Selective digestion of transcriptionally active ovalbumin genes from oviduct nuclei

Increased susceptibility of activated rat liver chromatin to DNAse I

Rat liver chromatin activated by partial hepatectomy is more susceptible to the action of DNAse I than control chromatin isolated from intact liver. The study on the transfer of chromatin material to the acid-soluble fraction reveals a higher rate of activated chromatin degradation. Activated chromatin shows also an increased capacity for ethidium bromide (EB) binding as estimated from the isotherms of adsorption. The difference in EB binding between activated and control chromatin is abolished after DNAse I treatment. Conditions of mild digestion with DNAse I have been found under which the number of binding sites for EB per nucleotide decreases to almost the same level in activated and non-activated chromatin. The results suggest a preferential degradation of those DNA sequences in activated chromatin that are responsible for the increase in the ligand binding.

Different nucleosome structures on transcribing and nontranscribing ribosomal gene sequences

Monomeric DNA lengths from Physarum nuclear chromatin occur in two subunit forms which differ from each other and from higher oligomers of nucleosomes in content of transcribed ribosomal DNA sequences. Labeled DNA restriction fragments from ribosomal RNA coding regions reanneal most rapidly with DNA from a monomeric subunit fraction. A particles, isolated from growing plasmodia and containing 144 base pairs of DNA in an extended conformation. Higher oligomers of nucleosomes are depleted in sequences from transcribing gene regions but are enriched in sequences from the nontranscribed central spacer of the ribosomal DNA palindrome. Nucleosome configuration on two 26S gene intervening sequences resembles that on adjacent coding regions.

Subnucleosome particles containing high mobility group proteins HMG-E and HMG-G originate from transcriptionally active chromatin

Subnucleosome particles SN2 and SN3 containing short DNA fragments and non-histone proteins of the high mobility group, HMG-G and HMG-E respectively, were purified from the chromatin preparations of mouse L cells partially digested with staphylococcal nuclease. Labeled DNAs prepared from these particles were hybridized to an excess of nuclear RNA. The binding of subnucleosomal DNA was about 3-fold higher comparing to total cellular DNA fragmented to the same size. Special control experiments showed that DNA.protein complexes present in subnucleosomes SN2 and SN3 preexisted in nontreated nuclei. The conclusion has been drawn that non-histone proteins HMG-G and HMG-E are associated with the DNA of transcriptionally active chromatin and are released by nuclease as subnucleosomes.

Structure of plant nuclear and ribosomal DNA containing chromatin

Digestion of plant chromatin from Brassica pekinensis and Matthiola incana with staphylococcus nuclease leads to a DNA repeat of 175 plus or minus 8 and a core size of 140 base pairs. DNase I digestion results in multiples of 10 bases. Ribosomal RNN genes were studied as a model system for active plant chromatin because of their great redundancy and their high transcriptional activity in growing and differentiating tissues. The actively transcribed genes were identified by nascent RNA of ribosomal origin still attached to its matrix DNA. Hybridization techniques were used to demonstrate that even transcriptionally active gene sequences are present in nuclease generated chromatin subunits. Comparison of the DNase I kinetics of chromatin digestion with the amount of ribosomal RNA genes which is available for hybridization at the given times indicated that ribosomal RNA genes are digested, but not preferentially degraded by DNase I.

Relaxation of chromatin structure induced by ethidium binding. Involvement of the intercalation process

In this paper we study the effects of the binding of ethidium on the structure of chromatin, using micrococcal nuclease as a structural probe. This binding induces two structural changes of chromatin either isolated or in the nuclei. (a) An unfolding of the overall structure which results in an activation of the rate of degradation by the nuclease. (b) A disorganisation of the core particle structure which has the effect of unwrapping the DNA from the histone core, this disruption can go on so far as to leave only 90 base pairs. By comparing the bindings of ethidium and tetramethylethidium, we conclude that the first type of structural change is due to an electrostatic effect and does not depend upon intercalation. On the other hand, the second one is due to the intercalation process and to the change of topological constraints on the DNA that such a process involves.

Assembly of an active chromatin structure during replication

MSB cells were pulse labeled with 3H-thymidine and the isolated nuclei digested with either staphylococcal nuclease (to about 40% acid solubility) or DNase I (to 15% acid solubility). The purified, nuclease resistant single-copy DNA was then hybridized to nuclear RNA (nRNA). The results of these experiments show that actively transcribed genes are assembled into nucleosome-like structures within 5-10 nucleosomes of the replication fork and that they also acquire a conformation characteristic of actively transcribed nucleosomes (ie, a DNase I sensitive structure) within 20 nucleosomes of the fork. Assuming DNA sequence specific interactions are required for establishing a DNase I sensitive conformation on active genes during each round of replication, our results indicate that a specific recognition event can occur very rapidly and very specifically in eukaryotic cells. The results are discussed in terms of the possible mechanisms responsible for propagating active, chromosomal conformations from mother cells to daughter cells.

A comparison of methods for extracting ribonucleic acid polymerases from rat liver nuclei

Nuclei were prepared from rat liver after homogenization of the tissue in hyperosmotic sucrose and RNA polymerases (EC 2.7.7.6) extracted by two methods applied sequentially. Optimal conditions for washing loosely bound enzymes out of nuclei were determined first, and involved short (10 min) incubations at 0 degrees C in the presence of 5 mM-Mg2+ and 60 mM-(NH4)2SO4. Subsequent sonication of the residual nuclear pellet after resuspension and lysis at high ionic strength resulted in further release of RNA polymerases. The primary wash yielded about 2 x 10(4) molecules of RNA polymerases I and III (altogether) and 1 x 10(4) molecules of form-II enzymes per original nucleus, whereas subsequent sonication released 2 x 10(4)-2.5 x 10(4) form-I and -III enzyme molecules (altogether) and a further 7 x 10(3)-8 x 10(3) form-II enzyme molecules, as measured by end-labelling of nascent RNA. RNA polymerase II was partially purified from both types of extracts and shown to initiate very poorly on high-molecular-weight homologous DNA irrespective of the source of the enzyme.

In vivo binding of N-2-acetylaminofluorene and its N-hydroxy derivative to the DNA of fractionated rat liver chromatin

The in vivo binding of radioactive N-2-acetylaminofluorene (AAF) and N-hydroxy-2-acetylaminofluorene (N-OH-AAF) to the DNA of rat liver chromatin was examined. The chromatin was fractionated into putative transcriptionally active and inactive fractions by hydrodynamic shearing and subsequent glycerol gradient centrifugation, DNAase II digestion followed by MgCl2 aggregation of transcriptionally inactive chromatin, or mild digestion with micrococcal nuclease. Carcinogens were administered for various times prior to sacrifice. Irrespective of the duration of exposure, no preferential binding of either carcinogen to DNA was detected in any of the fractions prepared by hydrodynamic shearing of DNAase II digestion. When micrococcal nuclease was utilized, a 2-fold increase in carcinogen bound to the DNA of that chromatin fraction containing the smallest molecular weight fragments was detected. These small molecular weight fragments produced by micrococcal nuclease have been postulated to be derived from in vivo transcriptional units. Additionally, when DNAase II was used to probe chromatin from rat livers which had been exposed to a carcinogenic regimen of AAF, no preferential binding of radioactive N-OH-AAF to the DNA of any chromatin fraction was detected.

The nature of the interaction of nucleosomes with a eukaryotic RNA polymerase II

The integrity and stability of nucleosomes under transcription assay conditions has been found to depend on concentration and ionic environment. Rifamycin AF/013, a commonly used inhibitor of initiation, is particularly effective in destabilisation of nucleosomes. Intact nucleosomes are refractory to transcription by wheat RNA polymerase II, the histone core preventing initiation. Template titration suggests that the polymerase can, however, bind to nucleosomes, and a 15--16S complex has been observed on sucrose gradients. DNase I digestion of polymerase-nucleosome incubations indicates that whilst histone is still present in the complex, the nucleosome conformation is altered resulting in enhanced nucleolysis at sites near the DNA centre but reduced overall kinetics of digestion.

Transcription of viral genes in chromatin from adenovirus 2 transformed cells by exogenous eukaryotic RNA polymerases

The transcription of chromatin from adenovrius 2 transformed rat cells by murine plasmacytoma RNA polymerases I, II and III has been studied. Both the total RNA synthesis and transcription of the integrated adenovirus 2 genes by RNA polymerase II represent de novo DNA transcription as assessed by their sensitivity to actinomycin D. It is shown that each RNA polymerase class has characteristic ionic strength activation profiles and metal ion requirements. RNA polymerase II transcribes the integrated adenovirus 2 genes in chromatin at a frequency 25- to 50-fold higher than their sequences are represented in the genome. In contrast, no detectable viral RNA is synthesized when deproteinized DNA is transcribed. In the presence of Mn2+, all three RNA polymerases (I, II and III) transcribe the integrated viral genes at approximately the same relative frequencey. However, the Mg2+ as divalent cation, the proportion of the total RNA which represents viral gene transcripts is increased 3- to 4-fold with RNA polymerase II, while it remains unchanged for RNA polymerases I or III.

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.

Chromatin replication revealed by studies of animal cells and papovaviruses (simian virus 40 and polyoma virus)

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Studies on the high-mobility-group non-histone proteins from hen oviduct

Nuclear high-mobility-group (HMG) proteins were isolated from hen oviduct. These were proteins HMG-1, -2, -3, -14 and -17, which are equivalent to the classification of calf thymus HMG proteins. Hen oviduct proteins HMG-1 and -2 were individually isolated by HCIO4.extraction and CM-Sephadex chromatographic separation. Their mol.wts. were determined as 28 000 and 27 000, respectively. The proteins have a high content of acidic and basic amino acids. The association of proteins HMG-1 and -2 with the genome of hen oviduct nuclei was probed by a limited digestion with nucleases. Hen oviduct nuclei were incubated with deoxyribonuclease I or micrococcal nuclease until 10% of the DNA was digested. The nuclear suspension was centrifuged and the contents of proteins HMG-1 and -2 in the supernatant and sediment fractions were analysed by polyacrylamide-gel electrophoresis. HMG proteins were found to be preferentially released by micrococcal-nuclease digestion rather than by deoxyribonuclease I.

Biochemical properties and localization of the chromosomal protein IP25

The protein IP25, which has previously been reported to accumulate in the chromatin during erythroid differentiation of Friend-virus-transformed erythroleukemia cells (FL cells), is shown to behave like histone H1 without being structurally related to it. Like H1, IP25 is not released by digestion of FL cells nuclei with DNAse I. After micrococcal digestion IP25 and H1 are differentially distributed in the nucleosome monomers and dimers. This distribution suggests an internucleosomal location for IP25 and H1. Different rates of digestion are observed between nuclei of differentiating and non-differentiating FL cells with both DNAse I and micrococcal nuclease. These differences could be due to the presence of IP25 in the chromatin of differentiating cells.

The variation with age of the structure of chromatin in three cell types from rat liver

The organization of chromatin in three rat liver nuclear populations, namely diploid stromal, diploid parenchymal, and tetraploid parenchymal nuclei, which were separated by zonal centrifugation, was studied by digestion with micrococcal nuclease and pancreatic deoxyribonuclease in 3-week-old rats in which the parenchymal cells contain diploid nuclei and in 2-and 4-month-old rats with a high proportion of tetraploid nuclei. Digestion by micrococcal nuclease allowed the estimation of DNA-repeat length in chromatin. Parenchymal nuclei have shorter repeat length than stromal nuclei and DNA-repeat length increases with the age in all three nuclei populations. The kinetics of digestion by micrococcal nuclease showed that nuclei with shorter repeat length are more sensitive to micrococcal nuclease and that the sensitivity of chromatin decreases with age for all the types of nuclei in this study. The kinetics of digestion by pancreatic deoxyribonuclease showed that sensitivity of chromatin is related to the repeat length and that the sensitivity decreases with the ages.

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].

Characteristics of transcriptionally active and inactive neuronal and nonastrocytic glial rat brain chromatin fractions

Rapid and reliable fractionation of neuronal and nonastrocytic glial (NAG) cerebral rat brain chromatin in transcribable and repressed portions was achieved employing the DNAase II/Mg++-solubility method of Gottesfeld et al. (1974). Compositional and transcriptional properties of these fractions have been investigated. Compared to transcriptionally repressed fractions, template-active neuronal and NAG chromatin fractions are associated with an increased content of nonhistone chromosomal (NHC-) proteins. Both of the transcribable as well as both of the repressed fractions are strikingly different in their composition as assessed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. Comparative acid urea gel electrophoretic patterns of histones revealed that histone fraction H 1 is almost completely absent in actively transcribed neuronal chromatin and reduced in the corresponding NAG fraction while in template-inactive neuronal and NAG chromatin all five main histone fractions are present in equal amounts. The total number of RNA initiation sites available for exogenously added homologous RNA polymerase on template-active and -inactive neuronal and NAG chromatin was quantitatively measured under assay conditions completely eliminating reinitiation. Unlike the template-active neuronal and NAG fractions which are differently enriched in RNA initiation sites, transcriptionally more repressed neuronal and NAG fractions demonstrated a minimal ability to initiate RNA synthesis. Under assay conditions allowing repeated initiation of RNA chains at the same initiation site, rat brain RNA polymerase molecules were found to utilize neuronal initiation sites more frequently than NAG ones.

Nucleosome-like structural subunits of intranuclear parental adenovirus type 2 DNA

The intranuclear structure of parental adenovirus 2 DNA was studied using digestion with micrococcal nuclease as a probe. When cultures were infected with 32P-labeled virions, at a multiplicity of 3,000 particles per cell, 14 to 21% of parental DNA penetrated the cell and reached the nucleus. Of this parental DNA, 60% could be solubilized by extensive digestion with micrococcal nuclease. The nuclease-resistant fraction contained viral deoxyribonucleoprotein monomers and oligomers. These nucleosome-like structures contained DNA fragments which are integral multiples of a unit-length DNA of approximately 185 base pairs. The monomeric DNA is similar in length to the unit-length DNA contained in cellular nucleosomes. However, the viral oligomers are slightly smaller than their cellular counterparts. DNA-DNA hybridization demonstrated that all segments of the viral genome, including those expressed as mRNA only at late times, are represented in the nucleosomal viral DNA. The amount of early intranuclear viral chromatin was proportional to multiplicity of infection up to multiplicities of 4,000 particles per cell. However, viral transcriptional activity did not increase in direct proportion to the amount of viral chromatin. Maximum accumulation of intranuclear viral chromatin was achieved by 3 h after infection. The intranuclear parental viral chromatin remained resistant to nuclease digestion even at late times in infection, after viral DNA replication had begun.

Comparison of non histone proteins selectively associated with nucleosomes with proteins released during limited DNase digestions

Cultured mammary cells from GR mouse were used to analyse proteins associated with the mononucleosomes and released by a short micrococcal DNase treatment of nuclei. On metrizamide density gradients, mononucleosomes appear to be heterogeneous according to their content of associated non-histone proteins. Proteins associated with the denser fraction (1.22 - 1.24 g/ml) were analysed by two dimensional electrophoresis and compared to the proteins released by DNase I treatment. All the proteins associated with mononucleosomes were also released by DNase I treatment. It could then be assumed that these proteins are associated with the active part of the genome. Additional proteins were released by micrococcal DNase treatment of the nuclei. They could be involved in a higher order organization of chromatin.

Simple isolation of DNA hydrophobically complexed with presumed gene regulatory proteins (M3)

Chromatin from chicken reticulocytes and mouse Ehrlich ascites tumor cells has been extracted with 2 M NaCl, leaving a portion of the DNA still complexed with a fraction of nonhistones (designated M3, since it can be dissociated from DNA in solutions of 3 M NaCl containing 5 M urea). The DNA complexed with M3, separated from the bulk DNA by centrifugation, was found to contain sequences poorly represented in bulk DNA. Specifically we found that DNA--M3 complexes isolated from chicken reticulocyte chromatin were enriched in globin gene sequences by 20-fold relative to unfractionated DNA and by over 1000-fold relative to DNA rendered free of protein following the extraction of chromatin with 2 M NaCl. We have therefore isolated DNA fractions complexed with M3 which are enriched in specific sequences as may be determined by M3.

Selective activation of human beta-but not gamma-globin gene in human fibroblast x mouse erythroleukaemia cell hybrids

The human alpha- and beta-globin genes have been activated in MEL X human fibroblast cell hybrids. However, even though the human gamma- and beta-globin genes are closely linked and were shown in these hybrid clones to be present in approximately equal numbers, no human gamma-globin mRNA was produced. Thus, the human beta- and gamma-globin genes in these cells are differentially regulated apparently by a positive regulatory factor(s) specific for individual globin genes.

Urea-induced binding of histone 1 to nucleosomes lacking linker DNA

The binding of H1 (and H5) to nucleosome core particles was demonstrated by separating mononucleosomes according to their DNA size on acrylamide gels containing high molarity urea. The presence of urea causes a redistribution of H1 so that it associates with some particles of all linker lengths, including no linker. When the urea is removed the H1 remains associated with particles of all DNA sizes if the different size classes are not mixed with each other. Therefore, urea can effect the transfer of H1 from particles with linker to particles with no linker. When nucleosomes of uniform DNA fragment length, some containing and some lacking H1, are re-electrophoresed under native conditions, they migrate as two widely separated bands. The mobilities of these variants do not depend on linker length and are identical to the mobilities of native H1-containing and H1-lacking particles. When the same collection of particles is electrophoresed in the presence of high molarity urea they migrate with a uniform mobility. These results suggest that H1-containing nucleosomes are conformationally different from H1-lacking particles, but that this difference is eliminated when histone-histone interactions are disrupted by urea.

A correlation between nucleosome spacer region susceptibility to DNase I and histone acetylation

Hepatoma tissue culture (HTC) cell nuclei were digested with either DNase I or micrococcal nuclease and the nucleohistone digestion products fractionated by gel electrophoresis or exclusion chromatography. Under appropriate conditions, gel electrophoresis demonstrates that for both nucleases, only cleavages within the nucleosome spacer regions and not within the nucleosome core lead to freely migrating nucleohistone particles. These particles consist of nucleosome cores, nucleosomes and nucleosome oligomers. Following DNase I digestion and fractionation by exclusion chromatography, analysis of the histones indicates a direct relationship between increased spacer region susceptibility to nuclease and increased nucleosomal histone acetylation. Evidently digestion sites outside the regions of DNA protected by core histones can reflect the degree of acetylation of core histones. Such a relationship is not found when micrococcal nuclease is used to digest the samples.

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.

Studies on the association of the high mobility group non-histone chromatin proteins with isolated nucleosomes

Nucleosomes have been isolated from rabbit thymus by sucrose gradient centrifugation, and their high mobility group (HMG) protein content analysed by electrophoresis on polyacrylamide gels. The results suggest that proteins HMG 14 and HMG 17 are associated with the core particle of the nucleosome, and that there are two or more sub-populations of both HMG 1 and HMG 2 molecules. One sub-population appears to be fairly tightly bound to the nucleosome, while another is rapidly released from the chromatin by digestion with micrococcal nuclease. The latter fraction may participate in a higher order folding of the nucleosomes.

In vitro DNA dependent synthesis of globin RNA sequences from erythroleukemic cell chromatin

Murine erythroleukemic cells in culture accumulate cytoplasmic globin mRNA during differentiation induced by dimethyl sulfoxide (DMSO)1. Chromatin was prepared from DMSO induced erythroleukemic cells that were transcribing globin RNA in order to determine whether in vitro synthesis of globin RNA sequences was possible from chromatin. RNA was synthesized in vitro using 5-mercuriuridine triphosphate and exogenous Escheria coli RNA polymerase. Newly synthesized mercurated RNA was purified from endogenous chromatin associated RNA by affinity chromatography on a sepharose sulfhydryl column, and the globin RNA sequence content of the mercurated RNA was assayed by hybridization to cDNA globin. The synthesis of globin RNA sequences was shown to occur and to be sensitive to actinomycin and rifampicin and insensitive to alpha-amanitin. In contrast, synthesis of globin RNA sequence synthesis was not detected in significant amounts from chromatin prepared from uninduced erythroleukemic cells, nor from uninduced cell chromatin to which globin RNA was added prior to transcription. Isolated RNA:cDNA globin hybrids were shown to contain mercurated RNA by affinity chromatography. These results indicated that synthesis of globin RNA sequences from chromatin can be performed by E. coli RNA polymerase.

Comparison on the structure and transcriptional capability of growing phase and stationary yeast chromatin: a model for reversible gene activation

We have compared the structure of intra-nuclear and isolated chromatin from logarithmically growing yeast cells to chromatin from cells which had entered the stationary phase and ceased growing. Both chromatins show a similar nucleosomal repeat pattern, 160 bp repeat size, with staphylococcal nuclease and similar variability in repeat sizes within the genome. DNase I produces the same ladder (less than 120 b) and a quite similar extended ladder (120-300 b) which shows that both chromatins have phased nucleosomes. However, the rate of DNase I digestion of growing phase is greater than in stationary. Functionally speaking, growing phase nuclei are 5-20 times as active in the rate of endogenous transcription (all three polymerases are involved). The transcriptional and DNase I susceptibility differences noted in nuclei are maintained in sucrose gradient isolated oligonucleosomes and mononucleosomes from the two states.

Cell specific antiserum to chromosome scaffold proteins

Antiserum has been raised to a chromosomal protein fraction specific for Hela cells. The immunoactivity is located in the transcriptionally inactive regions of log phase chromatin. Digestion of metaphase chromosomes results in the purification of the immunoactivity in the scaffold region of the chromosomes. Extensive nuclease digestion of the scaffolds results in loss of activity. The data suggest that some of the proteins in the scaffold area are both tight binding and cell specific and may therefore play a sophisticated role in gene expression.

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.

Regulation of mouse mammary tumor virus gene expression by glucocorticoid hormones

Several laboratories have documented that glucocorticoid hormones markedly stimulate the expression of mouse mammary tumor virus genes in a variety of mouse mammary tumor cells and in infected heterologous cells. The effect of the hormone appears to be a rapid and specific augmentation of the synthesis of viral RNA, mediated by interaction with glucocorticoid receptor proteins. The availability of virus-specific reagents and recent developments in the molecular biology of RNA tumor viruses now permit a highly refined analysis of hormonal regulation in this experimental system.

Lysine-rich histones and the selective digestion of the globin gene in avian red blood cells

Deoxyribonuclease I (DNase I) is known to preferentially digest the adult globin gene sequences in avian red blood cells. We have investigated the contribution of histones H1 and H5 in maintaining the nuclease-sensitive structure about the globin genes. When the lysine-rich histones H1 and H5 were selectively removed from avian red blood cell nuclei, the rate of digestion with DNase I increased several fold. However, the globin genes in H1-and H5-depleted nuclei were still selectively digested. Since histone H1 is necessary for the higher order folding of the nucleosomes, these data suggest that DNase I recognizes an aspect of structural heterogeneity within each core particle rather than some higher order packaging of the nucleosome cores.

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.

Hemoglobin switching in sheep: only the gamma gene is in the active conformation in fetal liver but all the beta and gamma genes are in the active conformation in bone marrow

Differential expression of the closely linked gamma, beta(A) (or beta(B)), and beta(C) globin genes in sheep results in the production of fetal hemoglobin (Hb F, alpha(2)gamma(2)) during gestation and the adult hemoglobins (Hb A, alpha(2)beta(2) (A), and Hb B, alpha(2)beta(2) (B)) after birth. Erythropoietic stress in certain animals leads to production of Hb C (alpha(2)beta(2) (C)). The molecular mechanism of differential expression of these genes in nuclei of fetal and adult erythroid cells has been investigated by analysis of their susceptibility to digestion by DNase I (genes that are in the conformation associated with active transcription are sensitive to this nuclease). The concentration of globin gene sequences in DNA from control and DNase I-digested nuclei was determined by annealing to synthetic DNAs and analogous cDNA probes derived from recombinant plasmids containing one of the sheep globin genes. In nuclei from sheep fetal liver erythroid cells, the gamma genes but not the beta genes were digested by DNase I; the gamma locus was open but the beta(A) or beta(C) loci was closed, consistent with synthesis of only Hb F by these cells. DNase I digestion of nuclei from bone marrow of anemic sheep making only Hb C or Hb B resulted in equivalent digestion of the beta and gamma gene sequences, although gamma mRNA was not detected in these cells. Digestion by DNase I did not decrease the globin gene sequence concentration in residual DNA of spleen nuclei. As a further control, DNA from digested bone marrow and spleen nuclei were shown to anneal equally well to a cDNA prepared from liver polysomal mRNA. Differential expression of the gamma and beta globin genes in sheep fetal erythroid cell appears to be based on differences in chromatin structure. The gamma globin gene remains in the active conformation in adult erythroid cells; failure of gamma mRNA to accumulate in these cells probably reflects transcriptional or post-transcriptional regulation.

The histone core complex: an octamer assembled by two sets of protein-protein interactions

A protein complex, extracted from calf thymus chromatin with 2 M NaCl, pH 7.5, containing approximately equal molar ratios of histones H2A, H2B, H3, and H4, has been characterized in this study. Gel filtration, sedimentation velocity, and sedimentation equilibrium experiments demonstrate that this complex, known as the core complex, has a molecular weight near that expected for a histone octamer (108 000 for a unit containing two each of the four inner histones) and far exceeding that of a histone tetramer (54 400). This finding suggests that the histone octamer, postulated to be the fundamental histone unit in chromatin, is stable in 2 M NaCl, pH 7.5, in the absence of DNA or chemical cross-linking reagents. In the second part of this study, we demonstrate that the bonds maintaining the octameric complex in 2 M NaCl are weak and distinctly different from the forces stabilizing the H2A-H2B dimer or H3-H4 tetramer. The octamer is dissociated into two H2A-H2B dimers and one H3-H4 tetramer by (i) increasing temperature; (ii) decreasing NaCl concentration; (iii) adding low concentrations of urea or guanidine hydrochloride; and (iv) lowering the pH below 7 or raising it above 10. These findings indicate that the octamer is assembled by two sets-of protein-protein interactions. The first set involves mostly hydrophobic interactions and yields the H2A-H2B dimer and the H3-H4 tetramer subunits. The second set involves the weak association of one H3-H4 tetramer with two H2A-H2B dimers to form an octamer. We suggest that these weak interactions might be derived predominantly from histidine-lysine or histidine-tyrosine hydrogen bonds between the dimer and tetramer subunits.

Non-histone proteins in mononucleosomes and subnucleosomes

Nucleosomes and subnucleosomes separated either by sucrose gradient ultracentrifugation or by polyacrylamide gel electrophoresis contain proteins incorporating [3H]tryptophan, i.e. non-histone proteins. The fractions of mononucleosomes MN3 and MN2 are enriched in these proteins as compared to the MN1 fraction. Two-dimensional gel electrophoresis of chromatin digests reveals a number of non-histone proteins comigrating with deoxyribonucleoprotein particles in the first direction (in non-dissociating conditions). A significant fraction of these proteins corresponds to basic non-histone proteins, so-called HMG (high-mobility-group) proteins. Two HMG proteins are present in mononucleosomes MN3 exclusively and three others in mononucleosomes MN3 and MN2. One of them is recovered also in subnucleosomes SN2, and another in SN3 subnucleosome fraction, At least three HMG proteins are rapidly released from the oligonucleosome fractions as well as from the insoluble DNA . protein residue. Thus, they are located in chromatin readily available to DNAase action. Apart from HMG proteins, a number of other non-histone proteins are present in mononucleosomes but their relative content in the oligonucleosome fraction is much higher. The conclusion has been drawn that many non-histone proteins, in particular HMG proteins, interact with linker DNA in chromatin.