Selective digestion of transcriptionally active ovalbumin genes from oviduct nuclei

DNaseI-hypersensitive sites at promoter-like sequences in the spacer of Xenopus laevis and Xenopus borealis ribosomal DNA

We have detected a DNAseI hypersensitive site in the ribosomal DNA spacer of Xenopus laevis and Xenopus borealis. The site is present in blood and embryonic nuclei of each species. In interspecies hybrids, however, the site is absent in unexpressed borealis rDNA, but is present normally in expressed laevis rDNA. Hypersensitive sites are located well upstream (over lkb) of the pre-ribosomal RNA promoter. Sequencing of the hypersensitive region in borealis rDNA, however, shows extensive homology with the promoter sequence, and with the hypersensitive region in X. laevis. Of two promoter-like duplications in each spacer, only the most upstream copy is associated with hypersensitivity to DNAaseI. Unlike DNAaseI, Endo R. MspI digests the rDNA of laevis blood nuclei at a domain extending downstream from the hypersensitive site to near the 40S promoter. Since the organisation of conserved sequence elements within this "proximal domain" is similar in three Xenopus species whose spacers have otherwise evolved rapidly, we conclude that this domain plays an important role in rDNA function.

Distribution of nucleosomes on reconstituted chromatin from cloned mouse beta-globin DNA

Relative abundance of nucleosomes on reconstituted chromatin was estimated with cloned mouse beta-globin gene DNA. Mononucleosomal DNA was isolated from reconstituted chromatin after digestion with micrococcal nuclease, nick-translated and used as a probe for blot hybridization. DNA fragments of restriction nuclease-digested globin DNA were transferred to DBM-paper and hybridized with mononucleosomal [32P] DNA probe. The results showed non-random distribution of nucleosomes.

The level of expression of the rat growth hormone gene in liver tumor cells is at least eight orders of magnitude less than that in anterior pituitary cells

Rat liver hepatoma cells (HTC) which express liver-specific gene products were assayed for the expression of the rat growth hormone (rGH) gene, which is normally expressed in anterior pituitary somatotrophs. The combination of immunoprecipitation and two-dimensional gel electrophoresis provided a highly sensitive assay for rGH synthesis at levels as low as one part in 10(9) of cell protein synthesis (or four molecules of rGH per cell). No rGH expression was detected at this level. The lack of expression in HTC cells did not derive from a deletion of the rGH gene, as shown by Southern hybridization analysis of genomic DNA. Because the gene is expressed at greater than 30% of anterior pituitary protein synthesis, differentiation regulated rGH expression by over 10(8)-fold between the two cell types. Additionally, DNA-excess solution hybridization was used to measure the level of rGH mRNA sequences. A novel and general method for preparing single-strand probes from recombinant plasmids was developed. Hybridization analyses with a sensitivity of detection of 1 part in 10(8) failed to detect any rGH RNA sequences in either the nucleus or cytoplasm of HTC cells. It is concluded, therefore, that the restriction in rGH expression in the liver tumor cells is likely to occur at the level of the transcription of the gene, and that for all practical purposes, the rGH gene is completely shut off in the hepatoma cells.

In situ nick-translation distinguishes between active and inactive X chromosomes

Template-active regions of chromatin are structurally distinct from nontranscribing segments of the genome. Recently, it was suggested that the conformation of active genes which renders them sensitive to DNase I may be maintained even in fixed mitotic chromosomes. We have developed a technique of mitotic cell fixation and DNase I-directed nick-translation which distinguishes between active and inactive X chromosomes. We report here that Gerbillus gerbillus (rodent) female cells contain easily identified composite X chromosomes each of which includes the original X chromosome flanked by two characteristic autosomal segments. After nick-translation the active X chromosome in each cell is labelled specifically in both the autosomal and X-chromosomal regions. The inactive X chromosome is labelled only in the autosomal regions and in a small early replicating band within the late replicating 'original X' chromosome. Our technique opens the possibility of following the kinetics of X-chromosome inactivation and reactivation during embryogenesis, studying active genes in the inactive X chromosome and mapping tissue-specific gene clusters.

A destabilized DNA conformation associated with tightly bound nuclear proteins in active genes of rat myoblast

Purified nuclei from tissue cultured myoblasts were disrupted and centrifuged to equilibrium in a sarcosyl-caesium chloride gradient. A small portion (1.3% - 1.9%) of the non histone proteins (NHP) were banded with DNA in a high density region of the gradient. The DNA tightly bound to proteins representing about 0.6% of the total nuclear DNA was degraded after treating cell nuclei with S1 nuclease or DNAse I but resisted to mild micrococcal nuclease digestion. A large portion of the DNA sequences complementary to homologous RNA was concentrated in this DNA-proteins fraction. These finding suggest that a subset of NHP strongly associated to the active DNA regions play a role in the destabilisation of the double helical DNA during transcriptional processes.

Induction of globin gene expression during erythroid cell differentiation

We can provide increasing insight, albeit still incomplete, into the changes in MELC that accompany globin gene expression induced by polar chemicals, such as DMSO, and other agents. These transformed, CFUe-like erythroid precursor cells exhibit in their uninduced state, a DNA methylation pattern and globin gene (formula; see text) chromatin configuration (DNase I sensitivity) that is compatible with actual or potential gene transcription. Such features may reflect alterations in chromatin configuration that have occurred at a stage prior to leukemic transformation, during the differentiation of earlier erythroid precursor cells and associated with the restriction in developmental potential characteristic of progression to the CFUe (or MELC) stage of erythropoiesis. Uninduced MELC display a low level of globin gene transcription, producing globin mRNA or mRNA precursors whose processing or stabilization is the target of action of hemin. The major increase in MELC globin gene transcription that is initiated by DMSO, HMBA, or butyric acid, is accompanied by, and perhaps preceded by, an increase in DNase I hypersensitivity in the regions 5' to the active globin genes. This suggests that reorganization of chromatin structure in the globin gene domains is associated with accelerated globin gene transcription and may be characteristic of a developmental transition during terminal differentiation in the erythroid cell lineage.

Actinomycin D-binding in vivo: active chromatin preferred

Escherichia coli RNA polymerase and the endogenous engaged RNA polymerase I were used as specific probes to monitor the physiologically inactive and active nucleolar chromatin template function, respectively. Actinomycin D bound preferentially to the physiologically active regions of rat liver nucleolar chromatin in vivo.

Mouse hepatic metallothionein-I gene cleavage by micrococcal nuclease is enhanced after induction by cadmium

Micrococcal nuclease has been shown to preferentially cleave chromatin in the region of genes actively engaged in transcription. We have used this preferential cleavage to show that the metallothionein (MT) gene in adult mouse liver, when induced to produce mRNA by injection of cadmium, becomes more susceptible to nuclease cleavage. However, the MT gene in uninduced liver, and the alphafoetal protein (AFP) gene in both induced and uninduced liver, remain relatively resistant to nuclease cleavage. The AFP gene is not normally expressed in cadmium induced or uninduced liver. Thus, susceptibility of genes to nuclease cleavage appears to rise with increasing transcription of the gene.

Resistance of Chinese hamster ovary cell chromatin to endonuclease digestion. I. Reversal by cAMP

A portion of the DNA within intact nuclei of a spontaneously transformed Chinese hamster ovary cell line (CHO-Kl) is relatively resistant to digestion by pancreatic deoxyribonuclease, as compared to nuclei from primary cultures of Chinese hamster ovary fibroblasts. Treatment of CHO-Kl cells with derivatives of 3',5' cyclic AMP (cAMP) under conditions which effect the reverse transformation (RT) of these cells, results in restoration of the increased sensitivity of their DNA to hydrolysis by pancreatic deoxyribonuclease, to the level characteristic of an untransformed, morphologically normal Chinese hamster fibroblast cell line. Dibutyryl (db-)cAMP and 8-bromo-cAMP (Br-cAMP) yielded similar results. The cAMP derivatives employed had no effect on the normal fibroblasts.

On the presence of two new high mobility group-like proteins in HeLa S3 cells

Two phosphorylated HMG-like proteins with Mr approximately 10 000 have been isolated from HeLa S3 cells, one being present in metaphase and one in interphase cells. The amino acid compositions of these proteins are very similar but differ from the known HMG proteins. However, they exhibit similarities being rich in proline, basic and acidic amino acids. A possible role in chromatin condensation of the HMG-like protein characteristic for metaphase cells is suggested.

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.

S1 sensitive sites in adenovirus DNA

S1 nuclease has been used as a probe for regions of DNA secondary structure in supercoiled recombinant plasmids containing adenovirus (Ad) DNA sequences. In the sequences examined two S1 sensitive sites were identified in the left-terminal 16.5% of Ad 12 DNA, one of which aligned approximately with an inverted repeat region in the DNA sequence. In addition an S1 sensitive site was dictated by a potential cruciform structure in the region of the Ad 2 major late promoter. In contrast to the expected cleavage site at the loop of the cruciform, cleavage occurred at the base of the stem in the region of the TATA box. All three S1 sensitive sites identified were more sensitive to S1 than the endogenous sites in the parent plasmids.

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.

Synthesis and characterization of a DNA complementary to Xenopus laevis albumin mRNA

Albumin complementary DNA (cDNA) was transcribed from purified albumin mRNA from the liver of Xenopus laevis. The resultant cDNA was an almost full length copy as defined by denaturing gel electrophoresis; was hybridized specifically to albumin mRNA with pseudo-first-order reaction kinetics and the mRNA . cDNA hybrid exhibited a sharp melting profile with a Tm of 83 degrees C. The identity of the cDNA was confirmed by gel electrophoresis following hybridization-arrested translation.

The ninth Frederick H. Verhoeff lecture. The life history of retinal cells

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Accurate transcription of simian virus 40 chromatin in a HeLa cell extract

During simian virus 40 viral maturation, a series of modifications occur which alter the composition of viral nucleoprotein complexes. As a consequence, the chromatin that is extracted from extracellular simian virus 40 virions exhibits properties that are similar to those of transcriptionally active eucaryotic chromatin. The influence of this chromatin structure on specific RNA initiation by RNA polymerase II was examined by using the in vitro HeLa cell extract of Manley et al. (Proc. Natl. Acad. Sci. U.S.A. 77:3855-3859, 1980). The 5' ends of RNA transcripts were positioned by the "run-off" assay, in which transcripts extend from the initiation site to termination sites created by restriction cleavage and by S1 nuclease analysis, using DNA probes labeled at their 5' termini. Two major early RNA transcripts, which originated at map positions 5,240 +/- 10 and 5,145 +/- 10, and two major late RNA transcripts, which originated at map positions 325 +/- 10 and 185 +/- 10, were identified. Transcripts were initiated with comparable relative efficiencies at the same 5' site when either purified DNA or chromatin was used as the template. Our results suggest that extracellular simian virus 40 virion chromatin modifications do not regulate simian virus 40 promoter selection but function to increase the accessibility of RNA promoter sequences to RNA polymerase II and allow efficient elongation of the RNA chain after the initiation event.

Distribution of chromatin proteins between fractions of hamster liver chromatin differing in their susceptibility to micrococcal nuclease

Hamster liver nuclei were fractionated by digestion with micrococcal nuclease into nuclease released (SP) and nuclease resistant (PP) fractions varying in chemical composition and transcriptional activity. Electrophoretic analysis of histones from SP and PP showed no qualitative and quantitative differences. Apparently chromatin-bound protease activity can be found in both fractions. Nonhistone chromatin proteins isolated from SP and PP under mild conditions were fractionated by hydroxyapatite chromatography into NHCP1, NHCP2, NHCP3 and molecular heterogeneity and specificity were tested by SDS-polyacrylamide gel electrophoresis. The differences observed in nonhistone proteins are mainly of quantitative nature, however some specific polypeptides for SP and PP are observed.

Globin synthesis in hybrid cells constructed by transplantation of dormant avian erythrocyte nuclei into enucleated fibroblasts

The polypeptides synthesized by mature embryonic erythrocytes prepared from the peripheral blood of 14- to 15-day-old chicken embryos were analyzed by two-dimensional gel electrophoresis. Fewer than 200 species of polypeptides were detected; the major polypeptides made at this time were identified as the alpha A-, alpha D-, and beta-globin chains. The dormant erythrocyte nuclei were next reactivated to transcriptional competence by transplantation into enucleated mouse or chicken embryo fibroblasts, with frequencies of cytoplast renucleation of about 50 and 90%, respectively. Since large numbers of hybrid cells could be constructed, a biochemical analysis was possible. Electrophoretic analysis of the [35S]methionine-labeled polypeptides made in the hybrid cell types showed that polypeptides having the mobilities of only two (alpha A and alpha D) of the three major adult globin chains were made as major constituents of the hybrid cells. However, analysis of 14C-amino acid-labeled polypeptides revealed that a beta-like polypeptide that lacked methionine was also synthesized in large amounts. This polypeptide was tentatively identified as the early embryonic globin species rho. Globin synthesis was detected as early as 3 h after nuclear transplantation and as late as 18 h, the last time measured in these experiments. It appeared that globin polypeptides made at very early times were translated at least partially from chicken messenger ribonucleic acid introduced into the hybrid cells during fusion, whereas those made at later times were translated primarily from newly synthesized globin messenger ribonucleic acid. The potential usefulness of this hybrid cell system in analyzing mechanisms regulating globin gene expression is discussed.

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.

Active genes are sensitive to deoxyribonuclease I during metaphase

The active exogenous murine leukemia virus sequences of mouse cells growing in culture are preferentially digested by deoxyribonuclease I in metaphase chromosomes. As determined by nuclear nick translation, all of the gene sequences of these cells active during interphase are in a deoxyribonuclease I-sensitive conformation during metaphase. This method of nick translation can therefore be used to label chromosomes in situ in order to visualize the active regions of the genome.

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.

The DNase I sensitivity of Xenopus laevis genes transcribed by RNA polymerase III

Since the initial discovery that the DNase I sensitivity of the globin genes in different cell types correlates with globin gene expression, this relationship has been shown to hold true for a variety of genes, including the genes for ovalbumin, conalbumun, alpha- and beta-globin in chicken, several heat-shock proteins in Drosophila, the r-chromatin of Tetrahymena and the viral polyoma minichromosome. Although genes transcribed by RNA polymerases I and II have been studied extensively, the genes transcribed by RNA polymerase III have not. We have therefore investigated the DNase I sensitivity of transfer RNA (tRNA) and oogenetic 5S RNA genes in the liver and erythocyte nuclei of Xenopus laevis. The oogenetic 5S genes are not transcribed in any known somatic cell, and tRNA genes are transcribed in the hepatocyte but are inactive in the erythrocyte. We show here that, although in these two cell types the correspondence between DNase I sensitivity and gene transcription holds good for globin and the ribosomal genes, the tRNA and oogenetic 5S genes are DNase I sensitive in both liver and erythrocyte nuclei. Thus for the genes transcribed by polymerase III the correspondence of sensitivity and expression breaks down.

The changes in proviral chromatin that accompany morphological variation in avian sarcoma virus-infected rat cells

The clone All of avian sarcoma virus B77-infected Rat-1 cells comprises both morphologically normal and morphologically transformed derivatives. Transformed subclones, in which virus-specific RNA is readily detectable, contain a provirus that is very sensitive to DNase 1 digestion of chromatin, and show DNase 1 hypersensitive sites at the 5' end of the provirus and in 5' flanking cell DNA. Normal subclones with no detectable virus-specific RNA, whether infected cells that have never been transformed or revertants derived from transformed cells, contain a provirus that is far more resistant to DNase 1 digestion. Moreover this provirus lacks hypersensitive sites at its 5' end, although DNase 1 hypersensitive sites were detected at the 3' end of the provirus in either normal or transformed clones. The pattern of cytosine methylation in the proviral restriction sites of the isoschizomers Msp I and Hpa II differed between transformed and revertant clones; the revertants show additional methylation at some CpG doublets.

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.

DNAase I sensitivity of genes expressed during myogenesis

Cultures of a rat myogenic cell line were used to examine the question of whether in proliferating precursor cells genes which are programmed to be expressed later in development, in the same cell lineage, differ in DNAase I sensitivity from genes which are never expressed in these cells. Nuclei isolated from proliferating mononucleated myoblasts, differentiated cultures containing multinucleaged fibers, and rat brain, were treated with DNAase I. The sensitivity of the genes coding for the muscle-specific alpha-actin, myosin light chain 2 and the nonmuscle beta-actin was measured by blot hybridization of nuclear DNA with the corresponding cloned cDNA and genomic DNA probes. The sensitivity of these genes was compared to that of a gene not expressed in the muscle tissue. The results showed that in the muscle precursor cells, the potentiality of tissue-specific genes to be expressed is not reflected in DNAase I sensitivity. The changes which render these genes preferentially sensitive to DNAase I take place during the transition to terminal differentiation. The results showed also that the region of DNAase I sensitivity of the alpha-actin gene in the differentiated cells ends between 40 to 700 bp 5' to the structural gene. No DNAase I hypersensitive site was detected 5' to the alpha-actin gene.

Participation of core histone "tails" in the stabilization of the chromatin solenoid

We show here that the solenoid is maintained by the combination of linker histones and the nonglobular, highly basic "tails" of the core histones, which play only a minor part in the formation of the nucleosome core (Whitlock and Simpson, 1977. J. Biol. Chem. 252:6,516--6,520; Lilley and Tatchell, 1977. Nucleic Acids Res. 4:2,039--2,055; and Whitlock and Stein, 1978. J. Biol. Chem. 253:3,857--3,861). Polynucleosomes that contain core histones devoid of tails remain substantially unfolded under conditions otherwise favorable for the formation of solenoids. The tails can be replaced by extraneous basic polypeptides and in the presence of the linker histones the solenoid structure is then spontaneously recovered, as judged by a wide variety of structural criteria. The inference is that the core histone tail segments function by providing electrostatic shielding of the DNA charge and at the same time bridging adjacent nucleosomes in the solenoid. Our results carry the further implication that posttranscriptional modifications, such as acetylation of epsilon-amino groups, that reduce the positive charge of the core histone tails will tend to destabilize the higher-order structure and could thus render the DNA with which they are associated more readily available for transcription.

Ultrastructural organization of yeast chromatin

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

Isolation of a mouse DNA fraction which encodes more informational than non informational RNA sequences

A small fraction of single-stranded DNA (ssDNA), amounting to 1.5--2% of the total DNA, was isolated from native nuclear DNA of mouse Ascites tumour cells. In RNA-driven annealing reactions, 40--42% of the ssDNA, (labelled with [3H]-thymidine or 125I) could be hybridized to cytoplasmic RNA was compared with 4--4.5% for the non repetitious component of bulk DNA and 60--63% of the ssDNA could be hybridized to nuclear RNA as compared with 20--22% for bulk DNA. It was also found that most of the ssDNA sequences which are hybridizable to homologous RNA, consisted of non self-reassociating DNA regions (which can be reassociated with non repetitious bulk DNA). These findings complete earlier data obtained in other cell systems and demonstrate that ssDNA mainly originates from active DNA transcription sites which encode informational RNA sequences. It is proposed that ssDNA is formed via selective endogenous nuclease attacks presumably at an early stage of the DNA purification procedure.

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.