Interaction of HMG 14 and 17 with actively transcribed genes

Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes

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

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.

Developmental switches in reiterated genes may reduce the rate of age changes in DNA

The possible role of the redundancy of genetic information in the regulation of the ageing rate has been discussed in several works. However, it was shown recently that the gene reiteration in most cases is represented by families of similar, but not identical genes. Their expression usually related to the different stages of development and when "early" embryonic or fetal genes are active, the "late" or adult genes are repressed. It is known that the DNA repair needs double stranded structure of DNA which is usual for inactive genes. Genes which are being transcribed and active are repressed by unwound, relaxed DNA which is less protected by the DNA repair enzymes. Aging of genetic information in somatic cells can be, therefore, considered as stage specific and alterations of "early" embryonic and fetal genes do not constitute the genetic load which influences the ageing rate of differentiated cells.

Antigens in chromatin associated with proliferating and nonproliferating cells

Xenoantisera were raised to total chromatin from the leukemia cell line K562, or materials released through limited deoxyribonuclease I digestion of nuclei or during the control incubation of nuclei without enzyme. The peroxidase-antiperoxidase method of antibody-antigen detection was employed to visualize individual antigens resolved on one-dimensional polyacrylamide gels following transfer to sheets of nitrocellulose (immunotransfers). Each antiserum contained multiple antigen specificities as evidenced by the diverse patterns of reactive bands displayed on the immunotransfers. The most striking difference in antigens recognized between the antisera was observed in the molecular weight region below 50,000, where two highly reactive bands were seen mainly with antiserum to nuclear materials released by deoxyribonuclease I digestion. The antigens detected with all of the antisera were present in chromatins prepared from proliferating cells, while the levels of antigens present in chromatin from non-proliferating peripheral blood lymphocytes were greatly reduced or not detected. Antigens in chromatin from proliferating cells that migrated with apparent molecular weights of 37,000 and 100,000 were not lost once the activities to antigens in lymphocyte chromatin were absorbed out. These two activities were absorbed from antisera with the same amount of chromatins from proliferating cells. Two antigens migrating at molecular weight 52,000 and 76,000 appeared more active in the chromatin from unstimulated lymphocytes than in chromatin from proliferating cells.

Tissue-specific distribution of DNA-binding nuclear proteins

The DNA-binding capacity of nuclear proteins of mouse cells was examined by the protein-blotting method. Under conditions in which the lac repressor specifically binds to the lac operator, the DNA-binding nuclear proteins from different tissues showed a tissue-specific distribution, suggesting that the species and amounts of nuclear proteins with DNA binding activity differ in different tissues. When cloned eukaryotic genes were used for binding, eukaryotic DNA showed stronger binding than prokaryotic DNA. Competition experiments suggested that many nuclear proteins have different DNA binding properties from that of the prokaryotic repressor.

Accessibility of ribosomal genes to trimethyl psoralen in nuclei of Physarum polycephalum

We have probed the accessibility of the genes for rRNA in Physarum polycephalum by using the photoreactive DNA cross-linking agent 4,5',8-trimethyl psoralen. Nuclei isolated from actively growing Physarum were treated with trimethyl psoralen and irradiated with 360-nm light in order to form cross-links. The palindromic, extrachromosomal rDNA then was isolated, and the positions of cross-links were determined by electron microscopy of the DNA under totally denaturing conditions. The results indicate that the frequency of cross-linking, after correction for base sequence bias of the reaction, is up to sixfold higher in the transcribed regions than in the central or the terminal spacer regions. There is no detectable heterogeneity among the different rDNA molecules or between the halves of a single molecule. Cross-linked molecules invariably occur in a linear as opposed to a cruciform structure. The preferential cross-linking of the transcribed region is nearly eliminated in spherules, a dormant transcriptionally inactive form in the Physarum life cycle.

Prolactin-deficient variants of GH3 rat pituitary tumor cells: linked expression of prolactin and another hormonally responsive protein in GH3 cells

GH3 cells normally synthesize and secrete two pituitary polypeptide hormones, prolactin and growth hormone. From an ethyl methane sulfonate-mutagenized population, prolactin low-producing variants have been isolated at a frequency near 20%. Intracellular prolactin synthesis in the variants was reduced 40- to 100-fold compared to wild-type cells while growth hormone synthesis varied less than 2-fold. This decrease was paralleled by a decrease in intracellular preprolactin mRNA. Although reduced, prolactin synthesis was still repressible by glucocorticoids. There was a coordinate loss of expression of p21, a thyroid and glucocorticoid hormone-regulated protein, in GH3 cells, whereas the synthesis and regulation of other hormonally responsive proteins were unimpaired in the variants. Since p21 expression was coordinately regained in a high-producing prolactin revertant cell, expression of the two proteins is tightly coupled in GH3 cells. The stability of the low-producing phenotype differed among variants. One (B2) gave rise to revertants at about 20% frequency even after two rounds of subcloning, whereas another (B3) was more stable in that only 1 weak revertant was found in 47 subclones. The reversion frequency of B3 cells was also measured at less than 0.5%. Unmutagenized GH3 cells were phenotypically stable in that no prolactin-deficient variant was found among 57 subclones. Since variants were ony found after ethyl methane sulfonate mutagenesis, the DNA alkylating agent appears to have promoted an epigenetic change in pituitary gene expression.

Conformation of the HMG 14 nucleosome core complex from flow birefringence

Flow birefringence and extinction angles have been measured for HMG 14 complexes with nucleosome core particles from chicken erythrocytes under cooperative "tight" binding conditions, and for the uncomplexed core particles used in the preparations. Results are interpreted using optical models for the observed DNA anisotropy, and are compared to recent small angle neutron scattering results. (19) The studies effectively rule out highly distorted DNA conformations and configurations in which DNA ends are unwound and extended. It is concluded that the most likely conformation of the complex is one in which the DNA superhelix is radially increased, either uniformly or bilaterally, with the DNA ends remaining tightly bound to the particle. This conformation does not require large changes in spatial relationships between the DNA ends compared to the uncomplexed core as would accompany, for example, significant unwinding of the ends. However, it may lead to more subtle but possibly highly significant differences in the angles at which the DNA exits the core particle.

Neutron scattering studies and modeling of high mobility group 14 core nucleosome complex

Considerable evidence relates the nonhistone proteins high mobility group (HMG) 14 and HMG 17 with the structure of active or potentially active chromatin. In this study, bulk nucleosome core particles prepared from chicken erythrocytes and the complex formed by binding two HMG 14 molecules per nucleosome core were studied by use of small-angle neutron scattering techniques. By varying the H2O/2H2O ratio, and hence the contrast between the solvent and the particles, it was possible to determine the radius of gyration of the protein and of the DNA independently and as a function of HMG 14 binding. The results show an increase of 0.9 +/- 0.6 A (mean +/- SEM) in the protein radius of gyration and of 2.7 +/- 0.6 A in the DNA radius of gyration upon binding of HMG 14 to the nucleosome. These changes are considered in the light of several postulated modes for the unfolding or perturbation of the nucleosome structure. Modeling calculations demonstrate that the observed changes in radius of gyration for the DNA and for the protein are too small to be consistent with an overall unfolding or opening of the core particle upon HMG 14 binding. However, the observed changes are consistent with several models that involve only minor changes in the structure. It is postulated that the differences observed may be an indication of the type of conformational change occurring in active nucleosomes.

Condensation of chromatin into chromosomes preserves an open configuration but alters the DNase I hypersensitive cleavage sites of the transcribed gene

DNase I was used to probe the molecular organization of the chicken ovalbumin (OV) gene and glyceraldehyde 3-phosphate dehydrogenase (GPD) gene in interphase nuclei and in metaphase chromosomes of cultured chicken lymphoblastoid cells (MSB-1 line). The OV gene was not transcribed in this cell line, whereas the GPD gene was constitutively expressed. The GPD gene was more sensitive to DNase I digestion than the OV gene in both interphase nuclei and metaphase chromosomes, as determined by Southern blotting and liquid hybridization techniques. In addition, we observed DNase I hypersensitive sites around the 5' region of the GPD gene. These hypersensitive sites were not always at the same locations between the interphase nuclei and metaphase chromosomes. Our results suggest that chromatin condensation and decondensation during cell cycle alters nuclease hypersensitive cleavage sites.

Replicative conformation of parental nucleosomes: salt sensitivity of deoxyribonucleic acid-histone interaction and alteration of histone H1 binding

The transiently altered DNA-histone interaction of parental chromatin during replication was studied by micrococcal nuclease digestion. A large amount of nuclease-resistant pulse-labeled DNA and a small fraction of nonreplicating DNA are released from chromatin fragments by treatment with 0.5 M NaCl and appear as protein-free DNA. As shown by reconstitution experiments, the salt sensitivity of digested nascent chromatin is most probably a consequence of the shorter DNA fragment size (55 +/- 15 base pairs) in these complexes. This new DNA is associated with parental chromatin fragments which are structurally changed in such a way that parts of nucleosomal DNA were more susceptible to nuclease attack. The core histones of these particles are probably not distinct from those of salt-stable nucleosomes. However, histone H1 and probably high-mobility group proteins appear to be more weakly bound during replication as shown by electrophoresis under nondenaturing conditions. The results agree with the assumption that the transient alteration of nucleosomal conformation describes a state in which DNA could be replicated without leaving the associated core histone complexes. A possible attachment of pulse-labeled chromatin with nuclear matrix is discussed.

A complex of interacting DNAase I-hypersensitive sites near the Drosophila glue protein gene, Sgs4

The chromatin structure adjacent to the Drosophila glue protein gene Sgs4 changes drastically when the gene is active. In nuclei from embryos or tissue culture cells in which Sgs4 is inactive, there are three DNAase I-hypersensitive sites 3' to the gene, but none near its 5' end. In the nuclei of late third instar salivary glands, Sgs4 is actively transcribed, and a complex of five DNAase I-hypersensitive sites appears 5' to the gene. Two of the sites are near the point of transcription initiation, at -70 and +30. The others are much farther from the gene at -330, -405 and -480 and are affected by small deletions: one deletion reduces expression about 50-fold and removes sequences corresponding to the -330 hypersensitive site; another makes no Sgs4 RNA and removes sequences corresponding to two hypersensitive sites, -405 and -480. Thus the hypersensitive sites, or DNA sequences within 50 bp of them, seem to be required for normal gene expression Distinct changes are seen in the chromatin from salivary glands of these mutant strains. The first strain is simply missing the -330 hypersensitive site, while the second is missing all of the tissue-specific 5' sites, even though sequences corresponding to three of them remain. This suggests that hierarchical interactions among the regions 5' to Sgs4 are required for its full expression. A sequence of 14 bp at the most prominent hypersensitive site (-405) is closely related to sequences 5' to several other eucaryotic genes.

Fractionation of mechanically sheared chromatin on ECTHAM-cellulose

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

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

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

Active chromatin

Active genes are packaged into an altered nucleosome structure forming a chromosomal domain defined by increased sensitivity to nucleases. This structure, reflecting a potential for transcription, contains sites hypersensitive to nuclease digestion adjacent to the coding regions and may also be distinguished by specific non-histone proteins, variant or modified histones or modified DNA. Its formation, by unfolding of a tightly packed chromatin fibre by factors which might affect DNA supercoiling, may be the first step in gene activation.

Detection of monoclonal antibody to high-mobility-group protein 17 from chick oviduct

Total chromosomal HMG (high-mobility-group) proteins have been isolated from oestrogen-stimulated chick oviduct. The antibodies against these proteins were induced in mice and subsequently their spleen cells were fused with myeloma cells to form hybridomas. A highly purified HMG protein, 17, was used to select for the hybridomas that produce antibody against HMG protein 17. The hybridomas were cultured and injected into mice to produce ascites. The antibody against HMG protein 17 in the IgG (immunoglobulin G) fraction of the ascites fluid was obtained by Protein A-Sepharose column chromatography. We have devised a solid-phase radioimmunoassay and enzyme-linked serological assay for the detection and characterization of this antibody directed against HMG protein 17. This anti-(HMG protein 17) IgG interacted only with HMG protein 17, but not with other chromosomal proteins, e.g. histone H1, "95K protein' (a chick oviduct-specific chromosomal protein) and HMG proteins 1, 2 and 14. The monospecific nature of this anti-(HMG protein 17) IgG fraction is confirmed.

The small chromatin fragments released by micrococcal nuclease from hepatoma tissue cultured cell nuclei are strongly enriched in coding DNA sequences and are related to an actively transcribed single-stranded DNA fraction

It was shown with the use of specific probes that mild micrococcal nuclease digestion released from chromatin actively-transcribed genes as small nucleosome oligomers. In the present work we demonstrate that most if not all of the active genes are accessible to the nuclease. It was found that the short released fragments are greatly enriched in transcribed DNA sequences, the most enriched being the dimers of nucleosomes since 35% of their DNA could be hybridized to cytoplasmic RNA. The results of cDNA-DNA hybridizations indicate that the monomers and dimers of nucleosomes contain most of the DNA sequences which encode poly(A+) RNAs, however larger released fragments include some transcribed sequences, while the nuclease resistant chromatin is considerably impoverished in coding sites. These evidences are the finding that about 25% of the DNA from the dimers of nucleosomes are exclusively located in this class of fragments, tend to prove that the active chromatin regions are attacked in a non-random way by micrococcal nuclease. We have previously isolated, without using exogenous nuclease, an actively transcribed genomic fraction amounting to 1.5-2% of the total nuclear DNA, formed of single-stranded DNA. In the present study we show that all or nearly all the single-stranded DNA sequences could be reassociated with the DNA fragments present in the released monomers and dimers of nucleosomes. Our observations confirmed our previous finding that the greatest part of single-stranded DNA selectively originates from the coding strand of genomic DNA.

Temperature-sensitive changes in the structure of globin chromatin in lines of red cell precursors transformed by ts-AEV

Chicken bone marrow cells infected in vitro with a temperature-sensitive avian erythroblastosis virus fall to produce hemoglobin at 36 degrees C. When the product or products of the transforming gene (erb) are inactivated by a temperature shift to 42 degrees C in culture, several different cloned lines of cells infected with the temperature-sensitive avian erythroblastosis virus begin to make hemoglobin. This shift in phenotype correlates with an increase in hemoglobin mRNA specific to both adult and embryonic alpha and beta globin. The switch is accompanied by the acquisition of DNAase I-hypersensitive sites in one cell line (clone 2); however, a hypothetically more mature line (clone 3) has already acquired globin DNAase-hypersensitive sites but does not express hemoglobin until the temperature shift. Several (but not all) specific restriction sites associated with both the alpha and beta domains become unmethylated after the switch from 36 degrees C to 42 degrees C. The magnitude of these methylation switches is small compared with changes that occur in these genes during normal avian erythropoiesis. The results suggest that changes in chromosomal structure precede transcription and are not a consequence of transcription. Since (presumptive) precursor cloned lines can be established with some, but not all, of the structural properties of active globin chromatin, it is likely that many of these properties can be independently established and are not obligatorily related.

The high mobility group proteins HMG 14 and 17, do not prevent the formation of chromatin higher order structure

The high mobility group proteins, HMG 14 and 17, have been associated with the chromatin of active genes (refs 1-8), although how they function is not known. We use sedimentation and electric dichroism to investigate the effect of HMG 14 and 17 on the condensation of chicken erythrocyte chromatin into higher order structure. We find no evidence that excess HMG 14 and 17 induce an extended configuration, either in bulk chromatin or in the chromatin of the chicken beta-globulin gene.

Properties of active nucleosomes as revealed by HMG 14 and 17 chromatography

Nucleosomes from actively transcribed genes (active nucleosomes) contain nonhistone proteins HMG 14 and 17 and are preferentially sensitive to digestion by DNAse I. Active nucleosomes isolated by chromatography on an HMG 14 and 17 glass bead affinity column were analyzed with respect to overall structure, accessory nonhistone components and modifications to the DNA and histones. The experiments lead to the following conclusions: the DNA in the active nucleosome is undermethylated compared to bulk DNA; topoisomerase I is a non-stoichiometric component of the active nucleosome fraction; the level of histone acetylation is enriched in active nucleosomes, but the extent of enrichment cannot account for HMG binding; and the two histone H3 molecules in the active nucleosome can dimerize more readily and are, therefore, probably closer together than those in the bulk of the nucleosomes. Additionally it is shown that HMG 14 and 17 prefer to bind to single- vs. double-stranded nucleic acids. The role of HMG 14 and 17 in producing a highly DNAse I sensitive structure and correspondingly helping to facilitate transcription is discussed in terms of these properties.

Autoantibodies to nucleosomal proteins: antibodies to HMG-17 in autoimmune diseases

The relative amounts of autoantibodies against defined nucleosomal proteins present in serums from patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and mixed connective tissue disease (MCTD) have been examined by an enzyme-linked immunoassay. Autoantibodies to nucleosomal proteins were detected in 45 percent of the patients with SLE, 18 percent of the MCTD patients, and none of the RA patients. The results suggest that, in SLE, antibodies are formed against a subset of nucleosomes which contain protein HMG-17.

Major high mobility group like proteins of Drosophila melanogaster embryonic nuclei

Nuclei from Drosophila melanogaster embryos contain three major proteins which are extracted by 0.35 M NaCl and by 2% perchloric acid. One of these is histone H1, and we refer to the other two as A63 and A13 in accordance with their molecular weights determined by electrophoresis on sodium dodecyl sulfate (NaDodSO4)-polyacrylamide gels (63,000 and 13,000, respectively). The molecular weight of A13, based on its amino acid composition, is approximately 10,000. The amino acid analyses of A63 and A13 show that both of these proteins have high proportions of acidic and basic amino acid residues, a property characteristic of the high mobility group proteins isolated from vertebrate tissues. While A13 comigrates with histone H2A on NaDodSO4-polyacrylamide gels and with H2B on acid/urea gels, it can be readily resolved from the histones by Triton/acid/urea-Na DodSO4 two-dimensional electrophoresis.

Accessibility of ribosomal genes to trimethyl psoralen in nuclei of Physarum polycephalum

We have probed the accessibility of the genes for rRNA in Physarum polycephalum by using the photoreactive DNA cross-linking agent 4,5',8-trimethyl psoralen. Nuclei isolated from actively growing Physarum were treated with trimethyl psoralen and irradiated with 360-nm light in order to form cross-links. The palindromic, extrachromosomal rDNA then was isolated, and the positions of cross-links were determined by electron microscopy of the DNA under totally denaturing conditions. The results indicate that the frequency of cross-linking, after correction for base sequence bias of the reaction, is up to sixfold higher in the transcribed regions than in the central or the terminal spacer regions. There is no detectable heterogeneity among the different rDNA molecules or between the halves of a single molecule. Cross-linked molecules invariably occur in a linear as opposed to a cruciform structure. The preferential cross-linking of the transcribed region is nearly eliminated in spherules, a dormant transcriptionally inactive form in the Physarum life cycle.

Murine erythroleukemia cell differentiation: DNase I hypersensitivity and DNA methylation near the globin genes

The sensitivity to digestion by DNase I of chromatin containing the alpha- and beta(major)-globin genes and the pattern of DNA methylation near these genes was examined during hexamethylenebisacetamide (HMBA)-mediated erythroid differentiation of murine erythroleukemia cells (MELC). In uninduced and induced cells, the chromatin regions containing the alpha- and beta-(major)-globin genes are more sensitive to digestion by DNase I than is the region containing an immunoglobulin gene (Igalpha) not expressed during erythroid differentiation. However, at low concentrations of DNase I, a 6- to 10-fold increase in site-specific cleavages was generated in chromatin regions near both the alpha- and beta(major)-globin genes in cells induced to differentiate by HMBA. The DNase I hypersensitive site near the beta(major)-globin gene maps to a small region near the 5' terminus of the gene. No detectable change in the pattern of DNA methylation around either the alpha- or beta-globin genes was observed during HMBA-mediated erythroid differentiation. Of the potentially methylated sites assayed and mapped near the beta(major)-globin gene, one site is fully methylated, one is partially methylated, and one is unmethylated both in uninduced and induced cells. Many (but not all) sites assayed near the alpha-globin genes are unmethylated in both uninduced and induced cells. These results show that specific alterations of chromatin structure occur during MELC differentiation and suggest that these changes may not involve alterations in the pattern of DNA methylation.

Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state

Cloned 5S RNA genes added to Xenopus oocyte nuclear extract assemble into stable active transcription complexes that persist for many rounds of 5S RNA synthesis. This stability of the complex has been demonstrated by its resistance to dilution and to competitor DNA. A stable complex is formed within minutes and lasts for at least 40 rounds of transcription per template over several hours. Stable, transcriptionally inactive complexes can be formed by incubation of cloned 5S RNA genes in an oocyte nuclear extract depleted of a 5S-specific transcription factor and supplemented with histones. The stable, transcriptionally active and inactive states of 5S RNA gene complexes that can be formed in vitro are analogous to the states of the somatic and oocyte 5S RNA genes as they exist in somatic cell chromatin. Oocyte 5S RNa genes remain repressed in chromatin isolated from somatic cells, but can be activated by washing chromatin with high salt. Maintenance of the differentiated state of cell requires that selected genes remain stably active while others are stably repressed for long periods of time. We propose that stable transcription complexes may play an important role in the maintenance of the differentiated state in eucaryotic cells.

Prolactin-deficient variants of GH3 rat pituitary tumor cells: linked expression of prolactin and another hormonally responsive protein in GH3 cells

GH3 cells normally synthesize and secrete two pituitary polypeptide hormones, prolactin and growth hormone. From an ethyl methane sulfonate-mutagenized population, prolactin low-producing variants have been isolated at a frequency near 20%. Intracellular prolactin synthesis in the variants was reduced 40- to 100-fold compared to wild-type cells while growth hormone synthesis varied less than 2-fold. This decrease was paralleled by a decrease in intracellular preprolactin mRNA. Although reduced, prolactin synthesis was still repressible by glucocorticoids. There was a coordinate loss of expression of p21, a thyroid and glucocorticoid hormone-regulated protein, in GH3 cells, whereas the synthesis and regulation of other hormonally responsive proteins were unimpaired in the variants. Since p21 expression was coordinately regained in a high-producing prolactin revertant cell, expression of the two proteins is tightly coupled in GH3 cells. The stability of the low-producing phenotype differed among variants. One (B2) gave rise to revertants at about 20% frequency even after two rounds of subcloning, whereas another (B3) was more stable in that only 1 weak revertant was found in 47 subclones. The reversion frequency of B3 cells was also measured at less than 0.5%. Unmutagenized GH3 cells were phenotypically stable in that no prolactin-deficient variant was found among 57 subclones. Since variants were ony found after ethyl methane sulfonate mutagenesis, the DNA alkylating agent appears to have promoted an epigenetic change in pituitary gene expression.

Structure of the active nucleolar chromatin of Xenopus laevis Oocytes

Active nucleolar chromatin of Xenopus laevis oocytes was prepared for electron microscopy by a step gradient method, which separates the chromatin from proteins and other constituents that might nonspecifically bind at low ionic strength. Between putative RNA polymerases and within the nontranscribed spacer region, the chromatin appears as smooth, thin filaments. For the first time, it is shown here that these filaments are indistinguishable from pure DNA absorbed to the same specimen, even when the ionic strength is raised up to 100 mM NaCl. Bulk rat liver chromatin, however, which was coprepared as a biochemically well-characterized standard with the active nucleolar chromatin, shows nucleosomes containing fibers, which condense into supranucleosomal structures with increasing ionic strength. Since the appearance and the behavior of active nucleolar chromatin at different ionic strengths and pHs resembles tht of pure DNA, but not of any known type of chromatin, it is suggested that, except for the transcription apparatus, very few macromolecular constituents are associated with ribosomal DNA during transcription. The observations described in this paper explain most of the published and partly conflicting results obtained by electron microscopy of nucleolar chromatin.