these proteins free in solution or in chromatin native structure, and the measurement of their accessibility. The sensitivity of the assay is comparable to that of the radioimmunoassay, with the advantage of avoiding the handling of radioactive materials.

Characteristics of chromatin release during digestion of nuclei with micrococcal nuclease: preferential solubilization of nascent RNA at low enzyme concentration

1. Extensive digestion of nuclei with micrococcal nuclease (MNase), commonly used in the analysis of chromatin structure, results in the production of mono- and dinucleosomal chromatin fragments. 2. Digestion of nuclei from a range of cell types with low enzyme concentrations solubilized high molecular weight polynucleosomal fragments, some greater than 22 kb long. 3. Such digestion conditions also resulted in extensive solubilization of nascent RNA which contributed considerably to the nucleic acid content of the soluble fraction. 4. We conclude that the contribution of RNA to total nucleic acid content of the soluble fraction should be taken into consideration when nuclei are digested with low concentrations of MNase.

Persistent and heritable structural damage induced in heterochromatic DNA from rat liver by N-nitrosodimethylamine

Analysis, by benzoylated DEAE-cellulose chromatography, has been made of structural change in eu- and heterochromatic DNA from rat liver following administration of the carcinogen N-nitrosodimethylamine (10 mg/kg body weight). Either hepatic DNA was prelabeled with [3H]thymidine administered 2-3 weeks before injection of the carcinogen or the labeled precursor was given during regenerative hyperplasia in rats treated earlier with N-nitrosodimethylamine. Following phenol extraction of either whole liver homogenate or nuclease-fractionated eu- and heterochromatin, carcinogen-modified DNA was examined by stepwise or caffeine gradient elution from benzoylated DEAE-cellulose. In whole DNA, nitrosamine-induced single-stranded character was maximal 4-24 h after treatment, declining rapidly thereafter; gradient elution of these DNA preparations also provided short-term evidence of structural change. Following incubation of purified nuclei with micrococcal nuclease, 10-12% of labeled DNA was solubilized (eu-chromatin) by 1.0 unit of micrococcal nuclease (5 mg of DNA)-1 mL-1 after 9 min. In prelabeled animals, administration of N-nitrosodimethylamine caused a marked fall in the specific radioactivity of solubilized DNA, while that of sedimenting DNA was not affected. Caffeine gradient chromatography suggested short-term nitrosamine-induced structural change in euchromatic DNA, while increased binding of heterochromatic DNA was evident for up to 3 months after carcinogen treatment. Preparations of newly synthesized heterochromatic DNA from animals subjected to hepatectomy up to 2 months after carcinogen treatment provided evidence of heritable structural damage. Carcinogen-induced binding of heterochromatic DNA to benzoylated DEAE-cellulose was indicative of specific structural lesions whose affinity equalled that of single-stranded DNA up to 1.0 kilobase in length.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of in vitro (ADP)ribosylation on transcription of the chromatin of the brain of developing rats

The template-engaged RNA polymerase II was assayed in the nuclei purified from the cerebral hemisphere of 3-, 14- and 30-day old rats. Its activity is the highest at 3-day and declines as development proceeds. Lower transcription at 30-day may either be due to a decrease in the active fraction of chromatin or to a decrease in the amount of RNA polymerase II that is active towards endogenous template, or both. The activity of RNA polymerase I (active in low salt) is also maximal at 3-day and declines as development proceeds. (ADP)ribosylation of chromatin depresses RNA synthesis. This may be due to inactivation of RNA polymerase itself by protein poly(ADP)ribosylation.

Correlations between prostate chromatin structure and transcriptional activity and acceptor site distribution

Androgen-receptor complexes are intimately involved in the maintenance of rat ventral prostate chromatin in a transcriptionally active structure. The presence or absence of androgens influenced the quantity of transcriptionally active chromatin and the distribution of acceptor sites for androgen-receptor complexes as probed by endonucleolytic cleavage. After castration, changes in the sedimentation rates of nucleosome oligomers were consistent with the absence of androgen-receptor complexes and elongating polyribonucleotide chains. These changes were accompanied by decreases in the ability of chromatin released under conditions of minimal nuclease digestion to bind androgen-receptor complexes and to support incorporation of RNA precursors responsive to androgenic stimulation. Saturation analyses of chromatin and nuclear fractions with partially purified androgen-receptor complexes revealed two affinity classes of acceptor sites. After castration, alterations in the intrachromatin distribution of acceptor sites were consistent with their redeployment into areas of decreased nuclease sensitivity, as previously shown for androgen-responsive genes.

Dense distribution of nuclear alkaline protease to nucleoli with increase in rapidly growing cells in rats

Neutral and alkaline proteases (chymotrypsin-like serine proteases) are tightly bound to chromatin in nuclei of various tissues of rats, and rapidly growing cells are abundant in the latter enzyme. Activities per mg DNA of these enzymes were measured with fractions of euchromatin, heterochromatin, nucleoli and extranucleoli from normal and regenerating livers, and Rhodamine sarcoma. With normal liver, both enzymes, respectively, were almost evenly distributed among the fractions, except that alkaline protease was significantly higher in nucleoli. The nucleolar alkaline protease increased by 30-60% with regenerating liver and by higher than 100% with the tumor.

Single-strand-specific degradation of DNA during isolation of rat liver nuclei

We have investigated structural change in rat liver DNA produced by different isolation procedures and specifically compared the integrity of DNA derived by phenol extraction from isolated and purified nuclei with preparations extracted immediately from a crude liver homogenate containing intact nuclei. As indicated by stepwise elution from benzoylated DEAE-cellulose, most structural change in DNA was evident following nuclei isolation. Damage principally involved generation of single-stranded regions in otherwise double-stranded DNA fragments; totally single-stranded DNA was not detected by hydroxylapatite chromatography. Caffeine gradient elution suggested formation of single-stranded regions extending for up to several kilobases. In neutral sucrose gradients, differences in sedimentation rates of respective DNA samples consequent upon S1 nuclease digestion could be detected after isolation of nuclei, though not in other circumstances. The observed single-strand-specific nuclease digestion of DNA could apparently be reduced if steps were taken to reduce autodigestion during nuclei isolation by reduction of temperature and covalent cation concentration. The results are discussed in terms of the use of exogenous and endogenous nucleases in chromatin fractionation studies involving isolated nuclei and possible artifactual findings that may be generated by single-strand-specific autodigestion.

Analysis of conformation and function of the chromatin of the brain of young and old rats

Digestion of nuclei of the cerebral hemisphere of young (18-20 week) and old (90-97 week) rats by DNase I shows that the rate and extent of digestion is lower in the old. Time course analysis of the DNA fragments produced by DNase I by polyacrylamide gel electrophoresis shows that more of the lower base pair fragments are produced in the young. Also, the rate of production of these fragments is higher in the young than in the old. Assay of template-engaged RNA polymerase II (alpha-amanitin sensitive) shows that in the old it is only about 50% of that of the young. Addition of exogenous eukaryotic (wheat germ) RNA polymerase II is not able to restore transcription of the chromatin in the old to the level of the young. These data show that chromatin undergoes increasing condensation as a function of age, resulting in decreased transcriptional activity in old age.

Initiated complexes of RNA polymerase II are concentrated in the nuclear skeleton associated DNA

Several preparations of nuclear matrices containing varying amounts of DNA were obtained from mouse plasmocytoma P3-X63-Ag8.653 cells and tested for the presence of RNA polymerase II activity. It has been demonstrated that about 25% of RNA polymerase II activity detected in the original nuclei can be recovered in isolated nuclear matrices. Only DNA-bound RNA polymerase II was found in the isolated matrices, while both free and DNA-bound RNA polymerase II activities were detected in the original nuclei. RNA polymerase II activity found in the isolated matrices did not depend on the portion of DNA recovered in the nuclear matrices in a large interval between 91 and 1.5% of DNA content in the original nuclei. The conclusion has been drawn that initiated RNA polymerase II molecules are non-randomly distributed along DNA loops. They are concentrated near the points of DNA attachment to the nuclear skeleton.

Analysis of chromatin of the brain of young and old rats by nick-translation

Chromatin of the brain of young (22-23 week) and old (118-119 week) rats has been analysed by nick-translation reaction following its digestion by DNaseI, EcoRI, MspI and HpaII. The incorporation of (3H)-dTMP in the old is only about 50 percent of that of the young. The difference in the incorporation following digestion of nuclei by MspI and HpaII that quantitate the degree of methylation of internal cytosines in the 5' CCGG 3' sequences, is nearly two-fold higher in the old. These data indicate that the chromatin undergoes increasing condensation as a function of age. One of the contributory factors may be increasing methylation of DNA. This may decrease the active fraction of chromatin.

In vivo distribution of dimethylnitrosamine metabolites in mouse liver and their binding to micrococcal nuclease sensitive and resistant chromatin

Mice were injected i.p. with a single dose (5 mg/kg body wt) of [14C]dimethylnitrosamine and killed at time intervals between 15 and 120 min. Isolated nuclei were incubated with micrococcal nuclease and the chromatin separated into a 1100 g pellet P1 and supernatant fraction S1. The incorporation of 14C from [14C]dimethylnitrosamine into chromatin was significantly higher in the P1 than the S1 fraction. The purine bases of the P1 DNA showed a lower methylation than those of the S1 DNA. In contrast, radioactivity of the proteins was higher in the P1 than the S1 fraction. It is concluded that the open structures of the S1 chromatin were preferentially attacked by the hepatotoxin leading to a high 14C-labelling of the DNA relative to that of the proteins.

Eukaryotic RNA polymerases

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

Age-related changes of the pattern of non-histone proteins in active and condensed fractions of mouse liver chromatin and hepatocarcinoma

Electrophoretic analysis of histones and non-histone acid-soluble proteins in active (nuclease sensitive) and inactive chromatin from liver of young and old CBA mice and in age-related hepatocarcinomas showed a higher ratio of NHP:histones in active chromatin in old cells. Some liver- and hepatoma-specific fractions of non-histone proteins have been identified as chromatin matrix proteins.

Binding of benzo[a]pyrene to different chromatin domains following activation at the nuclear membrane

When isolated liver nuclei from methylcholanthrene-treated rats are incubated with benzopyrene, covalent adducts are formed between DNA and the ultimate carcinogen, benzopyrene diol epoxide. Brief digestion with DNaseI, or micrococcal nuclease has been used to demonstrate that benzopyrene metabolites bind more readily to DNA in chromatin regions with a more open, active conformation than to inactive chromatin.

RNA synthesis in regenerating mouse liver evaluated by incorporation of [methyl-14C]methionine and by determination of RNA polymerase activity

The synthesis of RNA during mouse liver regeneration was studied by two different methods at 24 and 48 h after partial hepatectomy. Total chromatin-bound RNA polymerase activity showed an increase of 32% at 24 h after partial hepatectomy. At 48 h a slight increase in total activity was also observed in regenerating liver, but the difference was not significant. The increase in total RNA polymerase activity was due to a rise in RNA polymerase I plus III activity. This enzyme activity was increased at both 24 and 48 h. The increase was 57% at 24 h and 51% at 48 h. When [methyl-14C]methionine was used for labelling of methyl groups in rRNA, there was an increased specific radioactivity of this class of RNA at both 24 h and 48 h. The increases were 263 and 103% at 24 and 48 h respectively. Thus both methods revealed an increased synthesis of rRNA during mouse liver regeneration. The results are discussed in relation to previous results from this laboratory [Yngner, Carlberg, Lewan & Engelbrecht (1979) Hoppe-Seyler's Z. Physiol. Chem. 360, 1069-1074; Yngner, Engelbrecht, Lewan & Annerfeldt (1979) Biochem. J. 178, 1-8; Yngner, Bengtsson, Carlberg, Engelbrecht & Wieslander (1980) Exp. Cell. Biol. 48, 393-403], which have shown that the incorporation of orotic acid or uridine into RNA is not increased in mouse liver regenerating after partial hepatectomy.

Thyroxine preferentially stimulates transcription by isolated neuronal nuclei in the developing rat brain cortex

The administration of thyroxine to neonatal rats stimulates RNA synthesis by neuronal nuclei isolated from the developing rat brain cortex. Glial nuclei are relatively resistant to thyroxine treatment. The activity of neuronal RNA polymerase II is particularly stimulated by the hormone. Thyroxine also affects neuronal chromatin structure as shown by changes in the relative proportion of different subnuclear fractions obtained by gentle micrococcal nuclease digestion of nuclei from hormone-treated rats.

Effects of partial hepatectomy on RNA polymerase activities in mouse liver

Chromatin-bound and poly[d(A-T)]dependent RNA polymerase I plus III and II activities of mouse liver were analysed 24 and 48 hr after partial hepatectomy. Chromatin-bound RNA polymerase I plus III activity showed an increase of 57% at 24 hr and 51% at 48 hr after partial hepatectomy. There was a decrease in chromatin-bound RNA polymerase II activity of 15% at 24 hr and 34% at 48 hr after partial hepatectomy. There was no significant changes in poly[d(A-T)]dependent RNA polymerase activities. Heparin caused an approximately 10-fold increase in chromatin-bound RNA polymerase II activity. The stimulation by heparin was significantly increased 48 h after partial hepatectomy. Anaesthesia and/or surgery had great influence on RNA polymerase activities. At 24 hr after operation, chromatin-bound RNA polymerase I plus III and II activities were depressed, and the liver cell chromatin was more susceptible to stimulation by heparin.

Effects of thyrotropin on thyroid chromatin. Enhanced sensitivity to micrococcal nuclease and increased nuclear protein phosphorylation

Thyroid slices were incubated with or without TSH for 2 or 5 h. Nuclei were then prepared, subjected to mild digestion with micrococcal nuclease, and centrifuged at 1200 X g. The amount of DNA in 1200 X g supernatants was increased by TSH at 5 h, but not at 2 h. In parallel studies, thyroid slices were incubated with 32Pi and labeling of acid-soluble nuclear proteins was examined. TSH-dependent increases in labeling of histones H1 and H3, and of the high mobility group protein HMG 14, were observed at 2 h; however, there were no apparent changes in TSH-dependent labeling between 2 and 5 h, in nuclease-sensitive or in bulk chromatin. These results suggest that the observed TSH-dependent changes in the micrococcal nuclease-sensitivity of thyroid nuclear chromatin were not induced directly by changes in the phosphorylation of the histones or HMG 14.

Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes

Purified RNA polymerase II from calf thymus can bind to about 15% of the nucleosome core particles prepared from mouse myeloma cells, forming a discrete complex having a sedimentation coefficient of 18S. These bound nucleosome cores are heavily enriched in transcribed DNA sequences, are deficient in histones H2A and H2B, and undergo a reversible change in structure on RNA polymerase II binding.

Eukaryotic ternary transcription complexes. I. The release of ternary transcription complexes of RNA polymerases I and II by the endogenous nucleases of rat liver nuclei

Autodigestion of rat liver nuclei in magnesium-containing buffers leads to the release of about 80% of DNA-dependent RNA polymerases I and II, together with 4 to 8% of the DNA. The RNA polymerases are at least partially DNA bound as judged by the effect on in vitro transcription of (1) Actinomycin D, (2) preirradiation of the enzymes in the presence of 8-methoxypsoralen and (3) heparin. The released DNA migrates as ladders of nicked nucleosome-size fragments on electrophoresis. On sucrose gradients, most RNA polymerase activity sediments as two peaks: one slightly smaller than the 11S mononucleosome and the other with the dinucleosome. The released material can act as a source of ternary transcription complexes for further structural studies.

Fractionation of mechanically sheared chromatin on ECTHAM-cellulose

Chromatography of chromatin on the weak ion-exchange resin ECTHAM-cellulose was re-examined using the combined salt-pH elution conditions of Stratling, W.H., Van, N.T. and O'Malley, B.W. (1976) Eur. J. Biochem. 66, 423-433. When mechanically sheared rat liver chromatin was chromatographed on ECTHAM-cellulose the histone composition of eluted fractions was very similar, whereas early eluting fractions were enriched in non-histone proteins, including certain high mobility group proteins, and in hnRNP particles, containing newly synthesised RNA. Later eluting fractions were depleted in all of these components. The majority of hnRNP particles in early eluting chromatin were shown to be physically associated with chromatin by centrifugation in metrizamide. Hen erythrocyte chromatin contained no early eluting material. Size of DNA fragments was not a significant factor in determining the elution position of chromatin fragments. Early eluting material was not generated by endogenous nuclease and protease action. The conditions of chromatin preparation, and of elution of early chromatin fractions caused no gross disruption of chromatin structure, or dissociation of chromatin proteins, although some nucleosome sliding may have occurred. The conditions required for elution of some of the later fractions are sufficient to cause dissociation of protein, and alteration of chromatin conformation.

Fractionation of chromatin, released by nuclease digestion, on ECTHAM-cellulose. Separation of active and inactive chromatin

Chromatin released by two nucleases under various ionic conditions has been fractionated by chromatography on ECTHAM-cellulose. Mg2+ -soluble chromatin, which according to Gottesfeld and Partington is enriched in transcribed DNA sequences (Gottesfeld, J.M. and Partington, G.A., (1977) Cell 12, 953-962) and produced by DNAase II digestion at intermediate ionic strength, comprises material eluting from ECTHAM-cellulose at 80-100 mM Cl-, pH 6.8-7.0, whereas bulk, Mg2+ -insoluble chromatin comprises more tightly binding material. Free hnRNP particles elute at 30 mM Cl-, pH 6.8. Oligonucleosomes, which according to Dimitriadis and Tata are enriched in transcribed sequences (Dimitriadis, G.J. and Tata, J.R. (1980) Biochem. J. 187, 467-477) and produced by micrococcal nuclease digestion at physiological ionic strength, also elute predominantly at 80-100 mM Cl-, pH 6.8-7.0. When liver nuclei are digested with micrococcal nuclease at low ionic strength, the most rapidly released chromatin is enriched in nascent RNA and hnRNP particles, and binds weakly to ECTHAM-cellulose. More slowly solubilised chromatin, containing fewer hnRNP particles, binds much more strongly to ECTHAM-cellulose. In confirmation of results with mechanically sheared chromatin, the affinity of particular chromatin fractions is not dependent on the size of chromatin particles, rather it reflects the differing composition, and in particular the non-histone protein and hnRNP content, which, we propose, determines the conformation adopted by different chromatin fractions in the cation conditions used for elution from ECTHAM-cellulose.

Correlation of nitrosourea murine bone marrow toxicity with deoxyribonucleic acid alkylation and chromatin binding sites

All of the clinically available nitrosourea antitumor agents produce serious treatment-limiting bone marrow toxicity. A reduction in this toxicity can be achieved by attaching the chloroethylnitrosourea cytotoxic group to C2 (chlorozotocin) or C1 (1-(2-chloroethyl)-3-(beta-D-glucopyranosyl)-1-nitrosourea, GANU) of glucose. Both glucose analogs are less myelotoxic in mice than 1-(2-chloroethyl)-3-cyclohepyl-1-nitrosourea (CCNU) or 1-(4-amino-2-methylpyrimidin-5-yl)methyl-3-(2-chloroethyl)-3-nitrosourea (ACNU), while retaining comparable antitumor activity against the murine L1210 leukemia. To define the nuclear mechanisms for this reduced myelotoxicity, alkylation of L1210 and murine bone marrow DNA was quantitated. With the use of the endonuclease micrococcal nuclease and DNase I, the sites of alkylation within the chromatin substructure were determined. Experiments were performed on L1210 leukemia or bone marrow cells that had been incubated in vitro for 2 hr with 0.1 mM [14C]chloroethyl drug. The quantitative alkylation of DNA by GANU was 1.3-fold greater in L1210, as compared to bone marrow, cells. This ratio of DNA alkylation is comparable to the 1.3 ratio we previously reported for chlorozotocin [L. C. Panasci, D. Green and P. S. Schein, J. clin. Invest. 64, 1103 (1979)]. In contrast, the ratio of alkylation (L1210:bone marrow DNA) for the myelotoxic ACNU was 0.66, similar to 0.59 for CCNU. Nuclease digestion experiments demonstrated that chlorozotocin and GANU preferentially alkylated internucleosomal linker regions of bone marrow chromatin, while nucleosome core particles were the preferred targets of CCNU and ACNU. The reduced myelotoxicity of chlorozotocin and GANU may be correlated with the advantageous ratio of L1210:bone marrow DNA alkylation and preferential alkylation of internucleosomal regions of bone marrow chromatin.

Ultrastructural organization of yeast chromatin

The ultrastructural organization of yeast chromatin was examined in Miller spread preparations of samples prepared from spheroplasts or isolated nuclei of Saccharomyces cerevisiae. Micrographs from preparations dispersed in 1 mM Tris (pH 7.2) illustrate that the basic chromatin fiber in yeast exists in two ultrastructurally distinct conformations. The majority (up to 95%) of the chromatin displays a beaded nucleosomal organization, although adjacent nucleosomes are separated by internucleosomal linkers of variable lengths. Ribonucleoprotein (RNP) fibrils are only occasionally associated with chromatin displaying the conformation. The remaining 5-10% of the chromatin appears to be devoid of discrete nucleosomes and has a smooth contour with a fiber diameter of 30-40 A. Transcriptional units, including putative ribosomal precursor RNA genes, defined by the presence of nascent RNP fibrils are restricted to chromatin displaying this smooth morphology. Chromatin released from nuclei in the presence of 5 mM Mg++ displays higher-order chromatin fibers, 200-300 A in diameter, these fibers appear to be arranged in a manner than reflects the two forms of the basic chromatin fiber.

Isolation of active transcription complexes from animal cell nuclei by nitrocellulose binding

A method for the rapid isolation of active transcription complexes from animal cell nuclei is described. The method is based on the observation that, after lysis of nuclei with the detergents Sarkosyl and Triton X-100, transcription complexes are selectively bound to nitrocellulose. The nitrocellulose filters retain 80-90% o the RNA labelled briefly in vitro and about 10% of the nuclear DNA. The bulk of the retained DNA is in the size range of 20 kb. Transcription complexes involving both RNA polymerase I and II are retained by nitrocellulose. The nitrocellulose-bound transcription complexes preserve almost all of their RNA polymerase activity. The size distribution of the RNA product shows that bound transcription complexes retain also most of their growing RNA chains. The possibility to use selective retention by nitrocellulose in the analysis of transcriptionally active genes is discussed.

Responses to androgens of rat ventral prostate nuclear androgen-binding sites sensitive and resistant to micrococcal nuclease

Rat ventral prostate nuclei were separated into three major fractions by mild digestion with micrococcal nuclease and two fractions by extensive digestion. All fractions contained androgen-binding sites. Almost 50% of nuclear binding sites were resistant to enzymic digestion when only 5-15% of total DNA was resistant. Under milder digestion conditions, 21% of nuclear binding sites were associated with an intermediate fraction, representing 16% of total nuclear DNA, which was enriched in specific androgen-regulated gene sequences. This fraction was rapidly degraded by more extensive digestion. The nuclease sensitivity of these particular genes was markedly influenced by castration and the administration of dihydrotestosterone to castrated animals. The nuclear content of both nuclease-resistant and -sensitive androgen-binding sites was decreased by castration. Whereas the administration of androgen to animals castrated 1 day previously preferentially replenished nuclease-resistant sites, nuclease-sensitive sites, including those associated with transcriptionally active regions, had apparent priority when androgen was supplied to animals castrated 7 days previously. The significance of these observations to the regulation of nuclear processes and the possible interrelationships of nuclease-sensitive and -insensitive sites are discussed.

Characterization of rat liver oligonucleosomes enriched in transcriptionally active genes: evidence for altered base composition and a shortened nucleosome repeat

A transcriptionally active chromatin fraction of oligonucleosome size has been separated and isolated by a modified micrococcal nuclease fractionation procedure. After mild enzymatic digestion, rat liver nuclei were lysed, and the chromatin was separated by centrifugation on linear sucrose gradients. Fractions from four regions of the gradient were pooled and labeled, from the top to the bottom, A, B, C, and D, respectively. Fraction A, which contained 20% or less of the total DNA, was determined to have a mean size of a hexanucleosome. By hybridization with [3H]cDNA transcribed from total cytoplasmic poly(A) mRNA, DNA from fraction A was shown to be 10-15-fold enriched in transcribing genes when compared with total DNA. This fraction also has a somewhat higher concentration of AT base sequences. Significant differences were observed in nucleosome phasing. Fraction A has the shortest repeat length, fractions B and C are intermediate, and fraction D, which is depleted in transcribing DNA sequences, has the longest. Thus, we have isolated a chromatin fraction of oligonucleosome size enriched in transcribing genes and organized with reduced nucleosome spacing.

Characterisation of a chromatin fraction bearing pulse-labelled RNA. 1. Nascent RNA, RNA polymerase B and transcribed DNA sequence content

We have further characterised a fraction of polynucleosomal chromatin from mouse cells which is enriched in transcribing regions, after separation by multistep partition in a dextran /poly(ethylene glycol) two-phase mixture [Faber, A. J. (1972) Methods Cell Biol. 16, 447--457]. This fraction contains an average of 16% of the total DNA and 63% of the 3-min pulse-labelled RNA in chromatin which, by a number of criteria, represents nascent RNA transcripts. Of the total transcribing RNA polymerase B molecules in chromatin, 52% are found in this fraction by titration with radioactive alpha-amanitin. About 28% of the single-copy DNA sequences in this fraction hybridise to nuclear polyadenylated RNA, compared with only 1.5% of the single-copy sequences in the remaining (nontranscribing) chromatin fraction.

Different chromatin structures in Physarum polycephalum: a special form of transcriptionally active chromatin devoid of nucleosomal particles

Nonnucleolar chromatin from interphase nuclei of Physarum polycephalum plasmodia occurs in two different structural configurations as seen in electron microscopic spread preparations. While the majority of the chromatin is devoid of nascent ribonucleoprotein (RNP) fibrils and compacted into nucleosomal particles, a minor proportion (10-20%) is organized differently and reveals a smooth contour. It is this form of smooth chromatin which is rich in transcription units (mean length: 1.36 +/- 0.21 micrometer). Only occasionally are solitary nascent RNP fibrils observed which are associated with beaded strands of chromatin. In transcribed smooth chromatin nucleosomal particles are not only absent from the transcription units but also from their nontranscribed flanking regions, indicating that this special structural aspect is not merely a direct consequence of the transcriptional process. The existence of ca. 10-20% of Physarum chromatin in the smoothly contoured form is discussed in relation to reports of a preferential digestibility of a similar proportion of Physarum chromatin by DNAse I (Jalouzot et al., 1980) and to the altered configuration of "peak A" chromatin subunits after micrococcal nuclease digestion (Johnson et al., 1978 a, b).

Effect of thyrotropin on 32P-labelled histones H1 and H3 in specific populations of nucleosomes in the thyroid

Thyrotropin (TSH) increases the labeling of histones of H1 and H3 in thyroid slices incubated with 32Pi. We have prepared nuclei from control and TSH-treated thyroid slices, digested them with micrococcal nuclease, and extracted specific populations of nucleosomes by salt fractionation. Mononucleosomes, derived from the most nuclease-sensitive regions of chromatin, appeared to be selectively enriched in 32P-labeled H1 and H3. However, we were able to detect TSH enhancement of H1 and H3 labeling only in nucleosome multimers derived from less nuclease-sensitive chromatin. Recent studies have indicated that transcriptionally competent regions of chromatin may be more susceptible to micrococcal nuclease digestion than inactive regions. Our results therefore suggest that H1 and H3 may be actively phosphorylated in transcriptionally competent chromatin; however, they suggest either that hormone-dependent phosphorylation of H1 and/or H3 does not confer transcriptional competence, or that not all transcriptionally competent chromatin is nuclease sensitive.

Quantitation of transcribing native simian virus 40 minichromosomes extracted from CV1 cells late in infection

Simian virus 40 transcriptional complexes could be extracted from CV1 cells late in infection and separated from the bulk of inactive viral chromatin. Sucrose gradient sedimentation, cesium sulfate equilibrium density gradient centrifugation, and electron microscopy indicated that the viral transcriptional complexes corresponded to at least 0.5 to 1% of the viral minichromosomes extracted, about 5,000 copies per cell.

Partial characterization of RNA polymerase II complex released by micrococcal nuclease digestion of rat liver nuclei

Two forms of RNA polymerase II were released from rat liver chromatin by micrococcal nuclease digestion of the nuclei. One from behaved like a free RNA polymerase II and the other like a complex with other nuclear components. Both forms of RNA polymerase II activity were recovered in the 0.16 M NaCl-soluble fraction of the nuclear digest, and the complexed from the RNA polymerase II could transcribe its endogenous template under conditions permitting only of elongation of the RNA synthesis. The RNA polymerase II complex was further purified by gel filtration chromatography and column electrophoresis. Analysis of protein and DNA of the partially purified complex suggested that the RNA polymerase II was bound to mono- or dinucleosomes carrying some characteristic nonhistone proteins. Furthermore, in experiments on tissues from starved rats, the two forms of RNA polymerase II were found to originate from different functional states of the chromatin-bound enzyme in vivo.

The quinternary chromatin-DNA structure. Three-dimensional reconstruction and functional significance

Nuclear DNA-space images from Feulgen-stained HeLa cells synchronized at 1, 3, 5, 8, 12, 15, and 18 h following mitosis are digitized and their densitometric-geometric patterns are analyzed by means of a Quantimet 720-D image analyzer on line with a PDP11/40 computer. Frequency distributions of picture point optical densities for the phases and subphases as seen in nuclear images show that DNA packing changes are evident by means of ordinary optical microscopy. Radii of gyration of the images, and optical density profiles and distributions for several squashes of similar cells reveal that in particular instances chromatin DNA is distributed mostly towards the periphery, and usually with high circular isotropy. Cross power spectra of individual scan lines suggest that existence of higher order "quinternary" periodic structure for chromatin that modulates during the cell cycle. Three-dimensional reconstruction 2- micrometer sections of intact, Feulgen-stained mammalian tumor tissue show stainable material only toward the nuclear perimeter and not in the center (compatible with the evidence that initial thymidine incorporation in HeLa cells is generally at the nuclear border). Densitometric properties of reconstructed interphase chromatin-DNA bodies are highly coupled with similar properties of the whole nucleus, showing that a more condensed nucleus is always accompanied by a more condensed interphase chromatin DNA. The effect of micrococcal nuclease digestion on the digitized nuclear images is also presented. All the above data are then discussed in terms of a quinternary chromatin-DNA structure and its modulation during the cell cycle.