Active chromatin

Yeast DNA topoisomerase II is encoded by a single-copy, essential gene

The gene TOP2 encoding yeast topoisomerase II has been cloned by immunological screening of a yeast genomic library constructed in the phage lambda expression vector, lambda gt11. The ends of the message encoded by the cloned DNA fragment were delimited by the Berk and Sharp procedure (S1 nuclease mapping) for the 5' end and mapping of the polyA tail portion of a cDNA fragment for the 3' end. The predicted size of the message agrees with the length of the message as determined by Northern blot hybridization analysis. The identity of the gene was confirmed by expressing the gene in E. coli from the E. coli promoter lac UV5 to give catalytically active yeast DNA topoisomerase II. Disruption of one copy of the gene in a diploid yeast creates a recessive lethal mutation, indicating that the single DNA topoisomerase II gene of yeast has an essential function.

Heritable genetic variation via mutation-selection balance: Lerch's zeta meets the abdominal bristle

Most quantitative traits in most populations exhibit heritable genetic variation. Lande proposed that high levels of heritable variation may be maintained by mutation in the face of stabilizing selection. Several analyses have appeared of two distinct models with n additive polygenic loci subject to mutation and stabilizing selection. Each is reviewed and a new analysis and model are presented. Lande and Fleming analyzed extensions of a model originally treated by Kimura which assumes a continuum of possible allelic effects at each locus. Latter and Bulmer analyzed a model with diallelic loci. The published analyses of these models lead to qualitatively different predictions concerning the dependence of the equilibrium genetic variance on the underlying biological parameters. A new asymptotic analysis of the Kimura model shows that the different predictions are not consequences of the number of alleles assumed but rather are attributable to assumptions concerning the relative magnitudes of per locus mutation rates, the phenotypic effects of mutation, and the intensity of selection. This conclusion is reinforced by analysis of a model with triallelic loci. None of the approximate analyses presented are mathematically rigorous. To quantify their accuracy and display the domains of validity for alternative approximations, numerically determined equilibria are presented. In addition, empirical estimates of mutation rates and selection intensity are reviewed, revealing weaknesses in both the data and its connection to the models. Although the mathematical results and underlying biological requirements of my analyses are quite different from those of Lande , the results do not refute his hypothesis that considerable additive genetic variance may be maintained by mutation-selection balance. However, I argue that the validity of this hypothesis can only be determined with additional data and mathematics.

Barriers to nuclease Bal31 digestion across specific sites in simian virus 40 chromatin

A portion of the nucleoprotein containing viral DNA extracted from cells infected by simian virus (SV40) is preferentially cleaved by endonucleases in a region of the genome encompassing the origin of replication and early and late promoters. To explore this nuclease-sensitive structure, we cleaved SV40 chromatin molecules with restriction enzymes and digested the exposed termini with nuclease Bal31. Digestion proceeded only a short distance in the late direction from the MspI site, but some molecules were degraded 400 to 500 base pairs in the early direction. By comparison, BglI-cleaved chromatin was digested for only a short distance in the early direction, but some molecules were degraded 400 to 450 base pairs in the late direction. These barriers to Bal31 digestion (bracketing the BglI and the MspI sites) define the borders of the same open region in SV40 chromatin that is preferentially digested by DNase I and other endonucleases. In a portion of the SV40 chromatin, Bal31 could not digest through the nuclease-sensitive region and reached barriers after digesting only 50 to 100 base pairs from one end or the other. Chromatin molecules that contain barriers in the BglI to MspI region are physically distinct from molecules that are open in this region as evidenced by partial separation of the two populations on sucrose density gradients.

Gene control by phosphoproteins: a theoretical model for eukarotic DNA regulation

Although gene regulatory mechanisms in eukaryotic cells are complex, some progress is being made in understanding them. Chromosomal proteins may play a significant role in genome function and gene control. More specifically, a central role may be played by the nuclear nonhistone proteins. It appears that both viral transformation and steroid hormone action may be associated with the phosphorylation of these proteins. Recent studies have revealed that some oncogenic viruses are capable of producing viral transforming proteins with protein kinase activity. This suggests how they may subvert normal gene regulatory mechanisms. Furthermore, the effects of the steroid-receptor complex on nuclear nonhistone proteins may be similar to the effects of these viral transforming proteins, but in a controlled sense. A model of gene-regulatory, nuclear phosphorylation reactions is formulated which suggests how some oncogenic viruses may control normal gene regulatory mechanisms and how steroid hormones may interact with these same mechanisms. Such a model may reveal how disruption of these same mechanisms leads to carcinogenesis.

Mechanism of enhanced RNA synthesis in acute-phase rat liver and its relationship to chromatin structure

Nuclei isolated from the liver of rats undergoing an acute inflammatory reaction induced by turpentine treatment show increased RNA synthesis. This increase is essentially determined by a faster polyribonucleotide-elongation rate while the number of transcribing polymerase molecules is unchanged. The sensitivity of chromatin to micrococcal-nuclease digestion and the composition of chromosomal proteins are not affected by the acute-phase process. Therefore the increased RNA synthesis by liver nuclei from acutely inflamed rats does not seem to correlate with major changes in chromatin structure.

Unequal activation by estrogen of individual Xenopus vitellogenin genes during development

Using a technique of filter hybridization under very stringent conditions to HindIII fragments of complementary DNA cloned in plasmids, we have measured the accumulation in hepatocytes of mRNA specified by each of the four vitellogenin genes (A1, A2, B1, B2) at different stages of development of Xenopus laevis. The ontogenic competence of embryonic liver to respond to the first exposure to estradiol-17 beta, in terms of activation of transcription of this multigene family, is acquired late in metamorphosis at around Nieuwkoop-Faber stage 58. Upon hormonal induction, the four mRNAs accumulate under non-steady-state conditions at different rates and to different extents at all developmental stages in vivo and in cultured adult hepatocytes. A1 and B1 mRNAs appear more rapidly and accumulate to levels that are five- to eightfold those specified by genes A2 and B2, with higher amounts of B1 than A1 mRNA. A threefold higher absolute rate of synthesis of A1 and B1 mRNAs in hepatocyte cultures, relative to the A2-B2 pair, suggests that hormonal regulation of differential accumulation of vitellogenin mRNA occurs at the transcriptional level. At the early developmental stages (up to stage 61) of acquired competence, there appears to be no fixed pattern of expression, but a pattern of unequal activation of individual genes of the Xenopus vitellogenin multigene family is established thereafter and then retained at all developmental stages of tadpoles, froglets, and in both male and female adults.

Phosphorylation of some chromosomal nonhistone proteins in active genes is blocked by the transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB)

The distribution of rapidly phosphorylated chromosomal proteins between chromosome I, chromosome II + III, chromosome IV, and nuclear sap including the matrix was investigated in salivary gland cells of Chironomus tentans. Chromosome IV, which carries most active nonribosomal genes in the cell, was found to be enriched in four rapidly phosphorylated nonhistone polypeptides (Mr = 25,000, 30,000, 33,000, and 42,000) in parallel with the transcriptional activity rather than with the DNA content of the chromosome. Also the histones H2A and H4 are rapidly phosphorylated but the phosphorylation is proportional to the DNA content of each chromosome sample. The 32P-labeled Mr = 42,000 polypeptide immunologically cross-reacted with an antibody elicited against the transcription stimulatory factor S-II isolated from Ehrlich ascites tumor cells (Sekimizu, K., D. Mizuno, and S. Natori, 1979, Exp. Cell Res., 124:63-72). In addition, indirect immunofluorescence studies on chromosome IV with antisera against the stimulatory factor II revealed a selective staining of the active gene loci. The incorporation of 32P into three chromosome IV nonhistone polypeptides, especially into the Mr = 42,000 polypeptide, was lowered by 70-85% shortly after administration of 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), a likely inhibitor of heterogeneous nuclear RNA transcription at initiation level. The possibility of a causal relationship between inhibited phosphorylation of chromosomal proteins and blocked transcription of heterogeneous nuclear RNA genes by DRB is discussed.

Absence of detectable 5-methylcytosine in DNA of embryos of the brine shrimp, Artemia

DNA from three developmental stages of the brine shrimp, Artemia was found to be undermethylated compared to DNA from calf thymus and salmon sperm. Using high-performance liquid chromatography we found that DNA hydrolysates from both dormant cysts and prefeeding nauplii contain less than 1 residue of 5-methylcytosine per 59 kilobases, placing Artemia DNA in the "insect type" category. The absence of detectable 5-methylcytosine in DNA of developing Artemia supports the view that methylation status alone cannot account for regulation of transcription in protostomes, and that DNA methylation may be more common among deuterostomes.

Isolation and purification of transcriptionally active ribosomal chromatin from the slime mould, Physarum polycephalum

In the acellular slime mold Physarum polycephalum the ribosomal genes are all located on linear, extrachromosomal DNA molecules which are clustered in the nucleolus. This report describes the isolation and purification of these ribosomal genes as functionally active chromatin particles. Nucleolar lysates are fractionated by gel filtration to remove ribosomal precursors and other soluble material. The ribosomal chromatin is subsequently separated from contaminating nuclear chromatin by a sucrose gradient centrifugation step. This procedure allows the isolation of the ribosomal genes as intact nucleoprotein particles, which are now amenable to a biochemical analysis of their structural and functional properties.

Induction of altered chromatin structures by simian virus 40 enhancer and promoter elements

Two simian virus 40 transcriptional promoter elements, the 72-base pair (bp) repeat and the 21-bp repeat region, induce chromatin structures of increased DNase I sensitivity when transposed elsewhere in the viral genome. The induction of a sufficiently long stretch of DNase I-sensitive chromatin leads to the appearance of a visible nucleosome-free region.

Differential expression of porcine major histocompatibility DNA sequences introduced into mouse L cells

The expression of a porcine genomic DNA segment containing a major histocompatibility gene and its chromatin structure in mouse L cells have been investigated. The transformed cells, which contain about two copies of the 17.8-kilobase pig DNA insert per haploid genome, stably and uniformly express major histocompatibility antigen on their surfaces. This expression is the result of differential transcription of the 3-kilobase major histocompatibility gene; the other 14 kilobases of pig sequences flanking the coding sequence are not transcribed. Although the entire pig DNA segment is packaged into nucleosomes, only the transcriptionally active DNA sequences are packaged in a DNase I-sensitive conformation. These results suggest that the expression of this foreign DNA is actively regulated in L cells.

Formation of transcribing mononucleosome-eukaryotic RNA polymerase II complexes in vitro as a simple model of active chromatin

Mononucleosomes obtained from cultured mouse hepatoma cells were incubated with RNA polymerase II from wheat germ. No free DNA was liberated as available templates under the experimental condition employed. Size analysis of the transcripts showed that the polymerase initiated transcription from either terminus and read through the DNA template of mononucleosomes. Sucrose density gradient centrifugation of the reaction mixture resolved mononucleosome-polymerase complexes from free materials. The complexes were characterized by the enrichment of DNA fragments containing the nucleosome linker region, the presence of H1 histone, and the increased susceptibility to DNase I. Both the complexes formed in the presence and absence of precursor nucleotides were susceptible. These suggest that RNA polymerase II prefers to bind to the linker region, and the polymerase-bound nucleosomes are structurally altered. The data were discussed in context with possible mechanisms of transcription of the nucleosome structure.

Hormonal regulation and expression of vitellogenin multigene family

Yolk proteins are the most abundant egg proteins in oviparous animals. They are deposited during oocyte maturation for use after fertilization and are synthesized in the liver or fat body as a common precursor termed vitellogenin. Hybridization with cloned DNA complementary to vitellogenin messenger RNA has revealed a surprisingly high degree of evolutionary conservation of sequence of vitellogenin genes among insects, amphibians and birds. The synthesis of vitellogenin in vertebrates is directly under the control of oestrogen at the level of gene transcription. In the frog, Xenopus, vitellogenin genes occur as a multigene family, four of which are actively expressed and are grouped as A and B genes. This multiplicity offers a useful system for investigating the possible selective hormonal regulation of expression of individual members of multigene families. When X. laevis vitellogenin genes were activated by oestrogen in the liver of whole animals or in cultures of parenchymal cells, the two groups of expressed genes were not induced in an identical manner in cells from male and female animals. The activation of A and B groups of genes was non-coordinate in male hepatocytes and coordinate in female cells. Prior exposure of male hepatocytes to oestradiol in vivo or in culture caused the pattern of expression to shift to that in female cells. Since the X. laevis oocyte itself does not synthesize vitellogenin in response to oestrogen, an attempt was made to activate its dormant vitellogenin genes by transferring oestrogen-binding proteins from the liver. Preliminary results show that the microinjection into the oocyte of a preparation containing liver receptor-hormone complex led to the synthesis of vitellogenin by the oocyte. Extension of these experiments will not only enable a more precise analysis of the activation of the vitellogenin multigene family to be made but will also provide direct functional evidence for the role played by steroid hormone receptors in regulating gene expression.

Chromatin proteins of rat preputial-gland: acute changes in response to estrogen

The effects of estradiol-17 beta (E2 beta) at 2 or 15 min in vivo on chromatin proteins of rat preputial-gland were analyzed by a battery of electrophoretic methods. Among histones, E2 beta/control ratios for major bands of H1 decreased substantially between 2 and 15 min. In contrast, ratios of H4 increased (P less than 0.01), whereas, except for losses by 2 min in a H2B-like component and in H3.1, other core histones were unchanged. Among 0.35 M NaCl-soluble proteins, components at 34K-mol. wt and less than 21K -mol wt were increased after 2 min of E2 beta. The bulk of the hormone-responsive low-molecular weight proteins was basic in charge. Electrophoretic correlates of 6 basic lysosomal proteins corresponded to those of low-molecular weight salt-soluble chromatin proteins. Selective proteolysis initiated in vivo by E2 beta depleted some tightly-bound nonhistone proteins.

Gene control by phosphoproteins: a theoretical model for eukaryotic DNA regulation

Although gene regulatory mechanisms in eukaryotic cells are complex, some progress is being made in understanding them. Chromosomal proteins may play a significant role in genome function and gene control. More specifically, a central role may be played by the nuclear nonhistone proteins. It appears that both viral transformation and steroid hormone action may be associated with the phosphorylation of these proteins. Recent studies have revealed that some oncogenic viruses are capable of producing viral transforming proteins with protein kinase activity. This suggests how they may subvert normal gene regulatory mechanisms. Furthermore, the effects of the steroid-receptor complex on nuclear nonhistone proteins may be similar to the effects of these viral transforming proteins, but in a controlled sense. A model of gene-regulatory, nuclear phosphorylation reactions is formulated which suggests how some oncogenic viruses may control normal gene regulatory mechanisms and how steroid hormones may interact with these same mechanisms. Such a model may reveal how disruption of these same mechanisms leads to carcinogenesis.

Induced differentiation of murine erythroleukemia cells: cellular and molecular mechanisms

Study of inducer-mediated differentiation of murine erythroleukemia cells provides insights into the cellular and molecular mechanisms implicated in cell differentiation. The loss of proliferative capacity is revealed to be a complex multistep process during which the cells progress through a series of stages, including a precommitment "initiation" stage, a stage suggestive of the accumulation of commitment-related factors, and, finally, a stage of expression of the characteristics of the differentiated state. Cell cycle arrest in G1 phase of the cell cycle may, in part at least, be related to down-regulation of protein p53 synthesis. Expression of induced differentiation is accompanied by an acceleration of transcription at the globin loci, and possibly by posttranscriptional modulation of globin mRNA accumulation, as well. Cells at the stage of erythroid cell development represented by the transformed, differentiation-arrested MELC, have acquired a unique DNA structure and chromatin configuration around the globin genes which distinguish them from other, nonerythroid cells; additional complex changes in chromatin configuration accompany, and probably precede, inducer-mediated acceleration of globin gene transcription during terminal differentiation. Passage through G1 and early S phase of the cell cycle, in the presence of inducer, is critical for subsequent globin gene expression and may be important in establishing the chromatin reconfiguration required for gene expression.

Analysis of chromatin of skeletal muscle of developing rats using micrococcal nuclease and DNase I

Conformational changes in the chromatin of skeletal muscle of 3-, 14- and 30 day-old developing rats have been studied using DNase I and micrococcal nuclease (MCN). Purified nuclei were digested separately by MCN and DNase I. The rate and extent of digestion by MCN decreases gradually as development proceeds. The electrophoretic pattern of MCN digested DNA, however, shows no change. The kinetics of digestion of nuclei by DNase I show no change with development. However, the electrophoretic pattern of DNase I digested DNA shows a gradual decrease in the amount of 10-30 bp fragments with progressive development. These studies show that the chromatin of the skeletal muscle undergoes certain conformational changes during postnatal development, and such changes in chromatin may be necessary for terminal differentiation of this tissue.

An African trypanosome variant surface glycoprotein gene whose expression is not activated by duplication

A variant surface glycoprotein (VSG) of Trypanosoma brucei is encoded by a gene whose expression is not governed by duplication-transposition. There are two copies of this gene. The 5' flanking regions of the two genes are indistinguishable by restriction mapping, although each possesses approximately 5-10 Kbp of DNA which is devoid of restriction sites. All restriction enzymes tested appeared to cut genomic DNA at a uniform distance 3' of the gene. This, coupled with the observed sensitivity of both genes to BAL 31, indicates that they lie near chromosomal termini. Length variation occurs 3' of these genes in bloodstream clones and their procyclic derivatives, although the number of length variants is conserved. This suggests that length variation alone does not control VSG switching or gene expression and that constraints exist on the extent to which 3' flanking regions can vary in length.

Intranuclear localization of histone acetylation in Physarum polycephalum and the structure of functionally active chromatin

Based on studies of histone acetylation in vivo in Physarum polycephalum, we present the following hypotheses: (1) Transcription-specific histone acetylation on histones H3 and H4 is a localized process at the nuclear matrix; (2) Histone acetylation in the S phase, which is specific for newly synthesized histones, occurs in an intranuclear nonlocalized process. These hypotheses can explain: (1) the histone specificity of histone acetylation that is dependent on the functional state of the chromatin; (2) the apparent absence of turnover of histone acetylation in the bulk of the chromatin despite a definite low level of steady-state acetylation of all four core histones in bulk chromatin; (3) the pattern of butyrate-induced hyperacetylation observed for active and inactive chromatin.

Conformation of promoter DNA: fine mapping of S1-hypersensitive sites

Larsen and Weintraub showed that a feature of active (but not inactive) chromatin is the appearance of S1-nuclease-hypersensitive sites in the 5'-flanking regions of expressing genes. Such sites are also present in supercoiled, but not relaxed, plasmids carrying these gene sequences. We have developed an in vitro approach to map, at the nucleotide level, S1-hypersensitive sites in artificially generated supercoiled circles of naked DNA. In the case of the adult chicken beta-globin gene, our results correlate extremely well with the coarser in vivo mapping. These sites reside in homopurine-homopyrimidine tracts, and, despite their S1 sensitivity, they do not seem to be single-stranded.

HMG (high-mobility-group)-14/17-like proteins in calf thyroid. Thyrotropin-dependent phosphorylation and comparison with calf thymus proteins

Two-dimensional polyacrylamide-gel electrophoresis of acid extracts of thyroid and thymus tissue, and of thyroid nuclei, revealed the presence of three HClO4-soluble nuclear proteins, PS.1, PS.2 and PS.3, whose electrophoretic mobilities closely resembled those of HMG (high-mobility-group) proteins 14 and 17. PS.1 co-migrated with HMG 14 on CM-Sephadex column chromatography. Like HMG 14, PS.2 and PS.3 were phosphorylated in calf thyroid slices; 32P-labelling of PS.3 was stimulated by thyrotropin. Thyrotropin also induced a rapid increase in the labelling of A5, an HMG-14/17-like protein found in whole calf thyroid and thymus tissue, but not in thyroid nuclei.

Sequence-specific binding of glucocorticoid receptor to MTV DNA at sites within and upstream of the transcribed region

Glucocorticoid receptor protein stimulates transcription initiation within murine mammary tumor virus (MTV) DNA sequences in vivo, and interacts selectively with MTV DNA in vitro. We mapped and compared five regions of MTV DNA that are bound specifically by purified receptor; one resides upstream of the transcription start site, and the others are distributed within transcribed sequences between 4 and 8 kb from the initiation site. Each region contains at least two strong binding sites for receptor, which itself appears to be a tetramer of 94,000 dalton hormone-binding subunits. Three of the five binding regions contain nine nuclease footprints that lack extensive homology, although a family of related octanucleotides can be discerned. Receptor interacts with the different regions with similar efficiencies, suggesting that receptor affinity for upstream and internal regions may differ by less than one order of magnitude. Moreover, each region appears to be bound independent of the others. A restriction fragment containing four footprint sequences from one of the regions has previously been shown to act in vivo as a receptor-dependent transcriptional enhancer element, implying that the binding sites detected in vitro may be biologically functional.

Inhibition of transcription in somatic cells by microinjection of antibodies to chromosomal proteins

The in vivo function of defined chromosomal proteins was examined by microinjecting purified antibody and antibody fragments into living fibroblasts. The involvement of histones and chromosomal high mobility group proteins HMG-1, 2, and 17 in transcription was visualized by studying the [3H]uridine incorporation in KD human fibroblasts after microinjection of fluoresceinated antibodies to these proteins. Nuclear uridine incorporation was not affected by microinjection of control antibodies or by the presence of immune complexes formed after microinjection of antibodies to chromosomal proteins that are not involved in transcription. In contrast, injection of anti-histone IgG, F(ab')2, or Fab and anti-HMG-17 IgG causes a significant reduction in transcription. The reduction is proportional to the amount of antibody introduced into the cell. We conclude that histones and protein HMG-17 are present on transcribed regions of the genome and that passage of RNA polymerase along the chromatin fiber is prevented by antibody binding to these proteins.

Differential expression of porcine major histocompatibility DNA sequences introduced into mouse L cells

The expression of a porcine genomic DNA segment containing a major histocompatibility gene and its chromatin structure in mouse L cells have been investigated. The transformed cells, which contain about two copies of the 17.8-kilobase pig DNA insert per haploid genome, stably and uniformly express major histocompatibility antigen on their surfaces. This expression is the result of differential transcription of the 3-kilobase major histocompatibility gene; the other 14 kilobases of pig sequences flanking the coding sequence are not transcribed. Although the entire pig DNA segment is packaged into nucleosomes, only the transcriptionally active DNA sequences are packaged in a DNase I-sensitive conformation. These results suggest that the expression of this foreign DNA is actively regulated in L cells.

Correlation between phosphorylated H1 histone and condensed chromatin in Planococcus citri

Histones of the mealybug Planococcus citri have been isolated and characterised. Although no major differences were observed between the core histones of male and female insects, the pattern of H1 histones was significantly different between the sexes. A specific hyperphosphorylated H1 was found to be present only in male mealybugs, where the paternal chromosomes are condensed and transcriptionally inactive.

Nucleosome arrangement in green monkey alpha-satellite chromatin. Superimposition of non-random and apparently random patterns

We have studied the structure of tandemly repetitive alpha-satellite chromatin (alpha-chromatin) in African green monkey cells (CV-1 line), using restriction endonucleases and staphylococcal nuclease as probes. While more than 80% of the 172-base-pair (bp) alpha-DNA repeats have a HindIII site, less than 15% of the alpha-DNA repeats have an EcoRI site, and most of the latter alpha-repeats are highly clustered within the CV-1 genome. EcoRI and HindIII solubilize approximately 8% and 2% of the alpha-chromatin, respectively, under the conditions used. EcoRI is thus approximately 30 times more effective than HindIII in solubilizing alpha-chromatin, with relation to the respective cutting frequencies of HindIII and EcoRI on alpha-DNA. EcoRI and HindIII solubilize largely non-overlapping subsets of alpha-chromatin. The DNA size distributions of both EcoRI- and HindIII-solubilized alpha-chromatin particles peak at alpha-monomers. These DNA size distributions are established early in digestion and remain strikingly constant throughout the digestion with either EcoRI or HindIII. Approximately one in every four of both EcoRI- and HindIII-solubilized alpha-chromatin particles is an alpha-monomer. Two-dimensional (deoxyribonucleoprotein leads to DNA) electrophoretic analysis of the EcoRI-solubilized, sucrose gradient-fractionated alpha-oligonucleosomes shows that they do not contain "hidden" EcoRI cuts. Moreover, although the EcoRI-solubilized alpha-oligonucleosomes contain one EcoRI site in every 172-bp alpha-DNA repeat, they are completely resistant to redigestion with EcoRI. This striking difference between the EcoRI-accessible EcoRI sites flanking an EcoRI-solubilized alpha-oligonucleosome and completely EcoRI-resistant internal EcoRI sites in the same alpha-oligonucleosome indicates either that the flanking EcoRI sites occur within a modified chromatin structure or that an altered nucleosome arrangement in the vicinity of a flanking EcoRI site is responsible for its location in the nuclease-sensitive internucleosomal (linker) region. Analogous redigestions of the EcoRI-solubilized alpha-oligonucleosomes with either HindIII, MboII or HaeIII (both before and after selective removal of histone H1 by an exchange onto tRNA) produce a self-consistent pattern of restriction site accessibilities. Taken together, these data strongly suggest a preferred nucleosome arrangement within the EcoRI-solubilized subset of alpha-oligonucleosomes, with the centers of most of the nucleosomal cores being approximately 20 bp and approximately 50 bp away from the nearest EcoRI and HindIII sites, respectively, within the 172-bp alpha-DNA repeat. However, as noted above, the clearly preferred pattern of nucleosome arrangement within the EcoRI-solubilized alpha-oligonucleosomes is invariably violated at the ends of every such alpha-oligonucleosomal particle, suggesting at least a partially statistical origin of this apparently non-random nucleosome arrangement.(ABSTRACT TRUNCATED AT 400 WORDS)

In vitro methylation of histones in sea urchin nuclei during early embryogenesis

Nuclei isolated from sea urchin embryos incubated in vitro in the presence of S-adenosyl-[methyl-3H]methionine, methylate their own basic proteins. The protein methylase activity varies during the embryonic development with two peaks of activity at mesenchymal blastula and at young gastrula. Histones H3 and H4 are the main substrates of the reaction. The extent of methylation of the two histones depends on the S-adenosylmethionine concentration. At low S-adenosylmethionine concentrations, the in vitro methyl-accepting ability of H3 is 10-times that of H4, while at high concentrations it is 3-times that of H4. This finding is clearly evident in the equilibrium saturation experiments with blastula and gastrula nuclei, which both show two distinct Km values for S-adenosylmethionine. The major and perhaps only product of methylation is epsilon-N-methyl-lysine. Enzyme activity is clearly correlated with specific embryonic stages, while no correlation is apparent between enzyme activity and the amount of DNA in the embryos.

HMG 14/17 binding affinities and DNAase I sensitivities of nucleoprotein particles

We show that ordinary (bulk) chicken erythrocyte nucleosomes are digested more rapidly by DNAase I when they are associated with high mobility group (HMG) proteins 14/17. Digestion of HMG 14/17-nucleosome complexes, under conditions where the DNA in control nucleosomes is digested to 10 to 20% acid solubility, results in a particular depletion of single-strand DNA fragments greater than 80 nucleotides in length, relative to the DNA fragments produced from control nucleosomes. Additionally, we show that staphylococcal nuclease digests of H1/H5-depleted chromatin contain an abundant subclass of nucleosomes that are not present in appreciable amounts in digests of native chromatin. These nucleosomes contain longer lengths of DNA and have lower electrophoretic mobilities than core particles. HMG 14/17 associates highly preferentially with these nucleosomes and renders them sensitive to DNAase I, similar to what has been found for active nucleosomes.

A topological model for chromatin transcription and a role for nucleosome linkers

There is a good deal of evidence that transcribing RNA polymerase may translocate across nucleosomes without their displacement and (or) rearrangement. A topological model for RNA chain elongation on a nucleosome is considered here. A new mechanism of RNA polymerase translocation is suggested in order to avoid the steric hindrances inherent in the model. It is shown that a transcribed nucleoprotein fiber should be interrupted by protein-free DNA stretches (nucleosome linkers) to allow release of nascent RNA. Possible verifications and consequences of the model are discussed.

Eukaryotic DNA methylation

Eukaryotic genomes contain 5-methylcytosine (5mC) as a rare base.5mC arises by postsynthetic modification of cytosine and occurs, at least in animals, predominantly in the dinucleotide CpG. The base is not distributed randomly in these genomes but conforms to a pattern. This pattern varies between taxa but appears to be inherited in a semi-conservative fashion. At the level of the genome, gross changes in the level of DNA methylation have been noted. This has encouraged speculation that the modification may play a role in cellular differentiation. Tissue-specific patterns of DNA methylation, predicted by various models of differentiation, have been found for most vertebrate genes so far examined. A correlation has emerged between the undermethylation of these regions and their transcription, but this is not always the case. While data for eukaryotic viral sequences are less equivocal, studies of this kind cannot in isolation distinguish between undermethylation being a cause or a consequence of gene activity. If it were a cause, it is probable that the demethylation of specific CpG sites would be a necessary yet not a sufficient condition for transcription to occur. The introduction of artificially methylated DNA sequences into individual eukaryotic cells by microinjection or transformation may provide the means to elucidate these questions in the future. In the meantime, the study of eukaryotic DNA methylation promises to contribute much to our understanding of the regulation of gene expression in these organisms.

Protein-associated intercalator-induced DNA scission is enhanced by estrogen stimulation in human breast cancer cells

Estrogen-responsive human breast cancer cells (MCF-7) displayed a higher frequency of intercalator-induced protein-associated DNA scission after treatment with 17 beta-estradiol (E2) than did cells that had not received estrogen treatment. This effect was dependent on estrogen concentration (maximum enhancement at approximately equal to 1 nM E2) and time (maximum effect seen approximately equal to 24 hr after E2 addition). Human breast cancer cells lacking estrogen receptors did not display the enhanced response. Antiestrogens produced a slight decrease in intercalator-induced DNA scission, whereas insulin produced an enhanced effect. The DNA breaks produced by the intercalators 5-iminodaunorubicin and 4'-(9-acridinylamino)methanesulfon-m-anisidide (m-AMSA) in these cells were undetectable without enzymatic deproteinization of cell lysates prior to quantification by alkaline elution. Intercalator-induced DNA-protein crosslinking also was enhanced in E2-treated MCF-7 cells. Studies with m-[14C]AMSA revealed no estrogen-associated increases in drug uptake. The data suggest that E2 treatment, either by specifically and directly increasing active transcription in chromatin or through secondary effects on DNA that accompany alterations in cell growth or cell cycle distribution, alters the susceptibility of DNA to intercalator-induced protein-associated DNA scission. If this enhanced protein-associated scission is selectively localized to transcriptionally active chromatin, the adsorption of the DNA-bound proteins to membrane filters (DNA-protein crosslinking) may allow identification and isolation of estrogen-regulated gene sequences.

Expression of T-lymphoblast-encoded HLA-DR, MT, and SB antigens on human T-B lymphoblast hybrids

The Ia-like antigens of hybrids of the B-lymphoblastoid cell line (B-LCL) WI-L2 and a subline of the T-lymphoblastoid cell line (T-LCL) HSB were examined. Antigens of the HLA-DR and MT series were analyzed by indirect immunofluorescence with chimpanzee anti-DR sera and monoclonal antibodies, and antigens of the SB series were analyzed by primed lymphocyte typing (PLT). The WI-L2 X HSB hybrids expressed antigens of each series not found on either parent cell. In each case, the novel antigens were indistinguishable from those found on SB, a B-LCL established from the same individual as HSB, and are thus presumably HSB encoded.

DNase I hypersensitivity in the gamma globin gene locus of K562 cells

We have probed the chromatin conformation of the G gamma-A gamma-delta-beta globin gene locus of K562 cells, a human hematopoietic cell line, with the enzyme pancreatic DNAse I. This enzyme preferentially digests genes in an active configuration. We have found that in K562 cells, which produce embryonic and fetal but not adult hemoglobins, both the active gamma and inactive beta genes are DNAse I sensitive. However, only the active gamma genes have DNAse I hypersensitive regions. The hypersensitive regions have been mapped to an area approximately 100 base pairs 5' to the G gamma and A gamma genes.

ADP-ribosyl transferase, rearrangement of DNA, and cell differentiation

Cell differentiation is the process by which genetic information is selectively expressed to produce cells with various morphologies and functions. The integrated changes necessary for this fundamentally important process have recently been the subject of intense study. This review will summarize data from several laboratories correlating differentiation with the activity of the enzyme ADP-ribosyl transferase and with changes in single-strand DNA breaks in various diverse eukaryotic systems. We will then discuss the implications of these observations for differentiation in general, including the possibility that rearrangement of genetic material is a widespread mechanism for controlling gene expression.

Decondensation of mouse sperm chromatin and reassembly into nucleosomes mediated by polyglutamic acid in vitro

The organization of the mammalian sperm nucleus was probed with staphylococcal nuclease. Although isolated nuclei are resistant to cleavage, following reduction and alkylation, 30% of the sperm DNA could be digested and the remaining DNA had a heterodisperse size distribution. By morphological criteria, a model acidic protein, polyglutamic acid was capable of decondensing purified sperm nuclei that had been reduced and alkylated. The maximal extent of nuclease digestion increased to 85-90%. The subsequent addition of purified, exogenous core histones in 0.1 M NaCl partially reversed this vulnerability to nuclease cleavage such that only 55% of the DNA was digested. Furthermore, analysis of the remaining DNA revealed a nucleosome ladder pattern with unit length repeat of 150 bp. These results strongly suggest that polyglutamic acid can mediate not only decondensation of sperm nuclei but also the assembly of sperm chromatin into nucleosomes.

Restricted repair of aflatoxin B1 induced damage in alpha DNA of monkey cells

We have investigated the processing of adducts formed by covalent binding of aflatoxin B1 (AFB1) to DNA in confluent cultures of African green monkey cells. Repair synthesis elicited by AFB1 adducts was deficient in alpha DNA sequences compared to that in bulk DNA, although the initial levels of modification were the same for these DNAs. The removal of the primary initial adduct, AFB1-N7-Guanine, was deficient in alpha DNA and the kinetics of its loss resembled those previously reported for removal from total DNA in xeroderma pigmentosum cells of complementation group A. Spontaneous loss of the AFB1 moiety or the concomitant loss of the guanine to yield an apurinic site account for these results. The formation of the more chemically stable secondary product, AFB1-triamino-Pyrimidine, occurred more rapidly and to a greater extent in alpha DNA than in bulk DNA, probably because of slower removal of the primary product. The excision repair patch size for AFB1 adducts in alpha DNA was only 10 nucleotides compared to 20 nucleotides for repair of AFB1 adducts in bulk DNA. Irradiation of cells with low doses of UV prior to or immediately after treatment with AFB1 increased the rate and extent of removal of AFB1 adducts from alpha DNA to the levels found in the bulk DNA, indicating that the formation of pyrimidine dimers or their repair may alter the chromatin structure of alpha DNA sufficiently to facilitate its repair.

DNA methylation and the regulation of globin gene expression

We have studied the effect of DNA methylation on human gamma-globin gene expression, using a novel in vitro DNA methylation technique. With this method we have methylated specific segments of the gamma-globin gene and its 5'-flanking region, which were cloned for this purpose in the bacteriophage vector M13mp8. The vitro methylated DNA was introduced into mouse L-cells by cotransfer using the herpes simplex virus thymidine kinase gene as a selective marker. Transformed cell lines were isolated to examine the inheritance of the segmental methylation pattern and its effect on the expression of the gamma-globin gene. Cells transformed with DNA methylated throughout the M13 vector and gamma-globin DNA sequences do not express the gamma-globin gene. Methyl-C residues in either the M13 DNA sequences or the gamma-globin structural gene have, however, no inhibitory effect on globin transcription. In contrast, methylation in the 5' region of the gamma-globin gene (from nucleotides -760 to +100) prevents transcription. These data indicate that DNA methylation in the 5' region of a gene might play a direct role in the regulation of gene expression.

Structure of a nuclease-sensitive region inside the immunoglobin kappa gene: evidence for a role in gene regulation

A discrete chromatin region inside the active immunoglobulin kappa gene is preferentially accessible to cleavage by nucleolytic enzymes. This region comprises 200-250 bp of DNA, and is situated within the large intron of the gene, approximately 600 bp upstream from the constant region coding sequence. The local chromatin structure of this region correlates with tissue-specific kappa gene expression: it is resistant to nucleolytic digestion in the inactive kappa genes of murine brain and liver nuclei, but becomes uniquely sensitive to cleavage by deoxyribonuclease I or by a variety of restriction endonucleases in the chromatin of kappa-producing cells. Nuclease sensitivity at this site occurs in both rearranged and unrearranged kappa alleles, and can be maintained in the absence of ongoing kappa transcription. The nucleotide sequence of the hypersensitive region has been selectively conserved in evolution, and includes both a 7 bp inverted repeat sequence and a short segment homologous to the transcriptional enhancer elements of certain eukaryotic viruses. Molecular events occurring at this locus may play a role in the regulation of kappa gene expression, perhaps by influencing the activity of promoter sequences several kilobases upstream.

Transcribing chromatin is not preferentially enriched with acetylated histones

Chromatin fragments of the RNA polymerase II-transcriptional complex were purified from the micrococcal nuclease digest of rat liver nuclei in the presence of n-butyrate, a potent histone deacetylase inhibitor. Polyacrylamide gel electrophoretic analysis in Triton acid-urea revealed that the extent of histone acetylation of the complex did not differ markedly from that of the total chromatin.

Role of histones H1 and H3 in the maintenance of chromatin in a compact conformation. Study with an immobilized enzyme

Chromatin polynucleosomes have been digested with trypsin immobilized on collagen membranes. This method allows the mild removal of the most accessible histone fragments simply by dipping the enzymatic membrane into the chromatin solution, without modification of its ionic and chemical composition. These results demonstrate that the removal of H1 does not affect the higher-order structure of chromatin and that only the elimination of the terminal regions of H3 leads to the unfolding of H1-depleted fibres. This observation suggests that structural changes reported in many previous works were not due to only the removal of H1 but to a concomitant unbinding from DNA of the N-terminal domain of H3.

Detection of an altered DNA conformation at specific sites in chromatin and supercoiled DNA

We show that bromoacetaldehyde, which reacts selectively at the N-1 and N-6 positions of unpaired adenine and at the N-3 and N-4 positions of unpaired cytosine residues reacts with chromosomal DNA in intact cells at probable regulatory sequences near active genes. A region of about 200 base pairs 5' to the chicken beta A-globin gene, which contains sites sensitive to nuclease S1, to several restriction endonucleases, and to very low levels of DNase I, also contains DNA structures that are preferentially sensitive to bromoacetaldehyde. These altered DNA structures are found at reproducible positions relative to the beta A-globin gene regardless of whether the bromoacetaldehyde is presented to intact erythrocytes, erythrocyte nuclei, or the beta A-globin gene itself carried in pBR322 as purified supercoiled DNA. The unpaired DNA 5' to the adult beta A-globin gene in adult erythrocytes is not detectable in embryonic erythrocytes that express embryonic beta-globin in contrast to adult beta A-globin. Our results suggest that well-defined regions of DNA with effectively unpaired bases occur in intact nuclei and that these structures may be important for specific recognition because they are tissue specific and are found at putative regulatory regions.