Renaturation kinetics of cDNA complementary to cytoplamic polyadenylated RNA from rainbow trout testis. Accessibility of transcribed genes to pancreatic DNase

Distribution of histone variants in the sea urchin chromatin fractions obtained by selective micrococcal nuclease digestion

Chromatin fractions differing in their transcriptional activity were isolated by selective micrococcal nuclease digestion of nuclei from sea urchin embryos (Strongylocentrotus droebachiensis) at the gastrula and pluteus stage. The electrophoretic analysis of the chromatin proteins at the gastrula stage showed that a soluble, transcriptionally active fraction of chromatin was enriched with early variants of histones H1 and H2A. The early and late variants of histone H2A at the pluteus stage were distributed randomly between chromatin fractions. However, the content of both variants of histone H1 was essentially decreased in the soluble transcriptionally active fraction of chromatin.

Effects of pre-treatment with sodium butyrate on the frequencies of X-ray-induced chromosomal aberrations in human peripheral blood lymphocytes

The effects of sodium butyrate-mediated alterations in chromatin structure on the yields of X-ray-induced chromosomal aberrations were studied in human peripheral blood lymphocytes. Unstimulated (G0) lymphocytes were pre-treated with sodium butyrate (5 mM) for 24 h, X-irradiated and then stimulated to pass through the cell cycle. Cells in their first post-radiation metaphase were scored for chromosomal aberrations. In parallel biochemical experiments nucleoid sedimentation technique was used to examine the induction and repair of DNA-strand breaks. The results show that sodium butyrate pre-treatment leads to a significant increase in the frequencies of dicentrics and rings, but not of fragments. The data from biochemical studies suggest that the numbers and rates of repair of X-ray-induced DNA-strand breaks are the same in butyrate-treated and untreated cells. We therefore suggest that the observed effect is probably a consequence of butyrate-induced conformational changes in the chromatin of G0 lymphocytes.

HMG-like protein in barley and corn nuclei

Chromosomal proteins have been isolated from barley (Hordeum vulgare) and corn (Zea mays) nuclei by extraction with 5% perchloric acid. In each plant, one protein was shown to belong to the HMG proteins. Their molecular weights are very close to that of HMG 14 from chicken erythrocytes, as shown by electrophoretic mobility in SDS polyacrylamide gels. In acetic acid-urea-Triton polyacrylamide gels they migrate between HMG 1,2 and HMG 14, from chicken erythrocytes. Their amino acid compositions are typical of HMG proteins, with equivalent high values of acidic and basic residues.Extraction of HMG's from purified barley chromatin fractions with 0.35 M NaCl considerably reduces histone H2 contamination and increases the yield of HMG up to 0.7% of the total histones. In this technique a second protein was extracted which is soluble in 2% Trichloroacetic acid and shows electrophoretic mobility analogous to those of HMG 14 and 17 from chicken erythrocytes. Whether or not these proteins are counterparts of the animal HMG's 1-2 or HMG's 14-17 is discussed.

Associated effects of sodium butyrate on histone acetylation and estrogen receptor in the human breast cancer cell line MCF-7

Sodium butyrate at a concentration of 5mM causes significant hyperacetylation of the core histones in the human breast cancer cell line MCF-7. Histone hyperacetylation was achieved in rapidly-growing cells at 40% confluency after 24 hours in 5mM sodium butyrate. More nearly confluent cells did not reach as high a level of histone hyperacetylation. Upon assaying the estrogen receptors, both cytosolic and KCl-extractable nuclear, we found that butyrate treatment had lowered the estrogen receptor levels in both compartments. To our knowledge this is the first report of an effect of sodium butyrate on estrogen receptor levels.

DNase I sensitivity of transcriptionally active genes in intact nuclei and isolated chromatin of plants

We have investigated the DNase I sensitivity of transcriptionally active DNA sequences in intact nuclei and isolated chromatin from embryos of wheat (Triticum aestivum L.). Nuclei or isolated chromatin was incubated with DNase I, and the extent of DNA digestion was monitored as percentage acid solubility. The resistant DNA and DNA from sham-digested controls were used to drive reassociation reactions with cDNA populations corresponding to either total poly(A)+RNA from unimbibed wheat embryos or polysomal poly(A)+RNA from embryos that had imbibed for 3 hr. Sequences complementary to either probe were depleted in DNase I-resistant DNA from nuclei and from chromatin isolated under low-ionic-strength conditions. This indicates that transcriptionally active sequences are preferentially DNase I sensitive in plants. In chromatin isolated at higher ionic strength, cDNA complementary sequences were not preferentially depleted by DNase I treatment. Therefore, the chromatin structure that confers preferential DNase I sensitivity to transcriptionally active genes appears to be lost when the higher-ionic-strength method of preparation is used. Treatment of wheat nuclei with DNase I causes the release of four prominent nonhistone chromosomal proteins that comigrate with wheat high mobility group proteins on NaDodSO4 gels.

Association of thyroid hormone receptors with chromatin

A large body of circumstantial evidence indicates that receptors located in nuclei of T3 responsive tissues represent a site of initiation of thyroid hormone action at the cellular level. Partial characterization of T3 receptors indicates that these proteins are monomeric structures in nuclei and are chromatin-associated non-histone proteins. Treatment of rat liver nuclei with either pancreatic DNase I or micrococcal nuclease releases T3 receptors from nuclei in two forms: a predominant (95 400 Mr; 5.5-6.0S) and a minor (265 000-365 000 Mr; 12.5S) nucleoprotein complex. Similar structures are excised from rat kidney, brain, and heart nuclei and from GH1 pituitary cell nuclei by micrococcal nuclease digestion. These endonuclease-excised receptor-containing complexes are significantly larger than the salt-extracted receptor (50 000 Mr; 3.5S). The presence of DNA and other non-receptor proteins in these structures indicates that T3 receptors probably function within multimeric complexes in vivo. Although T3 receptors appear to be associated with DNA between nucleosomes, i.e. linker DNA, it is not entirely clear whether all or only a fraction of T3 receptors interact with nucleosomal components. The 12.5S receptor-containing nucleoprotein complex may represent T3 receptors in association with linker DNA and nucleosomal components. T3 receptors do not appear to be uniformly distributed to all chromatin fractions, but are associated with structures having characteristics of transcriptionally active chromatin. They are found in a region of chromatin which is enriched in RNA polymerase activity, rapidly labeled RNA and non-histone proteins, and depleted of histone Hl. This region is also highly sensitive to both micrococcal nuclease and pancreatic DNase I digestion. The association of receptors with transcriptionally active chromatin, however, must be considered provisional until additional details of the precise receptor-chromatin interaction have been established. The recent demonstration of a 20-fold increase in a specific hepatic mRNA four hours following administration of T3 to hypothyroid rats indicates that thyroid hormone potentially has very rapid effects on hepatic gene expression. However, significant changes in nuclear protein phosphorylation, nuclear protein composition, and chromatin structure have not been detected within this four-hour period. Thus, effects of T3 on hepatic gene expression are brought about by local and presumably subtle changes in nuclear function.

Enhanced myocardial RNA synthesis in spontaneously hypertensive rats possible role of high-mobility group non-histone proteins

Cardiac hypertrophy in spontaneously hypertensive rats is associated with increased nuclear RNA polymerase activity. In order to explore mechanisms facilitating the interaction of the enzyme with its endogenous template, we compared the structure of nuclear chromatin from myocytes of 20-week-old spontaneously hypertensive rats and normotensive Wistar-Kyoto controls. Enhanced RNA synthesis in hypertensive rats was accompanied by increased susceptibility to digestion by deoxyribonuclease I. Nick translation of nuclei also resulted in higher nucleotide incorporation in hypertensive rats. Salt-extraction abolished the differences in deoxyribonuclease I sensitivity between the two animal groups. Reconstitution with either 0.35 M NaCl-extract or high mobility group (HMG) non-histone proteins restored digestion susceptibility but did not equalize SHR and WKY cells. SDS-polyacrylamide gel electrophoresis of 0.35 M NaCl-extracts and supernatants from deoxyribonuclease I digestion revealed the presence of HMG proteins which were preferentially released in hypertensive rats. There was a small but statistically significant increase in nuclear HMG protein content in hypertensive rats (0.12 +/- 0.02 mg/mg DNA vs. 0.09 +/- 0.02 mg/mg DNA in Wistar-Kyotos, P less than 0.05) but no difference in their electrophoretic appearance. These results indicate that chromatin structure is altered in the hypertrophied myocardium with resultant increase in deoxyribonuclease I susceptibility. This increase appears to be partly dependent on the high-mobility group non-histone proteins.

Detailed analysis of the nucleosomal organization of transcribed DNA in yeast chromatin

The precise chromatin structure of actively transcribed DNA in yeast has been analyzed by electrophoretic transfer of high-resolution staphylococcal nuclease and DNase I chromatin digest DNA patterns to DBM paper and hybridization with active sequence probes. The DNA patterns of the transcribed DNA sequences resemble the DNA patterns produced by digestion of bulk yeast nucleosomes. Hence, these active sequences must be arranged in "typical" nucleosome structures. Furthermore, in details of the structure, the active sequence nucleosomes look almost exactly like the average yeast nucleosome in repeat length, in the length of DNA associated with the core particle, in the amount and type of heterogeneity found within and between the oligomeric and monomeric repeat lengths of DNA, in the occurrence of discrete spacer lengths including the characteristic five nucleotide increments (i.e., 5, 15, 25, ... base pairs), and in the length of DNA between yeast nucleosomes. Early in digestion, there are some differences: increases in peak breadths (i.e., in the distribution of spacer lengths) and some preferential release of monomer DNA. These results suggest that transcribed DNA can exist in the typical (yeast) type of nucleosome organization and thus that active chromatin regions do not necessarily require profound structural rearrangements. The slight differences noted are consistent with some slight, mainly spacer, modification in the vicinity of the transcription event itself.

Structure of transcriptionally active and inactive nucleosomes from butyrate-treated and control HeLa cells

Nuclei from butyrate-treated or control HeLa cells were separated into micrococcal nuclease sensitive and resistant chromatin. Those regions most sensitive to the nuclease, amounting to some 10% of the chromatin, consisted mainly of mononucleosomes with equimolar amounts of the inner histones H2A, H2B, H3, and H4, very little H1, and equimolar amounts of the two small high-mobility group (HMG) proteins, HMG-14 and -17. Both in butyrate-treated and in control cells, these nuclease sensitive monomers were some 5--7-fold enriched in DNA sequences which are transcribed into cytoplasmic polyadenylated RNA, while resistant monomers are depleted in the same sequences. Electrophoretic analyses of the transcriptionally active mononucleosomes revealed heterogeneity. Several subcomponents were resolved when monomers of butyrate-treated or control cells were electrophoresed at low ionic strength. Active monomer subcomponents differ in their molar content of HMG-14 and -17, in their content of H1 and A24, and in the length of their DNA. Some minor differences between nucleosomes of butyrate-treated and control cells were observed.

Heterogeneous binding of high mobility group chromosomal proteins to nuclei

A dramatic difference is observed in the intracellular distribution of the high mobility group (HMG) proteins when chicken embryo fibroblasts are fractionated into nucleus and cytoplasm by either mass enucleation of cytochalasin-B-treated cells or by differential centrifugation of mechanically disrupted cells. Nuclei (karyoplasts) obtained by cytochalasin B treatment of cells contain more than 90 percent of the HMG 1, while enucleated cytoplasts contain the remainder. A similar distribution between karyoplasts and cytoplasts is observed for the H1 histones and the nucleosomal core histones as anticipated. The presence of these proteins, in low amounts, in the cytoplast preparation can be accounted for by the small percentage of unenucleated cells present. In contrast, the nuclei isolated from mechanically disrupted cells contain only 30-40 percent of the total HMGs 1 and 2, the remainder being recovered in the cytosol fraction. No histone is observed in the cytosol fraction. Unike the higher molecular weight HMGs, most of the HMGs 14 and 17 sediment with the nuclei after cell lysis by mechanical disruption. The distribution of HMGs is unaffected by incubating cells with cytochalasin B and mechanically fractionating rather than enucleating them. Therefore, the dramatic difference in HMG 1 distribution observed using the two fractionation techniques cannot be explained by a cytochalasin-B-induced redistribution. On reextraction and sedimentation of isolated nuclei obtained by mechanical cell disruption, only 8 percent of the HMG 1 is released to the supernate. Thus, the majority of the HMG 1 originally isolated with these nuclei, representing 35 percent of the total HMG 1, is stably bound, as is all the HMGs 14 and 17. The remaining 65 percent of the HMGs 1 and 2 is unstably bound and leaks to the cytosol fraction under the conditions of mechanical disruption. It is suggested that the unstably bound HMGs form a protein pool capable of equilibrating between cytoplasm and stably bound HMGs.

Selective release of HMG nonhistone proteins during DNase digestion of Tetrahymena chromatin at different stages of the cell cycle

The possible role of LG-1, a Tetrahymena specific HMG protein found in the macronuclear chromatin (Hamana, K. and Iwai, K. (1979) J. Biochem. 86, 789-794), was examined in relation to the chromatin structure. The chromatin isolated from cells synchronized at different stages of the cell cycle contained about one molecule of LG-1 per nucleosome. Limited digestion of the chromatin with DNase I or micrococcal nuclease selectively released LG-1 with the nucleosomal core histones and H1 remained insoluble, bound to the resistant DNA. Depending on the cell stages several types of chromatin structure were distinguished by their nuclease sensitivity. However, the chromatin at different stages exhibited the similar behavior of the LG-1 release with the nucleases as a function of the degree of chromatin solubilization. The results suggest that LG-1 proteins play a role in the chromatin organization which is rather independent of the cell stages.

Thyroid hormone receptor-containing fragment released from chromatin by deoxyribonuclease I and micrococcal nuclease

Limited deoxyribonuclease I and micrococcal nuclease digestion of hepatic nuclei from euthyroid rats injected with 125I-labeled triiodothyronine ([125I]T3) releases a discrete [125I]T3-labeled chromatin fragment (5.8S) which is larger than the T3 receptor (3.5S). These results suggest the T3 receptor is associated with a restricted fraction of hepatic chromatin that has a nuclease sensitivity characteristic of transcriptionally active chromatin.

Distribution within chromatin of deoxyribonucleic acid repair synthesis occurring at different times after ultraviolet radiation

We have compared the initial distribution and subsequent redistribution within chromatin of nucleotides incorporated during the early ("rapid") phase and the late ("slow") phase of UV-induced DNA repair synthesis. As has been observed for the early repair phase, most or all of the nucleotides incorporated during the late repair phase are initially staphylococcal nuclease and DNase I "sensitive" (i.e., rapidly digested). This initial enhanced sensitivity is accompanied by both an underrepresentation of these nucleotides in the 145--165 base pari (core) DNA produced by staphylococcal nuclease digestion and an absence of these nucleotides in the approximately 20-base repeat pattern produced by DNase I digestion. Furthermore, nucleotides incorporated at late time after damage are involved in nucleosome rearrangements as reported previously for repair synthesis occurring at early times [Smerdon, M. J., & Lieberman, M. W. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4238--4241]. The kinetics of redistribution, however, appear to be more rapid than those observed for early times. Following redistribution the average nucleosome repeat length of DNA containing repair-incorporated nucleotides is the same as that of bulk DNA regardless of the time after damage that repair occurs; also, many of these nucleotides coelectrophorese with the approximately 10-base repeat fragments generated by DNase I. The results yield a new interpretation of our previous studies [Smerdeon, M. J., Tlsty, T. D., & Lieberman, M. W. (1978) Biochemistry 17, 2377--2386] on the distribution of nucleotides incorporated at long times after UV irradiation.

Partial inhibition of histone deacetylase in active chromatin by HMG 14 and HMG 17

Digestion of isolated Friend erythroleukemic cell nuclei with DNase I under conditions which selectively destroy the DNA of transcriptionally "active" genes releases into the supernatant fraction proteins of the non-histone "High Mobility Group" (HMGs). Two of these, HMG-14 and HMG-17(identified by solubility in trichloroacetic acid, electrophoretic mobility on SDS-polyacrylamide gels and by amino acid composition) will partially inhibit the endogenous mouse cell histone deacetylase enzymes when added to in vitro assay mixtures. Other closely related proteins do not share this inhibitory ability and thus the reaction with the enzymes appears to be specific. Since these two HMG proteins appear to be preferentially associated with the "active" fraction of chromatin, these findings have important implications for possible models of eukaryotic gene regulatory mechanisms.

Segregation of rapidly acetylated histones into a chromatin fraction released from intact nuclei by the action of micrococcal nuclease

It has been previously shown that micrococcal nuclease digestion and subsequent fractionation of hen oviduct nuclei generates fractions enriched (first supernatant fraction - 1SF) and depleted (second supernatant fraction - 2SF) in ovalbumin genes, while a third fraction, the pellet fraction, contains about the same level of this gene as whole chromatin (Bloom and Anderson (1978) Cell 15, 141-150). We have utilized this fractionation method in an attempt to assess the extent and kinetics of histone acetylation associated with chromatin from the 1SF, 2SF, and pellet fraction. Hepatoma Tissue Culture (HTC) cells were labelled for 30 minutes in vivo with 3H-acetate, nuclei isolated and the chromatin fractionated. The specific activity of the histones in the 1SF was slightly greater than that of the 2SF (1.2 to 1.6 fold difference) independent of the length of nuclease digestion. If the labelling period is followed by short (10 to 60 minute) treatment of the cells with sodium butyrate, the more rapidly as well as more extensively acetylated histones are also preferentially found in the 1SF. This is in part the result of segregation of chromatin particles into the 1SF as the histones associated with these particles become hyperacetylated. That is, the extent of histone acetylation regulates the distribution of chromatin in the 1SF, 2SF and pellet fraction.

Limited DNase I nicking as a probe of gene conformation

We have extended the use of pancreatic DNase I as a probe of chromatin structure by exploring the accessibility of an active gene to the introduction of the first single-stranded nick. We show by a target analysis that the beta-globin gene is about 25-fold more sensitive to single-site nicking than is an average sequence in the chicken erythrocyte nucleus or the nontranscribed albumin gene. The sites of initial DNase I nicking are shown to cluster within the transcribed sequence of the beta-globin gene.

Reconstitution of a deoxyribonuclease I-sensitive structure on active genes

Chicken erythrocyte nuclei have been labeled in the active regions of the chromosome by using the nick translation reaction. In this procedure, accessible areas of the genome are preferentially nicked by the action of pancreatic DNase I and subsequently labeled by using DNA polymerase I from Escherichia coli. These nuclei were employed as a substrate for studying the factors responsible for maintaining the special chromatin conformation of the overall population of active genes. Treatment of nuclei with 0.35 M NaCl resulted in the loss of DNase I sensitivity in the active genes, but this sensitivity could be restored when nuclei were reconstituted with the NaCl eluate. Further purification of the released factors revealed that the HMG (high-mobility group) proteins HMG-14 and HMG-17 are involved in maintaining the conformation of the active regions. These factors are not tissue specific and seem to be involved in the chromosomal structure of most of the active genes.

DNase I sensitivity of ribosomal genes in isolated nucleosome core particles

The level of chromatin structure at which DNase I recognizes conformational differences between inert and activated genes has been investigated. Bulk and ribosomal DNA's of Tetrahymena pyriformis were differentially labeled in vivo with [14C]- and [3H]-thymidine, respectively, utilizing a defined starvation-refeeding protocol. The 3H-labeled ribosomal genes were shown to be preferentially digested by DNase I in isolated nuclei. Staphylococcal nuclease digested the ribosomal genes more slowly than bulk DNA, probably owing to the higher GC content of rDNA. DNase I and staphylococcal nuclease digestions of purified nucleosomes and of nucleosome core particles isolated from dual-labeled, starved-refed nuclei were indistinguishable from those of intact nuclei. We conclude from these studies that DNase I recognizes an alteration in the internal nucleosome core structure of activated ribosomal genes.

Yeast chromatin is uniformly digested by DNase-I

The DNase I (EC 3.1.21.1) sensitivity of transcribed yeast chromatin has been examined. We find that, in contrast to chromatin from higher eukaryotes, transcribed yeast chromatin and total yeast chromatin are equally sensitive to DNase I digestion. We interpret these results to mean that the entire yeast genome exists in a state that represents a restricted proportion of total chromatin in higher eukaryotes.

Limited action of micrococcal nuclease on trout testis nuclei generates two mononucleosome subsets enriched in transcribed DNA sequences

Hybridization experiments show that DNA extracted from two distinct subsets of mononucleosomes (MNI and MN2) generated by a limited action of micrococcal nuclease on trout testis nuclei is enriched approximately 7-fold in sequences that are transcribed into cytoplasmic polyadenylated RNA in trout testis cells. Both subsets of mononucleosomes contain eight core histones, but MNI also possesses one or two molecules of a small, basic, high-mobility-group (HMG) protein H6 [Levy W., B., Connor, W. & Dixon, G. H. (1979) J. Biol. Chem. 254, 609-620], bound to a DNA fragment of 140 base pairs. In contrast, MN2 contains 1 molecule of H1 but no H6, and its DNA length is somewhat longer at 140-190 base pairs. The preferential release of these two subsets of mononucleosomes is correlated with the presence of a second larger HMG protein, HMG-T, in the linker regions flanking both types of mononucleosomes. The HMG-T-containing linker regions appear to be considerably more susceptible to attack by micrococcal nuclease than H1-containing linkers. Cross-reassociation reactions between the DNA from MN1 and MN2 subsets indicate that they share a significant extent of sequence overlap but also that each subset contains specific sequences that are absent in the other subset.

The complete amino-acid sequence of a trout-testis non-histone protein, H6, localized in a subset of nucleosomes and its similarity to calf-thymus non-histone proteins HMG-14 and HMG-17

The complete amino acid sequence of a basic non-histone protein, H6, isolated from the chromatin of rainbow trout (Salmo gairdnerii) testis cells, has been determined. Protein H6, first described by D. T. Wigle and G. H. Dixon [J. Biol. Chem. 246, 5636--5644 (1971)] was extracted with 5% trichloracetic acid and purified by ion-exchange chromatography on carboxymethyl-cellulose (CM-52). Sequence analysis was performed by automatic Edman degradation of the amino terminus of the intact protein and a series of large fragments derived by cleavage with chymotrypsin, staphylococcal protease and with mild acid to cleave at aspartic acid residues. Protein H6 possesses 69 residues and shows considerable similarities to the 89-residue calf thymus HMG-17 protein previously sequenced [Walker, J. M., Hastings, J. R. B. & Johns, E. W. (1977) Eur. J. Biochem. 76, 461--468]. B. Levy W. and G. H. Dixon [Proc. Natl Acad. Sci. U.S.A. 74, 2810--2814 (1977)] have shown that H6 is selectively solubilized when trout testis nuclei (or chromatin) are digested with DNase I under conditions which preferentially hydrolyze that portion of DNA enriched in transcribed sequences [Levy, W. B. & Dixon, G. H. (1977) Nucleic Acids Res. 4, 883--898]. Recently H6 has been located as a stoichiometric component of a distinct subset of trout testis nucleosomes that are complexed with a core nucleosome comprising 140 base pairs of DNA and the inner histones H2A, H2B, H3 and H4 [Levy, W. B., Connor, W. & Dixon, G. H. (1979) J. Biol. Chem., in the press].

Isolation of a subclass of nuclear proteins responsible for conferring a DNase I-sensitive structure on globin chromatin

The globin gene is preferentially sensitive to digestion by DNase I in erythrocyte chromatin but not in brain, fibroblast, or oviduct chromatin. Elution of the erythrocyte chromatin with 0.35 M NaCl leads to no detectable change in the gross structure of individual nucleosomes; however, in this depleted chromatin the globin gene is no longer preferentially sensitive to DNase I. Reconstitution of the depleted chromatin with either the entire 0.35 M NaCl fraction or a subclass from this fraction greatly enriched in two high mobility group proteins (nos. 14 and 17) results in the successful reconstitution of DNase I sensitivity of the globin gene. For all of these preparations, the inactive ovalbumin gene exhibited no preferential sensitivity to DNase I. Reconstitution of the erythrocyte 0.35 M NaCl fraction with depleted brain chromatin resulted in no preferential sensitivity of the globin gene in brain chromatin; however, reconstitution of the brain 0.35 M NaCl fraction with depleted erythrocyte chromatin led to successful reconstitution of DNase I sensitivity of the globin gene. Thus, the eluted proteins responsible for conferring DNase I sensitivity are probably not tissue-specific and probably do not recognize specific DNA sequences.

Multiacetylated forms of H4 are found in a putative transcriptionally competent chromatin fraction from trout testis

We have examined the distribution of acetylated histones derived from various trout testis chromatin fractions of different composition. Our results indicate that a chromatin fraction, preferentially solubilized by micrococcal nuclease, containing the bulk of the HMG proteins and similar to a fraction released from intact trout nuclei and previously shown to be enriched in transcribed DNA sequences also possesses high levels of multiacetylated species of H4. Histones 2A, 2B and 3 are also acetylated in this particular chromatin fraction. Monoacetylated species of the 4 inner nucleosomal histones appear to be characteristic of the nucleohistone portion of trout testis chromatin.

The influence of chromatin structure on the distribution of DNA repair synthesis studied by nuclease digestion

The influence of chromatin structure on the distribution of DNA repair synthesis was studied by enzymatic digestion of "repair labeled" nuclei of mouse mammary cells: "repair labeled" nuclei were isolated from pregnancy mammary tissue fragments, treated in vitro with methylmethanesulfonate (MMS) or methylnitrosourea (MNU), and pulse-labeled with 3H-thymidine in the presence of hydroxyurea in the culture medium. Micrococcal nuclease digestion of "repair labeled" nuclei indicates that at early hours after treatment with the alkylating agents 70-80% of the total repair synthesis is located in the linker portion of the nucleosome. However, 6-12 hours after treatment DNA repair synthesis is more evenly distributed throughout the core and linker portion of the nucleosome. "Repair labeled" mammary cell nuclei were also digested with DNase I under conditions selective for transcriptionally active chromatin. A two-fold higher level of repair synthesis was found in the transcriptionally active chromatin of "repair labeled" nuclei isolated from MMS or MNU treated mammary fragments, pulse-labeled at different times after treatment. The results indicate that structural constitution of the chromatin may influence the distribution of DNA repair synthesis both at the nucleosome level, and at higher levels of chromatin organization. This may be due to 1) nonrandom base alkylation in chromatin or 2) areas in chromatin with increased accessibility for the repair enzymes to the alkylated bases.

Responses of mammalian metaphase chromosomes to endonuclease digestion

Digestion of fixed metaphase chromosomes by endonucleases (micrococcal nuclease and DNase II) under optimal digestion conditions followed by Giemsa staining produces sharp banding patterns identical to G-bands. In 3H-thymidine labeled, synchronized metaphase cells of the chinese hamster (CHO line), the band induction is accompanied by the removal of DNA. The single strand specific nuclease S1 and DNase I do not produce such banding patterns.

Partial purification of transcriptionally active nucleosomes from trout testis cells

Mononucleosomes (MN1) enriched in structural non-histone proteins and transcribed DNA sequences were obtained by limited digestion of trout testis nuclei with micrococcal nuclease followed by selective solubilization in 0.1 M NaCl. These monosomes consist of the four inner histones plus stoichiometric amounts of the non-histone protein H6, of the HMG group, complexed with 140 base pairs of DNA. Hybridization experiments indicate that MN1 DNA is enriched in sequences complementary to cytoplasmic polyadenylated RNA.

Fractionation of nucleosomes by salt elution from micrococcal nuclease-digested nuclei

The solubilization of nucleosomes and histone H1 with increasing concentrations of NaCl has been investigated in rat liver nuclei that had been digested with micrococcal nuclease under conditions that did not substantially alter morphological properties with respect to differences in the extent of chromatin condensation. The pattern of nucleosome and H1 solubilization was gradual and noncoordinate and at least three different types of nucleosome packing interactions could be distinguished from the pattern. A class of nucleosomes containing 13--17% of the DNA and comprising the chromatin structures most available for micrococcal nuclease attack was eluted by 0.2 M NaCl. This fraction was solubilized with an acid-soluble protein of apparent molecular weight of 20,000 daltons and no histone H1. It differed from the nucleosomes released at higher NaCl concentrations in content of nonhistone chromosomal proteins. 40--60% of the nucleosomes were released by 0.3 M NaCl with 30% of the total nuclear histone H1 bound. The remaining nucleosomes and H1 were solublized by 0.4 M or 0.6 M NaCl. H1 was not nucleosome bound at these ionic strengths, and these fractions contained, respectively, 1.5 and 1.8 times more H1 per nucleosome than the population released by 0.3 M NaCl. These fractions contained the DNA least available for micrococcal nuclease attach. The strikingly different macromolecular composition, availability for nuclease digestion, and strength of the packing interactions of the nucleosomes released by 0.2 M NaCl suggest that this population is involved in a special function.

A protein released by DNAase I digestion of drosophila nuclei is preferentially associated with puffs

Antisera have been produced against five molecular weight subfractions of the Drosophila proteins readily extracted from nuclei following limited DNAase I digestion. Immunofluorescence staining techniques were used to assess the distributions of these proteins in the polytene chromosomes of Drosophila. In three cases, the antigens were widely distributed; in one case, the antigens appeared to be slightly more concentrated at active loci; and in one case, the antigens were strongly concentrated at a defined set of loci, including puffs and most of the loci which are active (puffed) at some time during third instar larval and prepupal development. The latter distribution pattern differs from that of RNA polymerase. Nonhistone chromosomal proteins of this type may have a key role in establishing and/or maintaining the altered chromatin structure characteristic of the active state.