Portrait of a gene

Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes

In growing eukaryotic cells, nuclear ribosomal (r)RNA synthesis by RNA polymerase (RNAP) I accounts for the vast majority of cellular transcription. This high output is achieved by the presence of multiple copies of rRNA genes in eukaryotic genomes transcribed at a high rate. In contrast to most of the other transcribed genomic loci, actively transcribed rRNA genes are largely devoid of nucleosomes adapting a characteristic "open" chromatin state, whereas a significant fraction of rRNA genes resides in a transcriptionally inactive nucleosomal "closed" chromatin state. Here, we review our current knowledge about the nature of open rRNA gene chromatin and discuss how this state may be established.

Stochastic kinetics description of a simple transcription model

We study a stochastic model of transcription kinetics in order to characterize the distributions of transcriptional delay and of elongation rates. Transcriptional delay is the time which elapses between the binding of RNA polymerase to a promoter sequence and its dissociation from the DNA template strand with consequent release of the transcript. Transcription elongation is the process by which the RNA polymerase slides along the template strand. The model considers a DNA template strand with one promoter site and n nucleotide sites, and five types of reaction processes, which we think are key ones in transcription. The chemical master equation is a set of ordinary differential equations in 3(n) variables, where n is the number of bases in the template. This model is too huge to be handled if n is large. We manage to get a reduced Markov model which has only 2n independent variables and can well approximate the original dynamics. We obtain a number of analytical and numerical results for this model, including delay and transcript elongation rate distributions. Recent studies of single-RNA polymerase transcription by using optical-trapping techniques raise an issue of whether the elongation rates measured in a population are heterogeneous or not. Our model implies that in the cases studied, different RNA polymerase molecules move at different characteristic rates along the template strand. We also discuss the implications of this work for the mathematical modeling of genetic regulatory circuits.

Characterization of the rRNA locus of Pfiesteria piscicida and development of standard and quantitative PCR-based detection assays targeted to the nontranscribed spacer

Pfiesteria piscicida is a heterotrophic dinoflagellate widely distributed along the middle Atlantic shore of the United States and associated with fish kills in the Neuse River (North Carolina) and the Chesapeake Bay (Maryland and Virginia). We constructed a genomic DNA library from clonally cultured P. piscicida and characterized the nontranscribed spacer (NTS), small subunit, internal transcribed spacer 1 (ITS1), 5.8S region, ITS2, and large subunit of the rRNA gene cluster. Based on the P. piscicida ribosomal DNA sequence, we developed a PCR-based detection assay that targets the NTS. The assay specificity was assessed by testing clonal P. piscicida and Pfiesteria shumwayae, 35 additional dinoflagellate species, and algal prey (Rhodomonas sp.). Only P. piscicida and nine presumptive P. piscicida isolates tested positive. All PCR-positive products yielded identical sequences for P. piscicida, suggesting that the PCR-based assay is species specific. The assay can detect a single P. piscicida zoospore in 1 ml of water, 10 resting cysts in 1 g of sediment, or 10 fg of P. piscicida DNA in 1 micro g of heterologous DNA. An internal standard for the PCR assay was constructed to identify potential false-negative results in testing of environmental sediment and water samples and as a competitor for the development of a quantitative competitive PCR assay format. The specificities of both qualitative and quantitative PCR assay formats were validated with >200 environmental samples, and the assays provide simple, rapid, and accurate methods for the assessment of P. piscicida in water and sediments.

Scanning force microscopy of chromatin fibers in air and in liquid

We have adapted specimen preparation techniques of conventional electron microscopy for visualizing chromatin structures in the scanning force microscope (SFM) in air and in liquid. The beaded substructure of the nucleoprotein filament was obtained after hypotonic lysis of chicken erythrocytes and air drying, whereas supranucleosomal structures were preserved after treatment of cell nuclei with detergent. In the latter case, the nucleosomes were still distinct but appeared more condensed. A modified droplet diffusion-spreading technique of chromatin from Namalwa cells (a human B-lymphoid line) yielded a uniform filamentous morphology and similar fiber appearance. A reversible swelling of spread chromatin was observed upon exposure of air-dried samples to solutions differing in salt concentrations.

Probing chromatin with the scanning force microscope

With the scanning force microscope (SFM), one can image the topography of biological material adsorbed at air-solid or liquid-solid interfaces with up to nanometer resolution. In principle, fixation, contrast enhancement, and labeling are not required. We have adapted specimen preparation techniques of conventional electron microscopy for visualizing chromatin ultrastructures in the SFM. A beaded substructure of the nucleoprotein filament was obtained after hypotonic lysis of chicken erythrocytes and air drying. The beads-on-a-string morphology of the basic nucleosomal assembly was well delineated. The nucleosomes appeared as round protrusions with an apparent height of 4-6 nm. The histogram of center-to-center distances between adjacent nucleosome cores along the filament axis had a peak at approximately 30 nm. Reversible changes in the three-dimensional structure were observed upon exposure of air-dried samples of metaphase chromosomes to solutions of different ionic strengths.

Ultrastructural aspects of oogenesis and oocyte growth in fish and amphibians

Oogenesis, the early events of primary oocyte growth (meiotic arrest, synapsis, ribosomal gene duplication), and folliculogenesis can be seen to particular advantage in the germinal ridge of the syngnathan ovary. After budding off the germinal ridge (a compartment of the luminal epithelium), nascent follicles then enter into a linear array of developing follicles within which temporal and stage-specific events can be correlated with spatial distribution. Prominent features of the later phase of primary oocyte growth include intense transcriptional activity and the formation and subsequent dispersal of the Balbiani vitelline body (mitochondrial cloud) concomitant with an increase in cytoplasmic organelles and volume. Further oocyte growth is characterized by a period of cortical alveolus (in teleosts) or cortical granule (in anurans) formation, in which Golgi elements play a predominant role, and finally vitellogenesis. The latter process, which is responsible for the preponderance of oocyte growth, includes the hepatic synthesis and secretion of vitellogenin (VTG), the uptake of VTG from the bloodstream into the oocyte by receptor-mediated endocytosis, and the transport of VTG via endosomes and multivesicular bodies to forming yolk platelets. In the process, VTG is proteolytically cleaved into the yolk proteins, which assume either a monoclinic (in cyclostomes) or orthorhombic (in teleosts and amphibians) crystalline array. Other structures associated with the growing oocyte are also briefly discussed, including nuage, the vitelline envelope, intercellular junctions between the oocyte and overlying follicle cells, pigment, intramitochondrial crystals in ranidae, and annulate lamellae.

Chromosomal loop/nuclear matrix organization of transcriptionally active and inactive RNA polymerases in HeLa nuclei

The relative distribution of transcriptionally active and inactive RNA polymerases I and II between the nuclear matrix/scaffold and chromosomal loops of HeLa cells was determined. Total RNA polymerase was assessed by immunoblotting and transcribing RNA polymerase by a photoaffinity labeling technique in isolated nuclei. Nuclear matrix/scaffold was isolated by three methods using high-salt, intermediate-salt or low-salt extraction. The distribution of RNA polymerases I and II were very similar within each of the methods, but considerable differences in distributions were found between the different preparation methods. Either intermediate-salt or high-salt treatment of DNase I-digested nuclei showed significant association of RNA polymerases with the nuclear matrix. However, intermediate-salt followed by high-salt treatment released all transcribing and non-transcribing RNA polymerases. Nuclear scaffolds isolated with lithium diiodosalicylate (low-salt) contained very little of the RNA polymerases. This treatment, however, caused the dissociation of RNA polymerase II transcription complexes. These results show unambiguously that RNA polymerases, both in their active and inactive forms, are not nuclear matrix proteins. The data support models in which the transcriptional machinery moves around DNA loops during transcription.

An assessment of the evidence for the role of ribonucleoprotein particles in the maturation of eukaryote mRNA

This article has sought to draw together, on the one hand, what is known of mRNA processing and its control and, on the other hand, what is known of the structure and validity of hnRNP and snRNP particles. At the same time, it has attempted to synthesize these two themes into a critical assessment of the evidence which suggests that the particles are intimately involved in processing. It cannot be said that the case is proven. The evidence is compelling but circumstantial. The last few years have seen the development of the first in vitro splicing systems (Weingartner and Keller, 1981; Goldenberg and Raskus, 1981; Kole and Weissman, 1982), the isolation of monoclonal antibodies to defined snRNP (Lerner et al., 1981a; Billings et al., 1982) and hnRNP proteins (Hugle et al., 1982), and the ability to use artificial lipid vesicles to transfer antisera (Lenk et al., 1982) and radioactive snRNA (Gross and Cetron, 1982) into cells. It is to be hoped that further refinements of these and other techniques will allow us to solve this, one of the major outstanding problems of molecular biology.

Chromatin structure of Xenopus rDNA transcription termination sites. Evidence for a two-step process of transcription termination

The ultrastructure of Xenopus laevis (X.l.) 40S pre-rRNA transcription termination sites was investigated by electron microscopy. Amplified nucleolar chromatin was rapidly dispersed and processed for chromatin spread preparations. This type of preparation revealed that many rDNA termination sites appeared as 50 nm long segments of chromatin axis covered by a complex of three closely spaced RNA polymerase particles. Particle (Ptl) was characterized by the association with the terminal full-length pre-rRNP fibril; particles (Pt2) and (Pt3) are located downstream from (Ptl) and appear to be devoid of transcript fibrils. This particular structural arrangement as well as sequence homology analyses of 3' adjacent spacer rDNA segments indicate that transcript release and dissociation of polymerase particles are not necessarily coupled and termination of X.l. rDNA transcription may occur as a two step process. The structural data are correlated with homologies of DNA sequences at Xenopus rDNA transcription termination regions and are discussed with respect to sequence data of 3' termination sites of rRNA genes from other species.

The influence of antigen density and a comparison of IgG and IgM antibodies in the anti-complementary modulation of lymphocytic surface immunoglobulin

Experiments were carried out to determine the influence of antigen density on anti-complementary modulation, defined here as the conferring by anti-immunoglobulin (Ig) of resistance to lysis of guinea pig L2C leukaemic cells varied widely in their quantitative expression of surface membrane Ig as judged by the binding to cells of 125I-labelled Fab' fragments from anti-Ig, and a good correlation between the bulk antigen density and the percentage of cells lysed by anti-Ig plus C was obtained (P=0.02). In the presence of 10 mM sodium azide, which has been shown to diminish the modulation occurring during simultaneous incubations with anti-Ig and C, this correlation was even stronger (P less than 0.001). No zone could be defined in which the level of surface Ig expression was sufficient to serve complement lysis but too low for modulation. Furthermore, both the degrees and rates of modulation occurring on incubation with antibody at 37 degrees C, either before C addition or in the presence of lytic C, were similar for populations of high, low, or intermediate antigen density. Separation of cells by their size or density failed to yield populations differing in either their susceptibility to humoral killing through anti-Ig or their modulating capacity. IgG and IgM antibodies to the L2C cell surface Ig evoked similar levels of killing with syngeneic C, and when compared for their ability to promote anti-complementary modulation, no difference was revealed in either the rate or degree of modulation occurring during incubations at 37 degrees C with the two isotopes. The findings are discussed with particular reference to observations on the modulation of mouse thymus leukaemia (TL) antigens.

Patterns of transcriptional activity of nucleolar genes during progesterone-induced maturation of oocytes of Xenopus laevis

Maturation has been induced in full grown oocytes of Xenopus laevis by incubation in progesterone, and the ultrastructure of their nucleoli has been examined by electron microscopy using the chromatin spreading technique. We show that in this species numerous extrachromosomal nucleoli maintain high levels of transcription of rDNA for up to 200 min after the application of the hormone, i.e., shortly before germinal vesicle breakdown. Transcription has been identified as normal arrays of matrix units containing densely packed transcriptional complexes. In addition to normal-sized arrays of gradients of nascent RNP fibrils, as typical of active pre-rRNA genes, a number of unusual structures are described which include situations of sparse coverage of lateral fibrils in some matrix units, indicative of reduced frequencies of initiation events. The observations are discussed in relation to the time course of nucleolar gene inactivation described in oocytes of other amphibian species, as well as in relation to inactivation of chromosomal genes characteristic of this step of meiotic prophase I.

Correlation of hnRNP structure and nascent transcript cleavage

Using electron microscopy of spread chromatin, we have observed nonnucleolar transcription units from Drosophila melanogaster and Calliphora erythrocephala that display specific cleavage of nascent transcripts. We have quantitatively analyzed 20 of these relatively long transcription units. The primary RNP structure of homologous transcripts is nonrandom with respect to both RNA sequence and the cleavage event. In general, released RNA fragments have a smooth fibrillar RNP morphology (approximately 50 A wide) and retained segments have a thicker particulate morphology (approximately 250 A diameter). A characteristic secondary structure formation also accompanies cleavage--that is, RNP fibril loops form by association of noncontiguous transcript sequences that correspond to the terminal regions of the segment to be released. RNP particles form at the loop base sequences prior to their association and apparently coalesce upon loop formation. These loops, and thus the released segments, range in length from 1 and 25 kb on the examples we have analyzed. Cleavage of nascent hnRNA transcripts appears to be a fairly common event in these organisms and occurs within 0.3-3 min after transcription of the cleavage site.

Macromolecule synthesis in Escherichia coli BB under various growth conditions

The kinetic behavior of the macromolecule synthesis of Escherichia coli during balanced growth in various media at different temperatures as investigated. The results indicate that macromolecule contents per cell can be expressed as exponential functions of the specific growth rate at a given temperature. It was shown that the content per cell at the zero growth rate was constant in each macromolecule component, irrespective of the growth temperature. The rate of ribonucleic acid (RNA) synthesis per unit weight of deoxyribonucleic acid and that of protein synthesis per unit weight of RNA were taken as efficiencies of RNA and protein synthesis, respectively; both of them were found to be dependent on the growth rate and temperature. The efficiency of RNA synthesis was found to be very high at a high growth rate, whereas that of protein synthesis was found to decrease above certain growth rate. At the same growth rate, an increase in the growth temperature resulted in a decrease in the efficiency of RNA synthesis but an increase in that of protein synthesis.

[Transcription complexes with nucleolar and chromosomal origins in oocytes of Pleurodeles waltlii and P. poireti (amphibia, urodela) (author's transl)]

The method of spreading transcription complexes has been applied to amphibian oocytes of Pleurodeles genus. Complexes of nucleolar origin show a regular and homogeneous organization similar to that described in other materials. The observations add to the interpretation as an amplification of nucleolar DNA and a redundancy of ribosomal cistrons in the two species studied. -- On the other hand, complexes of chromosomal origin display a great diversity. Two main characteristics can be drawn: the existence of several transcription units in a chromosomal organization unit and the possibility to point out a special architecture at the RNP fibril level. Applying a shadowing technique used for isolated molecules is an improvement compared with earlier methods based on PTA coloration.

Effects of actinomycin D on the association of newly formed ribonucleoproteins with the cistrons of ribosomal RNA in Triturus oocytes

The effect of actinomycin D(AMD) on the association of the nascent ribonucleo-protein (RNP) fibrils containing the precursors of ribosomal RNA (pre-rRNA) with their template deoxyribonucleoprotein (rDNP) strands has been studied in lampbrush stage oocytes from Triturus alpestris. Ovary pieces were incubated in vitro either in media containing radioactive ribonucleosides and then, for various times, in solutions containing 25 mug/ml AMD, or were directly exposed to the drug. The ultrastructure of the nucleoli and the nuclear periphery was studied by electron microscopy of thin sections and positively stained spread preparations of isolated nuclear contents, and by light and electron microscope autoradiography. The fate of the labeled pre-rRNA was followed by gel electrophoresis of RNA extracted from manually isolated nuclei. Our results show that the growing fibrils which contain the nascent pre-rRNA progressively detach from the DNP strands, the majority being released between 45 and 180 min after application of the drug. The release pattern seems to be random and does not show preference for regions close to the initiator or terminator sites of the transcribed rDNP units. There is a pronounced tendency to removal of groups of adjacent mascent fibrils. The effect of the drug is very heterogeneous. Even after 3 h of treatment with AMD the nucleoli exhibit several individual transcriptional units which appear almost completely covered with lateral fibrils. Autoradiography revealed that most of this released RNP remains within the confinements of the nucleoli which show some foci of aggregation and condensation of fibrillar components but no clear "segregation" phenomenon. In the gel-electrophoretic analysis, a significant but moderate decrease of labeled pre-rRNA was noted only in the first stable pre-rRNA component, whereas pre-rRNA classes of lower molecular weight are very stable under these conditions. The results are discussed in relation to the stability of rDNA transcription complexes and as a basis for an explanation of the ultrastructural changes which are generally observed in nucleoli of AMD-treated cells. It is postulated that inhibition of transcription results in a slow but progressive release of the arrested incomplete RNP fibrils from the template.

Visualization of chromatin substructure: upsilon bodies

Spread chromatin fibers, from isolated eucaryotic nuclei, reveal linear arrays of spherical particles (upsilon bodies), about 70 A in diameter, connected by thin filaments about 15 A wide. These particles have been observed in freshly isolated nuclei from rat thymus, rat liver, and chicken erythrocytes. In addition, upsilon bodies can be visualized in preparations of isolated sheared chromatin, and in chromatin reconstructed from dissociating solvent conditions (i.e., high urea-NaCl concentration). As a criterion for perturbation of native chromatin structure low-angle X-ray diffraction patterns were obtained from nuclear pellets at different stages in the preparation of nuclei fro electron microscopy. These results suggest that the particulate (upsilon body) structures observed by electron microscopy may be closely related to the native configuration of chromatin.

Ribosomal DNA in different members of a family of green algae (Chlorophyta, Dasycladaceae): an electron microscopisal study

Active cistrons and non-transcribed spacers of rDNA were made visible in spread preparations of nucleolar material from different species of the green alga family Dasycladaceae (Chlorophyta). The data observed show a difference in length in transcribed rDNA regions between Acetabularia peniculus Solms-Laubach, Acetabularia dentata Solms-Laubach on the one hand and Acetabularia ryukyuensis Okamura et Yamada, Dasycladus clavaeformis J. Agardh, Cymopolia van bosseae Solms-Laubach and Batophora oerstedii J. Agardh on the other: The large size difference between spacer intercepts of different species is very conspicuous. While the Acetabularia species have long non-transcribed spacers they are very short or even not observable in the other Dasycladaceen species studied. Peculiarities found in rDNA include extra long spacers between cistrons, single extra long cistrons together with rDNA cistrons on the same strand and rDNA-sized cistrons alternately arranged on one strand with larger sized cistrons. In spite of extensive searching, inversions were never found in spread nucleolar material. However, they were frequent in spread material of whole nuclei.

The three-dimensional organization of the amplified ribosomal DNA complex in Acheta

The major chromomere of pachytene chromosome 6 in the oocytes of Acheta (Orthoptera) is a region of amplification for ribosomal RNA cistrons (28 S and 18 S). This chromomere was isolated and studied with the scanning electron microscope. It has an outer shell that is smooth at early stages but divides into polygonal plates as indentations appear on its surface. These indentations increase in number as the DNA copies separate from each other and as the ribosomal RNA synthesis progresses. The vertices of the polygonal plates coincide with the positions at which the DNA copies reach the surface of the chromomere during their "puffing" process. The combined information gained from scanning and transmission electron microscopy, DNA measurements, DNA.RNA hybridization, and cytochemistry, leads to a three-dimensional picture of the organization of the amplified ribosomal DNA in its association with ribosomal RNA and protein.

Morphology of nucleolar cistrons in a plant cell, Acetabularia mediterranea

The structural organization of transcriptionally active DNA that contains cistrons for precursor molecules of ribosomal RNA is described in positively stained spread preparations from nuclei and nucleoli isolated from the green alga, Acetabularia mediterranea Lmx. These nuclei contain large aggregates of nucleolar subunits in which fibril-covered regions, the putative active cistrons for precursors of ribosomal RNA, alternate with fibril-free intercepts, the "spacers." The length distribution of the different intercepts of this DNA is given, and the pattern is compared with those shown in animal cell systems. The data are discussed in relation to problems of transcription and of amplification of ribosomal RNA genes.